https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=Lasso 2026-06-07T21:50:09Z User contributions MediaWiki 1.33.0 https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/Plastimatch&diff=64465 2026-01-04T22:02:19Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/PlmBSplineDeformableRegistration&diff=64464 2026-01-04T21:25:46Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DicomSroImport&diff=64463 2026-01-04T21:06:12Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DicomRtImport&diff=64462 2026-01-04T21:03:38Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SegmentMorphology&diff=64461 2026-01-04T20:59:19Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SegmentComparison&diff=64460 2026-01-04T20:55:12Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/Isodose&diff=64459 2026-01-04T20:49:27Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DoseComparison&diff=64458 2026-01-04T20:46:36Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DoseAccumulation&diff=64457 2026-01-04T20:42:15Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DoseVolumeHistogram&diff=64456 2026-01-04T20:41:00Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ExternalBeamPlanning&diff=64455 2026-01-04T20:29:35Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/SlicerRT/HowToReportAnError&diff=64454 2026-01-04T18:23:44Z

<p>Lasso: Moved to https://github.com/slicerrt/slicerrt</p> <hr /> <div>Moved to https://github.com/slicerrt/slicerrt</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/FAQ/Models&diff=64453 2025-12-30T22:17:59Z

<p>Lasso: /* Models */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;noinclude&gt;__TOC__<br /> ={{#titleparts: {{PAGENAME}} | | -1 }}=<br /> &lt;/noinclude&gt;&lt;includeonly&gt;<br /> {{#ifeq: {{#titleparts: {{PAGENAME}} | 3 }} | Documentation/{{documentation/version}}/Developers | | ='''User FAQ: {{{1}}}'''=}}<br /> &lt;/includeonly&gt;<br /> <br /> ==How can I transform a model for output?==<br /> <br /> Slicer performs all operations in millimeters, and all anatomy is referenced to the patient space. When the data from from DICOM or other formats with well-defined geometry mappings, all the dimensions are handled automatically.<br /> <br /> However some output formats, such as .stl format, do not have defined physical units, and some software will insist that data be saved with respect to units other than millimeters. In this case, you can pre-transform the data before saving using the following steps:<br /> <br /> #Create a linear transform using the [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms module]]<br /> #Enter the conversion factor along the main diagonal of the transform matrix (i.e. if the export should be in meters rather than millimeters, then enter 0.001 in place of 1.0 along the three locations in the main diagonal).<br /> #Apply the new transform to the model (it will appear much smaller now in slicer)<br /> #Go to the [[Documentation/{{documentation/version}}/Modules/Data|Data module]]<br /> ##Right-click on the model<br /> ##Pick the Harden Transform menu item.<br /> <br /> The model will not change size, but it will move out of the transform, meaning that the internal data points have been changed and is ready for saving.</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/FAQ&diff=64452 2025-12-30T22:17:33Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> __TOC__<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/General|Installation &amp; Generic}}<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/Wiki|Slicer Wiki}}<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/UserInterface|User Interface}}<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/DICOM|DICOM}}<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/Viewing and Resampling|Viewing and Resampling}}<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/Registration|Registration}}<br /> <br /> {{:Documentation/{{documentation/version}}/FAQ/Models|Models}}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/FAQ/General&diff=64451 2025-12-30T22:14:02Z

<p>Lasso: Moved &quot;how to access older releases&quot; to download.slicer.org page</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;noinclude&gt;__TOC__<br /> ={{#titleparts: {{PAGENAME}} | | -1 }}=<br /> &lt;/noinclude&gt;&lt;includeonly&gt;<br /> {{#ifeq: {{#titleparts: {{PAGENAME}} | 3 }} | Documentation/{{documentation/version}}/Developers | | ='''User FAQ: {{{1}}}'''=}}<br /> &lt;/includeonly&gt;<br /> ==What is Slicer?==<br /> {{:Documentation/{{documentation/version}}/Slicer}}<br /> ==Is Slicer really free?==<br /> <br /> Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).<br /> <br /> See [http://www.slicer.org/pages/LicenseText the Slicer License page] for the legal version of this.<br /> <br /> ==Can I use slicer for patient care?==<br /> <br /> Slicer is intended for research work and ''has no FDA clearances or approvals of any kind''. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.<br /> ==How do I create an account for the Slicer wiki?==<br /> <br /> Current content of this wiki will be moved to https://slicer.readthedocs.io, https://www.slicer.org, and https://github.com/Slicer/Slicer/wiki websites and legacy content will be archived. New user accounts are no longer offered for this wiki.<br /> <br /> ==How to uninstall Slicer?==<br /> <br /> *On Windows, choose &quot;Uninstall&quot; option from the Start menu.<br /> *On the Mac, remove the Slicer.app file. To clean up settings, remove &quot;~/.config/www.na-mic.org/&quot;<br /> *On Linux, remove the directory where the application is located. To clean up settings, remove &quot;~/.config/NA-MIC/&quot;<br /> <br /> See the information about the location of [[Documentation/{{documentation/version}}/SlicerApplication/Settings|Settings]] for all platforms. If the uninstaller is not working on windows you may need to remove the settings manually.</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly&diff=64450 2025-12-30T21:01:12Z

<p>Lasso: Removed obsolete content</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> __NOTOC__<br /> <br /> {{documentation/versionlist}}<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; border=&quot;0&quot; align=&quot;center&quot; valign=&quot;top&quot;<br /> |-<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> |- <br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Where to start ?&lt;/span&gt;<br /> ----<br /> <br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]<br /> <br /> :Quick overview about Slicer<br /> <br /> *[https://training.slicer.org/ Training pages]<br /> <br /> :Information on how to use Slicer {{documentation/version}}<br /> <br /> *[[Documentation/{{documentation/version}}/FAQ|FAQ]]<br /> <br /> :Set of common questions/answers<br /> <br /> *[https://discourse.slicer.org Discussion Forum]<br /> <br /> :The most effective way to get help from the community<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How to&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}<br /> <br /> ----<br /> {{:{{FULLPAGENAME}}/SlicerApplication}}<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Modules&lt;/span&gt;<br /> ----<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> | width=&quot;5%&quot; |<br /> &amp;nbsp;<br /> <br /> | width=&quot;45%&quot; |<br /> [[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]<br /> &lt;br /&gt;<br /> <br /> [[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]<br /> &lt;br /&gt;<br /> <br /> [[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]<br /> &lt;br /&gt;<br /> <br /> [[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerModels-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/models.html Models]<br /> &lt;br /&gt;<br /> <br /> [[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]<br /> &lt;br /&gt;<br /> <br /> [[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]<br /> &lt;br /&gt;<br /> <br /> [[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]<br /> &lt;br /&gt;<br /> <br /> [[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]<br /> &lt;br /&gt;<br /> <br /> [[Image:ViewControllersIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/viewcontrollers.html View Controllers]<br /> &lt;br /&gt;<br /> <br /> [[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]<br /> &lt;br /&gt;<br /> <br /> [[Image:Welcome.png|32px]] [https://slicer.readthedocs.io/en/latest/user_guide/modules/slicerwelcome.html Welcome to Slicer]<br /> &lt;br /&gt;<br /> <br /> |}<br /> <br /> <br /> &lt;!--<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Extension Categories&lt;/span&gt; {{new}}<br /> ----<br /> {{note}} What are these categories ? See [[Documentation/{{documentation/version}}/Extensions/CatalogPolicies|here]]<br /> --&gt;<br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Developers Corner&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}<br /> <br /> :Source code, contribute patch, develop modules<br /> <br /> &lt;!--<br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Developers mailing list] / [http://slicer-devel.65872.n3.nabble.com/ Browse archives]<br /> : Intended for discussion of programming related questions<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Miscellaneous&lt;/span&gt;<br /> ----<br /> &lt;!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --&gt;<br /> <br /> *[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]<br /> <br /> :Slicer user documentation principle and guidelines<br /> <br /> *[[Slicer4:VisualBlog|Visual blog]]<br /> <br /> :Set of screenshots showing Slicer in action.<br /> <br /> *[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br /> <br /> :Platform specific issues and considerations<br /> <br /> *[[Documentation/{{documentation/version}}/Announcements|Announcements]] &amp; [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]<br /> <br /> *[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]<br /> <br /> :Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.<br /> <br /> <br /> |}<br /> <br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Data_Conversion&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Tensor_Images&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Diffusion_Import_and_Export&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Diffusion_Process&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Endoscopy&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Filter&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Filtering&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Filtering_Arithmetic&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Filtering_Denoising&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Filtering_Morphology&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_IGT&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Informatics&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Informatics_Converters&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Legacy&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Legacy_Converters&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Legacy_Filtering&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Legacy_Registration&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Quantification&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Registration&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Registration_Specialized&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Segmentation&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Segmentation_Specialized&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Surface_Models&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Utilities&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Utilities_BRAINS&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Wizards&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Developer_Tools&quot;&gt;&lt;/span&gt;&lt;span id=&quot;Modules_by_category_Developer_Tools_DICOM_Plugins&quot;&gt;&lt;/span&gt;</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/FAQ/General&diff=64449 2025-12-30T20:48:49Z

<p>Lasso: Removed obsolete parts or parts that have been moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;noinclude&gt;__TOC__<br /> ={{#titleparts: {{PAGENAME}} | | -1 }}=<br /> &lt;/noinclude&gt;&lt;includeonly&gt;<br /> {{#ifeq: {{#titleparts: {{PAGENAME}} | 3 }} | Documentation/{{documentation/version}}/Developers | | ='''User FAQ: {{{1}}}'''=}}<br /> &lt;/includeonly&gt;<br /> ==What is Slicer?==<br /> {{:Documentation/{{documentation/version}}/Slicer}}<br /> ==Where can I download Slicer?==<br /> 3DSlicer is available for download by visiting the following link: '''http://download.slicer.org'''<br /> <br /> You can also get older releases by using the offset parameter in the download page. For example, download page from 7 days ago: http://download.slicer.org/?offset=-7<br /> <br /> To get a direct download link of previous revision on a selected operating system: http://download.slicer.org/download?os=macosx&amp;stability=any&amp;offset=-1<br /> <br /> Always include these parameters:<br /> <br /> *''stability'', which can be ''release'', ''nightly'', or ''any''<br /> *''os'', which can be ''win'', ''macosx'', or ''linux''<br /> <br /> Additional options:<br /> <br /> *revision built before or on the date: ''date=2015-01-01''<br /> *same but checkout date: ''checkout-date=2015-02-01''<br /> *exact revision: ''revision=27000''<br /> *revision less than of equal: ''closest-revision=26000''<br /> *latest revision of 4.3 branch, can include patch as well: ''version=4.3''<br /> <br /> Any of these queries can be combined with the offset param, which will step forward or backward a given number of revisions. So,<br /> ''stability=release&amp;version=4.5.0&amp;offset=-1'' should give you the revision just before the first 4.5 release.<br /> <br /> ==Where can I download older release of Slicer ?==<br /> <br /> Older releases of 3DSlicer are available here: https://slicer-packages.kitware.com/#collection/5f4474d0e1d8c75dfc70547e/folder/5f4474d0e1d8c75dfc705482<br /> <br /> Extensions can be downloaded for old Slicer releases manually from the Extensions Catalog at the URL: &lt;code&gt;https://extensions.slicer.org/catalog/All/(revision_number)/(operating_system)&lt;/code&gt;. Revision number is available in Slicer menu: Help / About Slicer (or in the [https://www.slicer.org/wiki/Release_Details#Slicer_4.8 Slicer Releases page]). Operating system can be: &lt;code&gt;win&lt;/code&gt;, &lt;code&gt;linux&lt;/code&gt;, or &lt;code&gt;macosx&lt;/code&gt;. For example for Slicer-4.8.0 on Windows extensions are available at: https://extensions.slicer.org/catalog/All/26489/win<br /> ==Is Slicer really free?==<br /> <br /> Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).<br /> <br /> See [http://www.slicer.org/pages/LicenseText the Slicer License page] for the legal version of this.<br /> <br /> ==Can I use slicer for patient care?==<br /> <br /> Slicer is intended for research work and ''has no FDA clearances or approvals of any kind''. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.<br /> ==How do I create an account for the Slicer wiki?==<br /> <br /> Current content of this wiki will be moved to https://slicer.readthedocs.io, https://www.slicer.org, and https://github.com/Slicer/Slicer/wiki websites and legacy content will be archived. New user accounts are no longer offered for this wiki.<br /> <br /> ==How to uninstall Slicer?==<br /> <br /> *On Windows, choose &quot;Uninstall&quot; option from the Start menu.<br /> *On the Mac, remove the Slicer.app file. To clean up settings, remove &quot;~/.config/www.na-mic.org/&quot;<br /> *On Linux, remove the directory where the application is located. To clean up settings, remove &quot;~/.config/NA-MIC/&quot;<br /> <br /> See the information about the location of [[Documentation/{{documentation/version}}/SlicerApplication/Settings|Settings]] for all platforms. If the uninstaller is not working on windows you may need to remove the settings manually.</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Build_Instructions/Prerequisites/Qt&diff=64448 2025-11-22T03:02:11Z

<p>Lasso: Replaced content with &quot;{{documentation/banner | text = [https://slicer.readthedocs.io/en/latest/developer_guide/build_instructions/index.html This page has been moved to read-the-docs.] | bac...&quot;</p> <hr /> <div>{{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/developer_guide/build_instructions/index.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SimpleFilters&diff=64270 2022-11-14T02:49:22Z

<p>Lasso: moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/simplefilters.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/Welcome&diff=64269 2022-11-14T02:48:40Z

<p>Lasso: moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/slicerwelcome.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly&diff=64268 2022-11-14T02:47:08Z

<p>Lasso: moved Welcome module to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> __NOTOC__<br /> <br /> {{documentation/versionlist}}<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; border=&quot;0&quot; align=&quot;center&quot; valign=&quot;top&quot;<br /> |-<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> |- <br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Where to start ?&lt;/span&gt;<br /> ----<br /> <br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]<br /> <br /> :Quick overview about Slicer<br /> <br /> *[[Documentation/{{documentation/version}}/Training|Training pages]]<br /> <br /> :Information on how to use Slicer {{documentation/version}}<br /> <br /> *[[Documentation/{{documentation/version}}/FAQ|FAQ]]<br /> <br /> :Set of common questions/answers<br /> <br /> *[https://discourse.slicer.org Discussion Forum]<br /> <br /> :The most effective way to get help from the community<br /> <br /> &lt;!--<br /> * [http://slicer-users.65878.n3.nabble.com/ Search users mailing list]<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How to&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}<br /> <br /> ----<br /> {{:{{FULLPAGENAME}}/SlicerApplication}}<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Modules&lt;/span&gt;<br /> ----<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> | width=&quot;5%&quot; |<br /> &amp;nbsp;<br /> <br /> | width=&quot;45%&quot; |<br /> [[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]<br /> &lt;br /&gt;<br /> <br /> [[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]<br /> &lt;br /&gt;<br /> <br /> [[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]<br /> &lt;br /&gt;<br /> <br /> [[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerModels-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/models.html Models]<br /> &lt;br /&gt;<br /> <br /> [[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]<br /> &lt;br /&gt;<br /> <br /> [[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]<br /> &lt;br /&gt;<br /> <br /> [[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]<br /> &lt;br /&gt;<br /> <br /> [[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]<br /> &lt;br /&gt;<br /> <br /> [[Image:ViewControllersIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/viewcontrollers.html View Controllers]<br /> &lt;br /&gt;<br /> <br /> [[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]<br /> &lt;br /&gt;<br /> <br /> [[Image:Welcome.png|32px]] [https://slicer.readthedocs.io/en/latest/user_guide/modules/slicerwelcome.html Welcome to Slicer]<br /> &lt;br /&gt;<br /> <br /> | width=&quot;50%&quot; |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}<br /> <br /> |}<br /> <br /> <br /> &lt;!--<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Extension Categories&lt;/span&gt; {{new}}<br /> ----<br /> {{note}} What are these categories ? See [[Documentation/{{documentation/version}}/Extensions/CatalogPolicies|here]]<br /> --&gt;<br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Developers Corner&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}<br /> <br /> :Source code, contribute patch, develop modules<br /> <br /> &lt;!--<br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Developers mailing list] / [http://slicer-devel.65872.n3.nabble.com/ Browse archives]<br /> : Intended for discussion of programming related questions<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Miscellaneous&lt;/span&gt;<br /> ----<br /> &lt;!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --&gt;<br /> <br /> *[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]<br /> <br /> :Slicer user documentation principle and guidelines<br /> <br /> *[[Slicer4:VisualBlog|Visual blog]]<br /> <br /> :Set of screenshots showing Slicer in action.<br /> <br /> *[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br /> <br /> :Platform specific issues and considerations<br /> <br /> *[[Documentation/{{documentation/version}}/Announcements|Announcements]] &amp; [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]<br /> <br /> *[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]<br /> <br /> :Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Documentation in other languages&lt;/span&gt;<br /> ----<br /> {{:{{FULLPAGENAME}}/Lang/ES}}<br /> <br /> <br /> |}<br /> <br /> &lt;!--<br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing}}<br /> --&gt;<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; border=&quot;0&quot; align=&quot;center&quot; valign=&quot;top&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}<br /> <br /> |<br /> &lt;br /&gt;<br /> &lt;br /&gt;<br /> =Modules by category=<br /> <br /> ==Converters==<br /> <br /> *[[Documentation/Nightly/Modules/CropVolume|Crop Volume]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/vectortoscalarvolume.html Vector To Scalar Volume] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOM Series]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==Diffusion==<br /> <br /> *[[Documentation/Nightly/Modules/DMRIInstall|DMRI Install]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Data_Conversion&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Data Conversion===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Tensor_Images&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Weighted Images===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Import_and_Export&quot;&gt;&lt;/span&gt;<br /> ===Import and Export===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Process&quot;&gt;&lt;/span&gt;<br /> ===Utilities===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Endoscopy&quot;&gt;&lt;/span&gt;<br /> ==Endoscopy==<br /> <br /> *[[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filter&quot;&gt;&lt;/span&gt;<br /> ==Filter==<br /> <br /> *IslandRemoval &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering&quot;&gt;&lt;/span&gt;<br /> ==Filtering==<br /> <br /> *[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4 ITK Bias Field Correction]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Arithmetic&quot;&gt;&lt;/span&gt;<br /> ===Arithmetic===<br /> <br /> *[[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Denoising&quot;&gt;&lt;/span&gt;<br /> ===Denoising===<br /> <br /> *[[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Morphology&quot;&gt;&lt;/span&gt;<br /> ===Morphology===<br /> <br /> *[[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_IGT&quot;&gt;&lt;/span&gt;<br /> ==IGT==<br /> <br /> *[[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLink IF]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics&quot;&gt;&lt;/span&gt;<br /> ==Informatics==<br /> <br /> *[[Documentation/Nightly/Modules/SEG2NRRD|SEG 2 NRRD]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Tables|Tables]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Data|Data]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *DumpSEGFrame &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Terminologies|Terminologies]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Units|Units]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SampleData|Sample Data]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Colors|Colors]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Annotations|Annotations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Markups|Markups]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/EncodeSEG|Encode SEG]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy&quot;&gt;&lt;/span&gt;<br /> ==Legacy==<br /> &lt;span id=&quot;Modules_by_category_Legacy_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Filtering&quot;&gt;&lt;/span&gt;<br /> ===Filtering===<br /> <br /> *[[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Registration&quot;&gt;&lt;/span&gt;<br /> ===Registration===<br /> <br /> *Test Grid Transform Registration &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==MultiVolume Support==<br /> <br /> *[https://slicer.readthedocs.io/en/latest/user_guide/modules/multivolumeimporter.html MultiVolume Importer] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[https://slicer.readthedocs.io/en/latest/user_guide/modules/multivolumeexplorer.html MultiVolume Explorer] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Quantification&quot;&gt;&lt;/span&gt;<br /> <br /> ==Quantification==<br /> <br /> *[[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *SegmentStatistics &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINSLabelStats &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataProbe|Data Probe]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration&quot;&gt;&lt;/span&gt;<br /> ==Registration==<br /> <br /> *[[Documentation/Nightly/Modules/Transforms|Transforms]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *BRAINSResize &lt;small&gt;(cli)&lt;/small&gt;<br /> *PerformMetricTest &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSResample|BRAINS Resample]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSFit|General registration (BRAINS)]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *[[Documentation/Nightly/Modules/ACPCTransform|AC-PC Transform]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINS Demon Warp]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Reformat|Reformat]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *VBRAINSDemonWarp &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation&quot;&gt;&lt;/span&gt;<br /> ==Segmentation==<br /> <br /> *[[Documentation/Nightly/Modules/Segmentations|Segmentations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Editor|Editor]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EMSegment|EMSegment]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> *EMSegmentQuick &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *BRAINS ROI Auto &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment CommandLine &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Surface_Models&quot;&gt;&lt;/span&gt;<br /> <br /> ==Surface Models==<br /> <br /> *[[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelMaker|Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelToLabelMap|Model To LabelMap]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MergeModels|Merge Models]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMap Smoothing]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities&quot;&gt;&lt;/span&gt;<br /> ==Utilities==<br /> <br /> *[[Documentation/Nightly/Modules/ScreenCapture|Screen Capture]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataStore|Data Store]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicompatcher.html DICOM Patcher] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINS Strip Rotation &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment Transform To New Format &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities_BRAINS&quot;&gt;&lt;/span&gt;<br /> ===BRAINS===<br /> <br /> *BRAINS Transform Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Wizards&quot;&gt;&lt;/span&gt;<br /> ==Wizards==<br /> <br /> *[[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools&quot;&gt;&lt;/span&gt;<br /> ==Developer Tools==<br /> <br /> *[[Documentation/Nightly/Modules/Cameras|Cameras]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/extensionwizard.html Extension Wizard] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EventBroker|Event Broker]]<br /> *Double Arrays &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools_DICOM_Plugins&quot;&gt;&lt;/span&gt;<br /> ===DICOM Plugins===<br /> <br /> *DICOMParametricMapPlugin<br /> *DicomUltrasoundPlugin<br /> *DICOMSegmentationPlugin<br /> *DICOMSlicerDataBundlePlugin<br /> *DICOMTID1500Plugin<br /> *[[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]<br /> *DICOMScalarVolumePlugin<br /> *DICOMDiffusionVolumePlugin<br /> *DICOMLongitudinalPETCTPlugin<br /> *DicomSroImportPlugin<br /> *[[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]<br /> *DicomRtImportExportPlugin<br /> *MultiVolumeImporterPlugin<br /> <br /> |}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly&diff=64267 2022-11-14T02:45:11Z

<p>Lasso: /* MultiVolume Support */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> __NOTOC__<br /> <br /> {{documentation/versionlist}}<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; border=&quot;0&quot; align=&quot;center&quot; valign=&quot;top&quot;<br /> |-<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> |- <br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Where to start ?&lt;/span&gt;<br /> ----<br /> <br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]<br /> <br /> :Quick overview about Slicer<br /> <br /> *[[Documentation/{{documentation/version}}/Training|Training pages]]<br /> <br /> :Information on how to use Slicer {{documentation/version}}<br /> <br /> *[[Documentation/{{documentation/version}}/FAQ|FAQ]]<br /> <br /> :Set of common questions/answers<br /> <br /> *[https://discourse.slicer.org Discussion Forum]<br /> <br /> :The most effective way to get help from the community<br /> <br /> &lt;!--<br /> * [http://slicer-users.65878.n3.nabble.com/ Search users mailing list]<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How to&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}<br /> <br /> ----<br /> {{:{{FULLPAGENAME}}/SlicerApplication}}<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Modules&lt;/span&gt;<br /> ----<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> | width=&quot;5%&quot; |<br /> &amp;nbsp;<br /> <br /> | width=&quot;45%&quot; |<br /> [[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]<br /> &lt;br /&gt;<br /> <br /> [[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]<br /> &lt;br /&gt;<br /> <br /> [[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]<br /> &lt;br /&gt;<br /> <br /> [[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerModels-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/models.html Models]<br /> &lt;br /&gt;<br /> <br /> [[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]<br /> &lt;br /&gt;<br /> <br /> [[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]<br /> &lt;br /&gt;<br /> <br /> [[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]<br /> &lt;br /&gt;<br /> <br /> [[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]<br /> &lt;br /&gt;<br /> <br /> [[Image:ViewControllersIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/viewcontrollers.html View Controllers]<br /> &lt;br /&gt;<br /> <br /> [[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]<br /> &lt;br /&gt;<br /> <br /> [[Image:Welcome.png|32px]] [[{{FULLPAGENAME}}/Modules/Welcome|Welcome to Slicer]]<br /> &lt;br /&gt;<br /> <br /> | width=&quot;50%&quot; |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}<br /> <br /> |}<br /> <br /> <br /> &lt;!--<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Extension Categories&lt;/span&gt; {{new}}<br /> ----<br /> {{note}} What are these categories ? See [[Documentation/{{documentation/version}}/Extensions/CatalogPolicies|here]]<br /> --&gt;<br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Developers Corner&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}<br /> <br /> :Source code, contribute patch, develop modules<br /> <br /> &lt;!--<br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Developers mailing list] / [http://slicer-devel.65872.n3.nabble.com/ Browse archives]<br /> : Intended for discussion of programming related questions<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Miscellaneous&lt;/span&gt;<br /> ----<br /> &lt;!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --&gt;<br /> <br /> *[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]<br /> <br /> :Slicer user documentation principle and guidelines<br /> <br /> *[[Slicer4:VisualBlog|Visual blog]]<br /> <br /> :Set of screenshots showing Slicer in action.<br /> <br /> *[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br /> <br /> :Platform specific issues and considerations<br /> <br /> *[[Documentation/{{documentation/version}}/Announcements|Announcements]] &amp; [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]<br /> <br /> *[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]<br /> <br /> :Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Documentation in other languages&lt;/span&gt;<br /> ----<br /> {{:{{FULLPAGENAME}}/Lang/ES}}<br /> <br /> <br /> |}<br /> <br /> &lt;!--<br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing}}<br /> --&gt;<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; border=&quot;0&quot; align=&quot;center&quot; valign=&quot;top&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}<br /> <br /> |<br /> &lt;br /&gt;<br /> &lt;br /&gt;<br /> =Modules by category=<br /> <br /> ==Converters==<br /> <br /> *[[Documentation/Nightly/Modules/CropVolume|Crop Volume]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/vectortoscalarvolume.html Vector To Scalar Volume] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOM Series]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==Diffusion==<br /> <br /> *[[Documentation/Nightly/Modules/DMRIInstall|DMRI Install]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Data_Conversion&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Data Conversion===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Tensor_Images&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Weighted Images===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Import_and_Export&quot;&gt;&lt;/span&gt;<br /> ===Import and Export===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Process&quot;&gt;&lt;/span&gt;<br /> ===Utilities===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Endoscopy&quot;&gt;&lt;/span&gt;<br /> ==Endoscopy==<br /> <br /> *[[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filter&quot;&gt;&lt;/span&gt;<br /> ==Filter==<br /> <br /> *IslandRemoval &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering&quot;&gt;&lt;/span&gt;<br /> ==Filtering==<br /> <br /> *[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4 ITK Bias Field Correction]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Arithmetic&quot;&gt;&lt;/span&gt;<br /> ===Arithmetic===<br /> <br /> *[[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Denoising&quot;&gt;&lt;/span&gt;<br /> ===Denoising===<br /> <br /> *[[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Morphology&quot;&gt;&lt;/span&gt;<br /> ===Morphology===<br /> <br /> *[[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_IGT&quot;&gt;&lt;/span&gt;<br /> ==IGT==<br /> <br /> *[[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLink IF]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics&quot;&gt;&lt;/span&gt;<br /> ==Informatics==<br /> <br /> *[[Documentation/Nightly/Modules/SEG2NRRD|SEG 2 NRRD]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Tables|Tables]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Data|Data]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *DumpSEGFrame &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Terminologies|Terminologies]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Units|Units]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SampleData|Sample Data]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Colors|Colors]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Annotations|Annotations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Markups|Markups]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/EncodeSEG|Encode SEG]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy&quot;&gt;&lt;/span&gt;<br /> ==Legacy==<br /> &lt;span id=&quot;Modules_by_category_Legacy_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Filtering&quot;&gt;&lt;/span&gt;<br /> ===Filtering===<br /> <br /> *[[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Registration&quot;&gt;&lt;/span&gt;<br /> ===Registration===<br /> <br /> *Test Grid Transform Registration &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==MultiVolume Support==<br /> <br /> *[https://slicer.readthedocs.io/en/latest/user_guide/modules/multivolumeimporter.html MultiVolume Importer] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[https://slicer.readthedocs.io/en/latest/user_guide/modules/multivolumeexplorer.html MultiVolume Explorer] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Quantification&quot;&gt;&lt;/span&gt;<br /> <br /> ==Quantification==<br /> <br /> *[[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *SegmentStatistics &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINSLabelStats &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataProbe|Data Probe]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration&quot;&gt;&lt;/span&gt;<br /> ==Registration==<br /> <br /> *[[Documentation/Nightly/Modules/Transforms|Transforms]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *BRAINSResize &lt;small&gt;(cli)&lt;/small&gt;<br /> *PerformMetricTest &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSResample|BRAINS Resample]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSFit|General registration (BRAINS)]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *[[Documentation/Nightly/Modules/ACPCTransform|AC-PC Transform]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINS Demon Warp]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Reformat|Reformat]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *VBRAINSDemonWarp &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation&quot;&gt;&lt;/span&gt;<br /> ==Segmentation==<br /> <br /> *[[Documentation/Nightly/Modules/Segmentations|Segmentations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Editor|Editor]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EMSegment|EMSegment]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> *EMSegmentQuick &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *BRAINS ROI Auto &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment CommandLine &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Surface_Models&quot;&gt;&lt;/span&gt;<br /> <br /> ==Surface Models==<br /> <br /> *[[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelMaker|Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelToLabelMap|Model To LabelMap]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MergeModels|Merge Models]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMap Smoothing]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities&quot;&gt;&lt;/span&gt;<br /> ==Utilities==<br /> <br /> *[[Documentation/Nightly/Modules/ScreenCapture|Screen Capture]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataStore|Data Store]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicompatcher.html DICOM Patcher] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINS Strip Rotation &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment Transform To New Format &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities_BRAINS&quot;&gt;&lt;/span&gt;<br /> ===BRAINS===<br /> <br /> *BRAINS Transform Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Wizards&quot;&gt;&lt;/span&gt;<br /> ==Wizards==<br /> <br /> *[[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools&quot;&gt;&lt;/span&gt;<br /> ==Developer Tools==<br /> <br /> *[[Documentation/Nightly/Modules/Cameras|Cameras]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/extensionwizard.html Extension Wizard] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EventBroker|Event Broker]]<br /> *Double Arrays &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools_DICOM_Plugins&quot;&gt;&lt;/span&gt;<br /> ===DICOM Plugins===<br /> <br /> *DICOMParametricMapPlugin<br /> *DicomUltrasoundPlugin<br /> *DICOMSegmentationPlugin<br /> *DICOMSlicerDataBundlePlugin<br /> *DICOMTID1500Plugin<br /> *[[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]<br /> *DICOMScalarVolumePlugin<br /> *DICOMDiffusionVolumePlugin<br /> *DICOMLongitudinalPETCTPlugin<br /> *DicomSroImportPlugin<br /> *[[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]<br /> *DicomRtImportExportPlugin<br /> *MultiVolumeImporterPlugin<br /> <br /> |}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/MultiVolumeImporter&diff=64266 2022-11-14T02:43:53Z

<p>Lasso: Moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/multivolumeimporter.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/MultiVolumeExplorer&diff=64265 2022-11-14T02:43:28Z

<p>Lasso: Moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/multivolumeexplorer.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/ModuleExtensionListing&diff=64264 2022-11-13T18:02:21Z

<p>Lasso: Updated link to point to readthedocs</p> <hr /> <div>__NOTOC__<br /> &lt;noinclude&gt;{{:Documentation/Nightly/ModuleExtensionListing/TOC}}&lt;/noinclude&gt;<br /> = Modules by category =<br /> 46 categories:<br /> * [[#Modules_by_category_Astronomy|Astronomy]]<br /> * [[#Modules_by_category_Cardiac|Cardiac]]<br /> * [[#Modules_by_category_Cardiac_MRI_Toolkit|Cardiac MRI Toolkit]]<br /> * [[#Modules_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]<br /> ** [[#Modules_by_category_Chest_Imaging_Platform_Toolkit|Toolkit]]<br /> *** [[#Modules_by_category_Toolkit_Particles|Particles]]<br /> *** [[#Modules_by_category_Toolkit_Processing|Processing]]<br /> *** [[#Modules_by_category_Toolkit_Quantification|Quantification]]<br /> *** [[#Modules_by_category_Toolkit_Registration|Registration]]<br /> *** [[#Modules_by_category_Toolkit_Segmentation|Segmentation]]<br /> *** [[#Modules_by_category_Toolkit_Utils|Utils]]<br /> * [[#Modules_by_category_CIP|CIP]]<br /> * [[#Modules_by_category_Converters|Converters]]<br /> * [[#Modules_by_category_Developer_Tools|Developer Tools]]<br /> ** [[#Modules_by_category_Developer_Tools_DICOM_Plugins|DICOM Plugins]]<br /> ** [[#Modules_by_category_Developer_Tools_Editor_Extensions|Editor Extensions]]<br /> ** [[#Modules_by_category_Developer_Tools_Matlab|Matlab]]<br /> ** [[#Modules_by_category_Developer_Tools_Segment_Editor_Extensions|Segment Editor Extensions]]<br /> ** [[#Modules_by_category_Developer_Tools_Utils|Utils]]<br /> * [[#Modules_by_category_Diffusion|Diffusion]]<br /> ** [[#Modules_by_category_Diffusion_Diffusion_Data_Conversion|Diffusion Data Conversion]]<br /> ** [[#Modules_by_category_Diffusion_Diffusion_Tensor_Images|Diffusion Tensor Images]]<br /> ** [[#Modules_by_category_Diffusion_Diffusion_Weighted_Images|Diffusion Weighted Images]]<br /> ** [[#Modules_by_category_Diffusion_Import_and_Export|Import and Export]]<br /> ** [[#Modules_by_category_Diffusion_Process|Process]]<br /> ** [[#Modules_by_category_Diffusion_Quantify|Quantify]]<br /> ** [[#Modules_by_category_Diffusion_Tractography|Tractography]]<br /> *** [[#Modules_by_category_Tractography_Region-based|Region-based]]<br /> ** [[#Modules_by_category_Diffusion_Utilities|Utilities]]<br /> * [[#Modules_by_category_Editor_Effects|Editor Effects]]<br /> * [[#Modules_by_category_EditorEffect|EditorEffect]]<br /> * [[#Modules_by_category_Endoscopy|Endoscopy]]<br /> * [[#Modules_by_category_Examples|Examples]]<br /> * [[#Modules_by_category_Exporter|Exporter]]<br /> * [[#Modules_by_category_Filter|Filter]]<br /> * [[#Modules_by_category_Filtering|Filtering]]<br /> ** [[#Modules_by_category_Filtering_Arithmetic|Arithmetic]]<br /> ** [[#Modules_by_category_Filtering_Denoising|Denoising]]<br /> ** [[#Modules_by_category_Filtering_Morphology|Morphology]]<br /> * [[#Modules_by_category_IGT|IGT]]<br /> * [[#Modules_by_category_Informatics|Informatics]]<br /> ** [[#Modules_by_category_Informatics_Converters|Converters]]<br /> * [[#Modules_by_category_Legacy|Legacy]]<br /> ** [[#Modules_by_category_Legacy_Converters|Converters]]<br /> ** [[#Modules_by_category_Legacy_Filtering|Filtering]]<br /> ** [[#Modules_by_category_Legacy_Registration|Registration]]<br /> ** [[#Modules_by_category_Legacy_Work_in_Progress|Work in Progress]]<br /> *** [[#Modules_by_category_Work_in_Progress_Diffusion_Tensor|Diffusion Tensor]]<br /> **** [[#Modules_by_category_Diffusion_Tensor_Test|Test]]<br /> * [[#Modules_by_category_Libraries|Libraries]]<br /> * [[#Modules_by_category_Machine_Learning|Machine Learning]]<br /> * [[#Modules_by_category_Margin_Calculator|Margin Calculator]]<br /> * [[#Modules_by_category_Mesh_Generation|Mesh Generation]]<br /> * [[#Modules_by_category_MeshGeneration|MeshGeneration]]<br /> * [[#Modules_by_category_Microscopy|Microscopy]]<br /> * [[#Modules_by_category_MultiVolume_Support|MultiVolume Support]]<br /> * [[#Modules_by_category_Pathology|Pathology]]<br /> * [[#Modules_by_category_Perk_Tutor|Perk Tutor]]<br /> * [[#Modules_by_category_Plastimatch|Plastimatch]]<br /> ** [[#Modules_by_category_Plastimatch_Registration|Registration]]<br /> ** [[#Modules_by_category_Plastimatch_Utilities|Utilities]]<br /> * [[#Modules_by_category_Quantification|Quantification]]<br /> ** [[#Modules_by_category_Quantification_ChangeQuantification|ChangeQuantification]]<br /> * [[#Modules_by_category_Radiology|Radiology]]<br /> * [[#Modules_by_category_Radiotherapy|Radiotherapy]]<br /> * [[#Modules_by_category_Registration|Registration]]<br /> ** [[#Modules_by_category_Registration_CMF_Registration|CMF Registration]]<br /> *** [[#Modules_by_category_CMF_Registration_Voxelbase_Registration|Voxelbase Registration]]<br /> ** [[#Modules_by_category_Registration_Label_Registration|Label Registration]]<br /> ** [[#Modules_by_category_Registration_Specialized|Specialized]]<br /> * [[#Modules_by_category_Segmentation|Segmentation]]<br /> ** [[#Modules_by_category_Segmentation_Specialized|Specialized]]<br /> * [[#Modules_by_category_Sequences|Sequences]]<br /> * [[#Modules_by_category_Slicelets|Slicelets]]<br /> * [[#Modules_by_category_SlicerProstate|SlicerProstate]]<br /> * [[#Modules_by_category_Surface_Models|Surface Models]]<br /> * [[#Modules_by_category_TestCases|TestCases]]<br /> * [[#Modules_by_category_Testing|Testing]]<br /> ** [[#Modules_by_category_Testing_IGT_Tests|IGT Tests]]<br /> ** [[#Modules_by_category_Testing_SlicerRT_Tests|SlicerRT Tests]]<br /> ** [[#Modules_by_category_Testing_TestCases|TestCases]]<br /> * [[#Modules_by_category_Ultrasound|Ultrasound]]<br /> * [[#Modules_by_category_Uncategorized|Uncategorized]]<br /> * [[#Modules_by_category_Utilities|Utilities]]<br /> ** [[#Modules_by_category_Utilities_BRAINS|BRAINS]]<br /> * [[#Modules_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]<br /> * [[#Modules_by_category_Virtual_Reality|Virtual Reality]]<br /> * [[#Modules_by_category_Web_System_Tools|Web System Tools]]<br /> * [[#Modules_by_category_Wizards|Wizards]]<br /> * [[#Modules_by_category_XNATSlicer|XNATSlicer]]<br /> &lt;span id='Modules_by_category_Astronomy'&gt;&lt;/span&gt;<br /> == Astronomy ==<br /> * [[Documentation/Nightly/Modules/AstroVolume|AstroVolume]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroReproject|AstroReproject]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroStatistics|AstroStatistics]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroMasking|AstroMasking]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroSampleData|AstroSampleData]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroProfiles|AstroProfiles]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroMomentMaps|AstroMomentMaps]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroPVSlice|AstroPVSlice]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroPVDiagram|AstroPVDiagram]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroModeling|AstroModeling]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroWelcome|AstroWelcome]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Cardiac'&gt;&lt;/span&gt;<br /> <br /> == Cardiac ==<br /> * [[Documentation/Nightly/Extensions/SlicerHeart|Philips4dUsDicomPatcher]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerHeart|ValveView]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Cardiac_MRI_Toolkit'&gt;&lt;/span&gt;<br /> == Cardiac MRI Toolkit ==<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitPVAntrumCut] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitBooleanREMOVEFilter] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentationWorkflow]] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistrationBRAINSFit] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAutomaticLeftAtrialScar] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitConnectedThresholdFilter] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitWizard] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitIsolatedConnectedFilter] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitInhomogeneityCorrection] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAxialDilate] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ScarVisualization|ScarVisualization]] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistration] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitLASegmentationGraphCuts] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Chest_Imaging_Platform'&gt;&lt;/span&gt;<br /> == Chest Imaging Platform ==<br /> * [http://www.chestimagingplatform.org CIP_MIPViewer] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_BodyComposition] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_InteractiveLobeSegmentation] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_TracheaStentPlanning] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_LesionModel] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org AirwayInspector] &lt;small&gt;(loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_PAARatio] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_CalciumScoring] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_ParenchymaAnalysis] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_ParenchymaSubtypeTraining] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_PointsLabelling] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Chest_Imaging_Platform_Toolkit'&gt;&lt;/span&gt;<br /> === Toolkit ===<br /> &lt;span id='Modules_by_category_Toolkit_Particles'&gt;&lt;/span&gt;<br /> ==== Particles ====<br /> * [http://www.chestimagingplatform.org ExtractParticlesFromChestRegionChestType] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterVesselParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RemoveParticlesFromParticlesDataSet] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org PerturbParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org MergeParticleDataSets] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterAirwayParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FitLobeSurfaceModelsToParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ClassifyFissureParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateStenciledLabelMapFromParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterFissureParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Toolkit_Processing'&gt;&lt;/span&gt;<br /> ==== Processing ====<br /> * [http://www.chestimagingplatform.org ResampleLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RescaleLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateMedianFilteredImage] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org LabelMapFromRegionAndTypePoints] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CropLung] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateNLMFilteredImage] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RemoveChestTypeFromLabelMapUsingParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateAtlasConvexHull] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RemapLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeFissureFeatureVectors] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateLobeSurfaceModels] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterConnectedComponents] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ExtractChestLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org PerformMorphological] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ExtractFissureBoundaryFromLobeMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org EnhanceFissuresInImage] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GraphCutsOptimization] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateDistanceMapFromLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ResampleCT] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeFeatureStrength] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeDistanceMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org QualityControl] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateImageSubVolumes] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Toolkit_Quantification'&gt;&lt;/span&gt;<br /> ==== Quantification ====<br /> * [http://www.chestimagingplatform.org EvaluateLungLobeSegmentationResults] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetTransformationKappa] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadWriteImageData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeIntensityStatistics] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeCrossSectionalArea] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateParenchymaPhenotypes] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org LabelParticlesByChestRegionChestType] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetTransformationSimilarityMetric] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetTransformationKappa2D] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Toolkit_Registration'&gt;&lt;/span&gt;<br /> ==== Registration ====<br /> *[[:Category:Documentation/Nightly/Modules/Registration|Introduction to Registration]] &lt;small&gt;(by Dominik Meier)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegisterLungAtlas] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegisterLabelMaps] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegisterCT] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Toolkit_Segmentation'&gt;&lt;/span&gt;<br /> <br /> ==== Segmentation ====<br /> * [http://www.chestimagingplatform.org GenerateOtsuLungCast] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org SegmentLungAirways] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org SegmentLungLobes] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GeneratePartialLungLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateSimpleLungMask] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org SplitLeftLungRightLung] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateBinaryThinning3D] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateLesionSegmentation] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Toolkit_Utils'&gt;&lt;/span&gt;<br /> ==== Utils ====<br /> * [http://www.chestimagingplatform.org ConvertDicom] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegionTypeLocationsToROIVolume] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadVTKWriteNRRDs] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateModel] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateOverlayImages] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ExecuteSystemCommand] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetStructuresInLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FindPatchMatch] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ConvertChestRegionChestTypeToLabelMapValue] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org MaskOutLabelMapStructures] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadNRRDsWriteVTK] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ConvertLabelMapValueToChestRegionChestType] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadWriteRegionAndTypePoints] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org MergeChestLabelMaps] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadVidaWriteCIP] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadDicomWriteTags] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org TransferRegionAndTypeIndicesToFromPoints] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_CIP'&gt;&lt;/span&gt;<br /> == CIP ==<br /> * [http://www.chestimagingplatform.org CIP_] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_Common] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Converters'&gt;&lt;/span&gt;<br /> == Converters ==<br /> * [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|QuadEdgeSurfaceMesher]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CropVolume|CropVolume]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/OrientScalarVolume|OrientScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/UKFTractography|ConvertVTK]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VectorToScalarVolume|VectorToScalarVolume]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CreateDICOMSeries|CreateDICOMSeries]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ParticlesDisplay] &lt;small&gt;(loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegionType] &lt;small&gt;(loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Developer_Tools'&gt;&lt;/span&gt;<br /> == Developer Tools ==<br /> * [[Documentation/Nightly/Modules/Cameras|Cameras]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ExecutionModelTour|ExecutionModelTour]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DebuggingTools|NodeModifiedStatistics]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DebuggingTools|PyDevRemoteDebug]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ExtensionWizard|ExtensionWizard]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DebuggingTools|NodeInfo]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ImageMaker|ImageMaker]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ExtensionStats|ExtensionStats]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/EventBroker|EventBroker]]<br /> * DoubleArrays &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Developer_Tools_DICOM_Plugins'&gt;&lt;/span&gt;<br /> === DICOM Plugins ===<br /> * DICOMParametricMapPlugin<br /> * DicomUltrasoundPlugin<br /> * DICOMSegmentationPlugin<br /> * DICOMSlicerDataBundlePlugin<br /> * DICOMTID1500Plugin<br /> * [[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]<br /> * DICOMScalarVolumePlugin<br /> * DICOMDiffusionVolumePlugin<br /> * DICOMLongitudinalPETCTPlugin<br /> * DicomSroImportPlugin<br /> * [[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]<br /> * DicomRtImportExportPlugin<br /> * MultiVolumeImporterPlugin<br /> &lt;span id='Modules_by_category_Developer_Tools_Editor_Extensions'&gt;&lt;/span&gt;<br /> === Editor Extensions ===<br /> * [[Documentation/4.3/Modules/FastGrowCut|FastGrowCutEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/4.3/Modules/FastGrowCut|FastGrowCutEffect]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSliceEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGAEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PETTumorSegmentationEffect|PETTumorSegmentationEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|BinaryWatershedEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|DoubleThresholdEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Developer_Tools_Matlab'&gt;&lt;/span&gt;<br /> === Matlab ===<br /> * [[Documentation/Nightly/Modules/MatlabModuleGenerator|MatlabModuleGenerator]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MatlabCommander|MatlabCommander]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Developer_Tools_Segment_Editor_Extensions'&gt;&lt;/span&gt;<br /> === Segment Editor Extensions ===<br /> * [[Documentation/Nightly/Extensions/PETTumorSegmentation|SegmentEditorPETTumor]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Developer_Tools_Utils'&gt;&lt;/span&gt;<br /> === Utils ===<br /> * [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion'&gt;&lt;/span&gt;<br /> == Diffusion ==<br /> * [[Documentation/Nightly/Modules/DMRIInstall|DMRIInstall]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Diffusion_Data_Conversion'&gt;&lt;/span&gt;<br /> === Diffusion Data Conversion ===<br /> * DWIConvert &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Diffusion_Tensor_Images'&gt;&lt;/span&gt;<br /> === Diffusion Tensor Images ===<br /> * [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Diffusion_Weighted_Images'&gt;&lt;/span&gt;<br /> === Diffusion Weighted Images ===<br /> * BRAINSDWICleanup &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Import_and_Export'&gt;&lt;/span&gt;<br /> === Import and Export ===<br /> * DWIConvert &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerDMRI|DICOMTract_to_VTK]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerDMRI|VTK_to_DICOMTract]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Process'&gt;&lt;/span&gt;<br /> === Process ===<br /> * [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|DiffusionWeightedVolumeMasking]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DWIToDTIEstimation|DWIToDTIEstimation]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Quantify'&gt;&lt;/span&gt;<br /> === Quantify ===<br /> * [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|DiffusionTensorScalarMeasurements]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiberTractMeasurements|FiberTractMeasurements]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Tractography'&gt;&lt;/span&gt;<br /> === Tractography ===<br /> * [[Documentation/Nightly/Modules/TractographyInteractiveSeeding|TractographyInteractiveSeeding]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TractographyDisplay|TractographyDisplay]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Tractography_Region-based'&gt;&lt;/span&gt;<br /> ==== Region-based ====<br /> * [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|TractographyLabelMapSeeding]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiberBundleLabelSelect|FiberBundleLabelSelect]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Diffusion_Utilities'&gt;&lt;/span&gt;<br /> === Utilities ===<br /> * BRAINSDWICleanup &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ResampleDTIVolume|ResampleDTIVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiberBundleToLabelMap|FiberBundleToLabelMap]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerDMRI|DICOM2FullBrainTractography]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Editor_Effects'&gt;&lt;/span&gt;<br /> == Editor Effects ==<br /> * [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_EditorEffect'&gt;&lt;/span&gt;<br /> == EditorEffect ==<br /> * [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Endoscopy'&gt;&lt;/span&gt;<br /> == Endoscopy ==<br /> * [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Examples'&gt;&lt;/span&gt;<br /> == Examples ==<br /> * [[Documentation/Nightly/Modules/FastGrowCut|FastGrowCut]] &lt;small&gt;(loadable, bundled in [[Documentation/4.3/Modules/FastGrowCut|FastGrowCutEffect]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGA]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|FastGrowCutSegmenter]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutCore]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> * [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutInteractiveSegmenter] &lt;small&gt;(loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Exporter'&gt;&lt;/span&gt;<br /> == Exporter ==<br /> * [[Documentation/Nightly/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Filter'&gt;&lt;/span&gt;<br /> == Filter ==<br /> * IslandRemoval &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Filtering'&gt;&lt;/span&gt;<br /> == Filtering ==<br /> * [[Documentation/Nightly/Modules/SegmentationSmoothing|SegmentationSmoothing]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBiasFieldCorrection]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ImageLabelCombine|ImageLabelCombine]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|VotingBinaryHoleFillingImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CheckerBoardFilter|CheckerBoardFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [https://slicer.readthedocs.io/en/latest/user_guide/modules/extractskeleton.html ExtractSkeleton] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [https://slicer.readthedocs.io/en/latest/user_guide/modules/simplefilters.html SimpleFilters] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [https://slicer.readthedocs.io/en/latest/user_guide/modules/thresholdscalarvolume.html ThresholdScalarVolume] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [https://slicer.readthedocs.io/en/latest/user_guide/modules/histogrammatching.html HistogramMatching] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Filtering_Arithmetic'&gt;&lt;/span&gt;<br /> === Arithmetic ===<br /> * [[Documentation/Nightly/Modules/MultiplyScalarVolumes|MultiplyScalarVolumes]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AddScalarVolumes|AddScalarVolumes]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MaskScalarVolume|MaskScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SubtractScalarVolumes|SubtractScalarVolumes]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CastScalarVolume|CastScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/OpenCVExample|BlendVectorVolumes]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Filtering_Denoising'&gt;&lt;/span&gt;<br /> === Denoising ===<br /> * [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|CurvatureAnisotropicDiffusion]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|GradientAnisotropicDiffusion]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MedianImageFilter|MedianImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GaussianBlurImageFilter|GaussianBlurImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Filtering_Morphology'&gt;&lt;/span&gt;<br /> === Morphology ===<br /> * [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|GrayscaleFillHoleImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|GrayscaleGrindPeakImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_IGT'&gt;&lt;/span&gt;<br /> <br /> == IGT ==<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|Viewpoint]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CollectFiducials|CollectFiducials]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|TransformFusion]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GyroGuide|GyroGuide]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|PlusModelCatalogBrowser]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|CreateModels]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TrackerStabilizer|TrackerStabilizer]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/TrackerStabilizer|TrackerStabilizer]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PathExplorer|PathExplorer]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|UltrasoundSnapshots]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|BreachWarning]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|FiducialRegistrationWizard]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|ModelRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ResectionVolume|ResectionVolume]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|PivotCalibration]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VolumeResliceDriver|VolumeResliceDriver]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|FiducialsToModelRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Watchdog|Watchdog]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CornerAnnotation|CornerAnnotation]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|MarkupsToModel]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/iGyne|iGyne]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|iGyne]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PlusRemote|PlusRemote]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Informatics'&gt;&lt;/span&gt;<br /> == Informatics ==<br /> * [[Documentation/Nightly/Extensions/DCMQI|tid1500writer]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/mpReview|mpReviewPreprocessor]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SEG2NRRD|SEG2NRRD]] &lt;small&gt;(cli)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|segimage2itkimage]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/mpReview|mpReview]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Tables|Tables]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Data|Data]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * DumpSEGFrame &lt;small&gt;(cli)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|tid1500reader]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * Terminologies &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Units|Units]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DICOM|DICOM]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SampleData|SampleData]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Colors|Colors]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Annotations|Annotations]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Markups|Markups]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SubjectHierarchy|SubjectHierarchy]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Informatics_Converters'&gt;&lt;/span&gt;<br /> === Converters ===<br /> * [[Documentation/Nightly/Extensions/DCMQI|itkimage2paramap]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|paramap2itkimage]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|itkimage2segimage]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/EncodeSEG|EncodeSEG]] &lt;small&gt;(cli)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Legacy'&gt;&lt;/span&gt;<br /> == Legacy ==<br /> &lt;span id='Modules_by_category_Legacy_Converters'&gt;&lt;/span&gt;<br /> === Converters ===<br /> * [[Documentation/Nightly/Modules/BSplineToDeformationField|BSplineToDeformationField]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Legacy_Filtering'&gt;&lt;/span&gt;<br /> === Filtering ===<br /> * [[Documentation/Nightly/Modules/OtsuThresholdImageFilter|OtsuThresholdImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ResampleScalarVolume|ResampleScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Legacy_Registration'&gt;&lt;/span&gt;<br /> === Registration ===<br /> * TestGridTransformRegistration &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ExpertAutomatedRegistration|ExpertAutomatedRegistration]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Legacy_Work_in_Progress'&gt;&lt;/span&gt;<br /> === Work in Progress ===<br /> &lt;span id='Modules_by_category_Work_in_Progress_Diffusion_Tensor'&gt;&lt;/span&gt;<br /> ==== Diffusion Tensor ====<br /> &lt;span id='Modules_by_category_Diffusion_Tensor_Test'&gt;&lt;/span&gt;<br /> ===== Test =====<br /> * DiffusionTensorTest &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Libraries'&gt;&lt;/span&gt;<br /> == Libraries ==<br /> * [[Documentation/Nightly/Extensions/SlicerOpenCV|OpenCV]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Machine_Learning'&gt;&lt;/span&gt;<br /> == Machine Learning ==<br /> * [[Documentation/Nightly/Modules/DeepInfer|DeepInfer]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Margin_Calculator'&gt;&lt;/span&gt;<br /> == Margin Calculator ==<br /> * [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/MarginCalculator|DoseMorphology]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/MarginCalculator|SyntheticRTDose]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Mesh_Generation'&gt;&lt;/span&gt;<br /> == Mesh Generation ==<br /> * [[Documentation/Nightly/Extensions/CleaverExtension|CleaverCLI]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_MeshGeneration'&gt;&lt;/span&gt;<br /> == MeshGeneration ==<br /> * [[Documentation/Nightly/Modules/BodyCentricCubicMesh|BodyCentricCubicMesh]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Microscopy'&gt;&lt;/span&gt;<br /> == Microscopy ==<br /> * [[Documentation/Nightly/Extensions/IASEM|IASEMImportSeries]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|BinShrink]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|LabelObjectStatistics]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|SpacingAwareCurvatureDiffusion]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_MultiVolume_Support'&gt;&lt;/span&gt;<br /> == MultiVolume Support ==<br /> * [[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolumeImporter]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolumeExplorer]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Pathology'&gt;&lt;/span&gt;<br /> == Pathology ==<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Perk_Tutor'&gt;&lt;/span&gt;<br /> == Perk Tutor ==<br /> * [[Documentation/Nightly/Extensions/PerkTutor|PythonMetricsCalculator]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TransformRecorder|TransformRecorder]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PerkEvaluator|PerkEvaluator]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/WorkflowSegmentation|WorkflowSegmentation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Plastimatch'&gt;&lt;/span&gt;<br /> == Plastimatch ==<br /> * [[Documentation/Nightly/Modules/DicomSroExport|DicomSroExport]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|PlmRegister]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Plastimatch_Registration'&gt;&lt;/span&gt;<br /> === Registration ===<br /> * [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_bspline]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_landwarp]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Plastimatch_Utilities'&gt;&lt;/span&gt;<br /> === Utilities ===<br /> * [[Documentation/Nightly/Extensions/SlicerRT|PlastimatchPy]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Quantification'&gt;&lt;/span&gt;<br /> == Quantification ==<br /> * [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] &lt;small&gt;(cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/PET-IndiC|PETIndiC]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Q3DC|Q3DC]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/HeterogeneityCAD|HeterogeneityCAD]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ShapeQuantifier|ShapeQuantifier]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|QuantitativeIndicesCLI]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandardUptakeValueComputation]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactorCalculator]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PETDICOM|PETDICOMExtension]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|SpinalCurvatureMeasurement]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/QuantitativeIndicesTool|QuantitativeIndicesTool]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)&lt;/small&gt;<br /> * SegmentStatistics &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelStatistics|LabelStatistics]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MeshStatistics|MeshStatistics]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/MeshStatistics|MeshStatisticsExtension]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DWModeling|DWModeling]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> * BRAINSLabelStats &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PkModeling|PkModeling]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|PkModeling]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImageMaker]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DataProbe|DataProbe]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AnglePlanes|AnglePlanes]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/dPetBrainQuantification|dPetBrainQuantification]] &lt;small&gt;(scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PickAndPaint|PickAndPaint]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PickAndPaint|PickAndPaintExtension]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DiceComputation|DiceComputation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Quantification_ChangeQuantification'&gt;&lt;/span&gt;<br /> === ChangeQuantification ===<br /> * [[Documentation/Nightly/Modules/IntensityDifferenceMetric|IntensityDifferenceMetric]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Radiology'&gt;&lt;/span&gt;<br /> <br /> == Radiology ==<br /> * [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerZFrameRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Radiotherapy'&gt;&lt;/span&gt;<br /> == Radiotherapy ==<br /> * [[Documentation/Nightly/Extensions/SlicerRT|Beams]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|DvhComparison]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DoseVolumeHistogram|DoseVolumeHistogram]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|DicomRtImportExport]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DoseAccumulation|DoseAccumulation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|ExternalBeamPlanning]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentComparison|SegmentComparison]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|PlanarImage]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Isodose|Isodose]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DoseComparison|DoseComparison]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentMorphology|SegmentMorphology]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DicomSroImport|DicomSroImport]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Registration'&gt;&lt;/span&gt;<br /> == Registration ==<br /> * [[Documentation/Nightly/Modules/Transforms|Transforms]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * BRAINSResize &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * PerformMetricTest &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Registration_CMF_Registration'&gt;&lt;/span&gt;<br /> === CMF Registration ===<br /> * [[Documentation/Nightly/Extensions/CMFreg|ApplyMatrix]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelExtraction|LabelExtraction]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelAddition|LabelAddition]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Downsize|Downsize]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SurfaceRegistration|SurfaceRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_CMF_Registration_Voxelbase_Registration'&gt;&lt;/span&gt;<br /> ==== Voxelbase Registration ====<br /> * [[Documentation/Nightly/Modules/NonGrowing|NonGrowing]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Growing|Growing]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MaskCreation|MaskCreation]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Registration_Label_Registration'&gt;&lt;/span&gt;<br /> === Label Registration ===<br /> * [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|DistanceMapBasedRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Registration_Specialized'&gt;&lt;/span&gt;<br /> === Specialized ===<br /> * [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiducialRegistration|FiducialRegistration]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemonWarp]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Reformat|Reformat]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] extension)&lt;/small&gt;<br /> * VBRAINSDemonWarp &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Segmentation'&gt;&lt;/span&gt;<br /> == Segmentation ==<br /> * [[Documentation/Nightly/Modules/ROBEXBrainExtraction|ROBEXBrainExtraction]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]] extension)&lt;/small&gt;<br /> * EMSegmentQuick &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithModel]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)&lt;/small&gt;<br /> * [http://www.nitrc.org/projects/abc ABC] &lt;small&gt;(cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|VolumeClipToLabel]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentationCLI]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LAScarSegmenter|LAScarSegmenter]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AirwaySegmentation|AirwaySegmentation]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SkullStripper|SkullStripper]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]] extension)&lt;/small&gt;<br /> * [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFastMarching] &lt;small&gt;(scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SobolevSegmenter|SobolevSegmenter]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithRoi]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentCAD|SegmentCAD]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SwissSkullStripper|SwissSkullStripper]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]] extension)&lt;/small&gt;<br /> * [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFloodFilling] &lt;small&gt;(scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)&lt;/small&gt;<br /> * [https://github.com/Tomnl/Slicer-Wasp Wasp] &lt;small&gt;(scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Editor|Editor]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/EMSegment|EMSegment]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] extension)&lt;/small&gt;<br /> * [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorWatershed] &lt;small&gt;(scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Segmentation_Specialized'&gt;&lt;/span&gt;<br /> === Specialized ===<br /> * BRAINSROIAuto &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|RobustStatisticsSegmenter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * EMSegmentCommandLine &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Sequences'&gt;&lt;/span&gt;<br /> == Sequences ==<br /> * [[Documentation/Nightly/Extensions/Sequences|Sequences]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/Sequences|SequenceBrowser]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/Sequences|MetafileImporter]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Slicelets'&gt;&lt;/span&gt;<br /> == Slicelets ==<br /> * [[Documentation/Nightly/Modules/FilmDosimetry|FilmDosimetryAnalysis]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Modules/FilmDosimetry|FilmDosimetryAnalysis]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysisAlgo]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_SlicerProstate'&gt;&lt;/span&gt;<br /> == SlicerProstate ==<br /> * [[Documentation/Nightly/Extensions/SliceTracker|ZFrameCalibration]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Surface_Models'&gt;&lt;/span&gt;<br /> == Surface Models ==<br /> * [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GrayscaleModelMaker|GrayscaleModelMaker]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ModelMaker|ModelMaker]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ModelToLabelMap|ModelToLabelMap]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MergeModels|MergeModels]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/EasyClip|EasyClip]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|EasyClip]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMapSmoothing]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ProbeVolumeWithModel|ProbeVolumeWithModel]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|TextureModel]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_TestCases'&gt;&lt;/span&gt;<br /> == TestCases ==<br /> * SEGExporterSelfTest<br /> &lt;span id='Modules_by_category_Testing'&gt;&lt;/span&gt;<br /> == Testing ==<br /> * CLI4Test<br /> * ThresholdThreadingTest<br /> * [[Documentation/Nightly/Extensions/Scoliosis|ScoliosisMonitoring]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)&lt;/small&gt;<br /> * SlicerMRBSaveRestoreCheckPathsTest<br /> * CLIROITest &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * PerformanceTests<br /> * SlicerMRBMultipleSaveRestoreTest<br /> * SlicerMRBTest<br /> * SEGExporterSelfTest<br /> * SelfTests<br /> * SlicerMRBMultipleSaveRestoreLoopTest<br /> &lt;span id='Modules_by_category_Testing_IGT_Tests'&gt;&lt;/span&gt;<br /> === IGT Tests ===<br /> * BreachWarningSelfTest<br /> * WatchdogSelfTest<br /> &lt;span id='Modules_by_category_Testing_SlicerRT_Tests'&gt;&lt;/span&gt;<br /> === SlicerRT Tests ===<br /> * IGRTWorkflow_SelfTest<br /> * [[Documentation/Nightly/Extensions/SlicerRT|BatchStructureSetConversion]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Testing_TestCases'&gt;&lt;/span&gt;<br /> === TestCases ===<br /> * AtlasTests<br /> * AddStorableDataAfterSceneViewTest<br /> * test_tractography_display<br /> * SlicerTransformInteractionTest1<br /> * RSNAQuantTutorial<br /> * NeurosurgicalPlanningTutorialMarkupsSelfTest<br /> * ChangeTrackerSelfTest<br /> * FiducialLayoutSwitchBug1914<br /> * GraphCutSegmentSelfTest<br /> * SlicerBoundsTest<br /> * UtilTest<br /> * Charting &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures] &lt;small&gt;(scripted, bundled in [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures] extension)&lt;/small&gt;<br /> * fiber_visibility_crash2438<br /> * RSNAVisTutorial<br /> * JRC2013Vis<br /> * AddManyMarkupsFiducialTest<br /> * CropVolumeSelfTest<br /> * SliceLinkLogic &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * VolumeRenderingSceneClose &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * slicerCloseCrashBug2590<br /> * CLIEventTest<br /> * [[Documentation/Nightly/Extensions/SlicerDMRI|NsgPlanTracto]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * MarkupsWidgetsSelfTest<br /> * TablesSelfTest<br /> * SlicerOrientationSelectorTest<br /> * MarkupsInViewsSelfTest<br /> * TwoCLIsInParallelTest<br /> * SubjectHierarchyCorePluginsSelfTest<br /> * SubjectHierarchyGenericSelfTest<br /> * ScenePerformance &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * MarkupsInCompareViewersSelfTest<br /> * sceneImport2428<br /> * RSNA2012ProstateDemo<br /> * DTINotReproducibleIssue3977<br /> * TwoCLIsInARowTest<br /> * ColorsScalarBarSelfTest<br /> * BRAINSFitRigidRegistrationCrashIssue4139<br /> * Slicer4Minute &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * ViewControllersSliceInterpolationBug1926<br /> &lt;span id='Modules_by_category_Ultrasound'&gt;&lt;/span&gt;<br /> == Ultrasound ==<br /> * [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertCurvilinearArray] &lt;small&gt;(cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)&lt;/small&gt;<br /> * [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertPhasedArray3D] &lt;small&gt;(cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)&lt;/small&gt;<br /> * [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertSliceSeries] &lt;small&gt;(cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Uncategorized'&gt;&lt;/span&gt;<br /> == Uncategorized ==<br /> * [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifierCore]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractorLib]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Utilities'&gt;&lt;/span&gt;<br /> == Utilities ==<br /> * [[Documentation/Nightly/Modules/ScreenCapture|ScreenCapture]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DataStore|DataStore]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * DICOMPatcher &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * BRAINSStripRotation &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * EMSegmentTransformToNewFormat &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Utilities_BRAINS'&gt;&lt;/span&gt;<br /> === BRAINS ===<br /> * BRAINSTransformConvert &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Vascular_Modeling_Toolkit'&gt;&lt;/span&gt;<br /> == Vascular Modeling Toolkit ==<br /> * [http://slicer.vmtk.org/ CenterlineComputation] &lt;small&gt;(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)&lt;/small&gt;<br /> * [http://slicer.vmtk.org/ LevelSetSegmentation] &lt;small&gt;(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)&lt;/small&gt;<br /> * [http://slicer.vmtk.org/ VesselnessFiltering] &lt;small&gt;(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Virtual_Reality'&gt;&lt;/span&gt;<br /> == Virtual Reality ==<br /> * [[Documentation/Nightly/Modules/VirtualReality|VirtualReality]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Web_System_Tools'&gt;&lt;/span&gt;<br /> == Web System Tools ==<br /> * [[Documentation/Nightly/Modules/DatabaseInteractor|DatabaseInteractor]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_Wizards'&gt;&lt;/span&gt;<br /> == Wizards ==<br /> * [[Documentation/Nightly/Modules/CompareVolumes|CompareVolumes]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ChangeTracker|ChangeTracker]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)&lt;/small&gt;<br /> &lt;span id='Modules_by_category_XNATSlicer'&gt;&lt;/span&gt;<br /> == XNATSlicer ==<br /> * [[Documentation/Nightly/Extensions/XNATSlicer|XnatSlicer]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]] extension)&lt;/small&gt;<br /> <br /> = Modules by name =<br /> 367 modules:<br /> * [http://www.nitrc.org/projects/abc ABC] &lt;small&gt;(cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AddScalarVolumes|AddScalarVolumes]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org AirwayInspector] &lt;small&gt;(loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AirwaySegmentation|AirwaySegmentation]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentationCLI]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/AirwaySegmentation|AirwaySegmentation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AnglePlanes|AnglePlanes]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Annotations|Annotations]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/CMFreg|ApplyMatrix]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroMasking|AstroMasking]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroModeling|AstroModeling]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroMomentMaps|AstroMomentMaps]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroProfiles|AstroProfiles]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroPVDiagram|AstroPVDiagram]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroPVSlice|AstroPVSlice]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroReproject|AstroReproject]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerAstro|AstroSampleData]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroStatistics|AstroStatistics]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/AstroVolume|AstroVolume]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerAstro|AstroWelcome]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|Beams]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|BinShrink]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/OpenCVExample|BlendVectorVolumes]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/BodyCentricCubicMesh|BodyCentricCubicMesh]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemonWarp]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * BRAINSDWICleanup &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * BRAINSLabelStats &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * BRAINSResize &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * BRAINSROIAuto &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * BRAINSStripRotation &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * BRAINSTransformConvert &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|BreachWarning]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CastScalarVolume|CastScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://slicer.vmtk.org/ CenterlineComputation] &lt;small&gt;(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ChangeTracker|ChangeTracker]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CheckerBoardFilter|CheckerBoardFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_BodyComposition] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_CalciumScoring] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_Common] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_InteractiveLobeSegmentation] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_LesionModel] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_MIPViewer] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_PAARatio] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_ParenchymaAnalysis] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_ParenchymaSubtypeTraining] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_PointsLabelling] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CIP_TracheaStentPlanning] &lt;small&gt;(scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ClassifyFissureParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/CleaverExtension|CleaverCLI]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAutomaticLeftAtrialScar] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAxialDilate] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitBooleanREMOVEFilter] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitConnectedThresholdFilter] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitInhomogeneityCorrection] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitIsolatedConnectedFilter] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitLASegmentationGraphCuts] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitPVAntrumCut] &lt;small&gt;(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistration] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistrationBRAINSFit] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitWizard] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CollectFiducials|CollectFiducials]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Colors|Colors]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CompareVolumes|CompareVolumes]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeCrossSectionalArea] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeDistanceMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeFeatureStrength] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeFissureFeatureVectors] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ComputeIntensityStatistics] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ConvertChestRegionChestTypeToLabelMapValue] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ConvertDicom] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ConvertLabelMapValueToChestRegionChestType] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/UKFTractography|ConvertVTK]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CornerAnnotation|CornerAnnotation]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CreateDICOMSeries|CreateDICOMSeries]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|CreateModels]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org CropLung] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CropVolume|CropVolume]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|CurvatureAnisotropicDiffusion]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Data|Data]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DatabaseInteractor|DatabaseInteractor]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractorLib]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DataProbe|DataProbe]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DataStore|DataStore]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DeepInfer|DeepInfer]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DiceComputation|DiceComputation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DICOM|DICOM]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerDMRI|DICOM2FullBrainTractography]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * DICOMPatcher &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|DicomRtImportExport]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DicomSroExport|DicomSroExport]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DicomSroImport|DicomSroImport]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerDMRI|DICOMTract_to_VTK]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|DiffusionTensorScalarMeasurements]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|DiffusionWeightedVolumeMasking]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|DistanceMapBasedRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DMRIInstall|DMRIInstall]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DoseAccumulation|DoseAccumulation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DoseComparison|DoseComparison]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/MarginCalculator|DoseMorphology]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DoseVolumeHistogram|DoseVolumeHistogram]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Downsize|Downsize]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/dPetBrainQuantification|dPetBrainQuantification]] &lt;small&gt;(scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis] extension)&lt;/small&gt;<br /> * [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] &lt;small&gt;(cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)&lt;/small&gt;<br /> * DumpSEGFrame &lt;small&gt;(cli)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|DvhComparison]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * DWIConvert &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DWIToDTIEstimation|DWIToDTIEstimation]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/DWModeling|DWModeling]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/EasyClip|EasyClip]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|EasyClip]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Editor|Editor]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/EMSegment|EMSegment]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * EMSegmentCommandLine &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * EMSegmentQuick &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * EMSegmentTransformToNewFormat &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/EncodeSEG|EncodeSEG]] &lt;small&gt;(cli)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org EnhanceFissuresInImage] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org EvaluateLungLobeSegmentationResults] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ExecuteSystemCommand] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|ExternalBeamPlanning]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ExtractChestLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ExtractFissureBoundaryFromLobeMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ExtractParticlesFromChestRegionChestType] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ExtractSkeleton|ExtractSkeleton]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FastGrowCut|FastGrowCut]] &lt;small&gt;(loadable, bundled in [[Documentation/4.3/Modules/FastGrowCut|FastGrowCutEffect]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|FastGrowCutSegmenter]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiberBundleLabelSelect|FiberBundleLabelSelect]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiberBundleToLabelMap|FiberBundleToLabelMap]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiberTractMeasurements|FiberTractMeasurements]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FiducialRegistration|FiducialRegistration]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|FiducialRegistrationWizard]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|FiducialsToModelRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/FilmDosimetry|FilmDosimetryAnalysis]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Modules/FilmDosimetry|FilmDosimetryAnalysis]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterAirwayParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterConnectedComponents] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterFissureParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FilterVesselParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FindPatchMatch] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org FitLobeSurfaceModelsToParticleData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GaussianBlurImageFilter|GaussianBlurImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysisAlgo]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Modules/GelDosimetry|GelDosimetryAnalysis]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateAtlasConvexHull] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateBinaryThinning3D] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateDistanceMapFromLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateImageSubVolumes] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateLesionSegmentation] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateLobeSurfaceModels] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateMedianFilteredImage] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateModel] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateNLMFilteredImage] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateOtsuLungCast] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateOverlayImages] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateParenchymaPhenotypes] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GeneratePartialLungLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateSimpleLungMask] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GenerateStenciledLabelMapFromParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetStructuresInLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetTransformationKappa] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetTransformationKappa2D] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GetTransformationSimilarityMetric] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|GradientAnisotropicDiffusion]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutInteractiveSegmenter] &lt;small&gt;(loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org GraphCutsOptimization] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|GrayscaleFillHoleImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|GrayscaleGrindPeakImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GrayscaleModelMaker|GrayscaleModelMaker]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Growing|Growing]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/GyroGuide|GyroGuide]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/HeterogeneityCAD|HeterogeneityCAD]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/HistogramMatching|HistogramMatching]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|IASEMImportSeries]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/iGyne|iGyne]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|iGyne]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ImageLabelCombine|ImageLabelCombine]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/IntensityDifferenceMetric|IntensityDifferenceMetric]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] extension)&lt;/small&gt;<br /> * IslandRemoval &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Isodose|Isodose]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|itkimage2paramap]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|itkimage2segimage]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|KUtil]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelAddition|LabelAddition]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelExtraction|LabelExtraction]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org LabelMapFromRegionAndTypePoints] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMapSmoothing]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|LabelObjectStatistics]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org LabelParticlesByChestRegionChestType] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LabelStatistics|LabelStatistics]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LAScarSegmenter|LAScarSegmenter]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentationWorkflow]] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [http://slicer.vmtk.org/ LevelSetSegmentation] &lt;small&gt;(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Markups|Markups]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|MarkupsToModel]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MaskCreation|MaskCreation]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org MaskOutLabelMapStructures] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MaskScalarVolume|MaskScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MedianImageFilter|MedianImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org MergeChestLabelMaps] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MergeModels|MergeModels]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org MergeParticleDataSets] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MeshStatistics|MeshStatistics]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/MeshStatistics|MeshStatisticsExtension]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/Sequences|MetafileImporter]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ModelMaker|ModelMaker]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|ModelRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Models|Models]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ModelToLabelMap|ModelToLabelMap]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/mpReview|mpReview]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/mpReview|mpReviewPreprocessor]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MultiplyScalarVolumes|MultiplyScalarVolumes]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolumeExplorer]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolumeImporter]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBiasFieldCorrection]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/NonGrowing|NonGrowing]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerOpenCV|OpenCV]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/OrientScalarVolume|OrientScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|paramap2itkimage]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ParticlesDisplay] &lt;small&gt;(loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PathExplorer|PathExplorer]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)&lt;/small&gt;<br /> * PerformMetricTest &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org PerformMorphological] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PerkEvaluator|PerkEvaluator]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org PerturbParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/PET-IndiC|PETIndiC]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandardUptakeValueComputation]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImageMaker]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerHeart|Philips4dUsDicomPatcher]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PickAndPaint|PickAndPaint]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PickAndPaint|PickAndPaintExtension]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|PivotCalibration]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PkModeling|PkModeling]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|PkModeling]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|PlanarImage]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_bspline]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_landwarp]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|PlastimatchPy]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|PlmRegister]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|PlusModelCatalogBrowser]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/PlusRemote|PlusRemote]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ProbeVolumeWithModel|ProbeVolumeWithModel]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/PerkTutor|PythonMetricsCalculator]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Q3DC|Q3DC]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|QuadEdgeSurfaceMesher]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org QualityControl] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|QuantitativeIndicesCLI]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/QuantitativeIndicesTool|QuantitativeIndicesTool]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGA]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadDicomWriteTags] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadNRRDsWriteVTK] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadVidaWriteCIP] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadVTKWriteNRRDs] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadWriteImageData] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ReadWriteRegionAndTypePoints] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Reformat|Reformat]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegionType] &lt;small&gt;(loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegionTypeLocationsToROIVolume] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegisterCT] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegisterLabelMaps] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RegisterLungAtlas] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RemapLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RemoveChestTypeFromLabelMapUsingParticles] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RemoveParticlesFromParticlesDataSet] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ResampleCT] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ResampleDTIVolume|ResampleDTIVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org ResampleLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org RescaleLabelMap] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ResectionVolume|ResectionVolume]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ROBEXBrainExtraction|ROBEXBrainExtraction]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|RobustStatisticsSegmenter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SampleData|SampleData]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertCurvilinearArray] &lt;small&gt;(cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)&lt;/small&gt;<br /> * [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertPhasedArray3D] &lt;small&gt;(cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)&lt;/small&gt;<br /> * [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertSliceSeries] &lt;small&gt;(cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ScarVisualization|ScarVisualization]] &lt;small&gt;(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SceneViews|SceneViews]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ScreenCapture|ScreenCapture]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SEG2NRRD|SEG2NRRD]] &lt;small&gt;(cli)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|segimage2itkimage]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Segmentations|Segmentations]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentationSmoothing|SegmentationSmoothing]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentCAD|SegmentCAD]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentComparison|SegmentComparison]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFastMarching] &lt;small&gt;(scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)&lt;/small&gt;<br /> * [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFloodFilling] &lt;small&gt;(scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)&lt;/small&gt;<br /> * [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorWatershed] &lt;small&gt;(scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org SegmentLungAirways] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org SegmentLungLobes] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SegmentMorphology|SegmentMorphology]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * SegmentStatistics &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/Sequences|SequenceBrowser]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/Sequences|Sequences]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ShapeQuantifier|ShapeQuantifier]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifierCore]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutCore]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SimpleFilters|SimpleFilters]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SkullStripper|SkullStripper]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerZFrameRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SobolevSegmenter|SobolevSegmenter]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/IASEM|SpacingAwareCurvatureDiffusion]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|SpinalCurvatureMeasurement]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org SplitLeftLungRightLung] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SubjectHierarchy|SubjectHierarchy]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SubtractScalarVolumes|SubtractScalarVolumes]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SurfaceRegistration|SurfaceRegistration]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactorCalculator]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/PETDICOM|PETDICOMExtension]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/SwissSkullStripper|SwissSkullStripper]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/MarginCalculator|SyntheticRTDose]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Tables|Tables]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)&lt;/small&gt;<br /> * Terminologies &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|TextureModel]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ThresholdScalarVolume|ThresholdScalarVolume]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|tid1500reader]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/DCMQI|tid1500writer]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TrackerStabilizer|TrackerStabilizer]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/TrackerStabilizer|TrackerStabilizer]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TractographyDisplay|TractographyDisplay]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TractographyInteractiveSeeding|TractographyInteractiveSeeding]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|TractographyLabelMapSeeding]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [http://www.chestimagingplatform.org TransferRegionAndTypeIndicesToFromPoints] &lt;small&gt;(cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|TransformFusion]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/TransformRecorder|TransformRecorder]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Transforms|Transforms]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|UltrasoundSnapshots]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Units|Units]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerHeart|ValveView]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)&lt;/small&gt;<br /> * VBRAINSDemonWarp &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VectorToScalarVolume|VectorToScalarVolume]] &lt;small&gt;(scripted, built-in)&lt;/small&gt;<br /> * [http://slicer.vmtk.org/ VesselnessFiltering] &lt;small&gt;(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerRT|VffFileReader]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/ViewControllers|ViewControllers]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerIGT|Viewpoint]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VirtualReality|VirtualReality]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|VolumeClipToLabel]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithModel]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithRoi]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VolumeRendering|VolumeRendering]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VolumeResliceDriver|VolumeResliceDriver]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Volumes|Volumes]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|VotingBinaryHoleFillingImageFilter]] &lt;small&gt;(cli, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SlicerDMRI|VTK_to_DICOMTract]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)&lt;/small&gt;<br /> * [https://github.com/Tomnl/Slicer-Wasp Wasp] &lt;small&gt;(scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Watchdog|Watchdog]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/Welcome|Welcome]] &lt;small&gt;(loadable, built-in)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Modules/WorkflowSegmentation|WorkflowSegmentation]] &lt;small&gt;(loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/XNATSlicer|XnatSlicer]] &lt;small&gt;(scripted, bundled in [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]] extension)&lt;/small&gt;<br /> * [[Documentation/Nightly/Extensions/SliceTracker|ZFrameCalibration]] &lt;small&gt;(cli, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)&lt;/small&gt;</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/Data&diff=64263 2022-11-13T17:57:44Z

<p>Lasso: moved page to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/simplefilters.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Tutorials/MigrationGuide/Slicer&diff=64187 2022-09-14T16:43:06Z

<p>Lasso: /* Slicer 5.3: Removed Annotation module */</p> <hr /> <div>&lt;noinclude&gt;__TOC__&lt;/noinclude&gt;<br /> ==Slicer backward incompatible changes==<br /> <br /> ===Slicer 5.0: API changes since 4.10===<br /> <br /> *Removed protected method &lt;tt&gt;vtkMRMLModelDisplayableManager::FindPickedDisplayNodeFromMesh&lt;/tt&gt;<br /> <br /> ==== Supporting only Python 3.6 and above ====<br /> Slicer python code has been updated to support Python 3.6 and above syntax using [https://github.com/asottile/pyupgrade pyupgrade] to automatically update the syntax.<br /> <br /> Install pyupgrade: &lt;code&gt;PythonSlicer -m pip install pyupgrade&lt;/code&gt;<br /> <br /> * Running:<br /> ** On 1 file: &lt;code&gt;PythonSlicer -m pyupgrade --py36-plus MyPythonFile.py&lt;/code&gt;<br /> ** On multiple files: Here is my pyupgrade-script.py written to automate running pyupgrade across all python files in the Slicer repo. It was run by &lt;code&gt;PythonSlicer pyupgrade-script.py&lt;/code&gt;<br /> &lt;syntaxhighlight lang=&quot;python&quot;&gt;<br /> # pyupgrade-script.py<br /> import os<br /> import subprocess<br /> <br /> search_directory = &quot;C:/Users/MyUserName/Documents/GitHub/Slicer&quot;<br /> for root, _, files in os.walk(search_directory):<br />   for file_item in files:<br />     file_path = os.path.join(root, file_item)<br />       if os.path.isfile(file_path) and file_path.endswith(&quot;.py&quot;):<br />         subprocess.call([&quot;PythonSlicer&quot;, &quot;-m&quot;, &quot;pyupgrade&quot;, &quot;--py36-plus&quot;, file_path])<br /> &lt;/syntaxhighlight&gt;<br /> <br /> ====Python 2 to Python 3====<br /> <br /> Slicer core has been updated to only support Python 3.<br /> <br /> C++ classes and python scripts have been updated to use idioms and constructs only available in Python 3.<br /> <br /> Update to python scripts have been done leveraging the CLI provided by https://python-future.org by (1) iteratively applying each one of the associates &quot;fixes&quot;, (2) reviewing associated changes and (3) updating as needed.<br /> <br /> Updates specific to extensions are discussed in [[Documentation/Nightly/Developers/Tutorials/MigrationGuide#Slicer_5.0:_Python2_to_Python3]]<br /> <br /> ====Interactor styles====<br /> <br /> Limitations of VTK widgets (editable points, lines, curves, etc.) prevented Slicer from having sophisticated user interaction in slice and 3D views. In Slicer5, we replaced VTK widgets with MRML widgets. These widgets are still VTK-based and somewhat similar to VTK widgets, but they operate directly on MRML nodes, they use direct method calls between widgets and their representation, and they use a more efficient and flexible event processing. Instead of hardcoding how viewers behave in response to interaction (mouse move, button click, keyboard, ...) events in an interactor style, all these events are translated to actions and performed in a MRML widget. Most modules are not expected to observe interactor events or styles directly, but if they did, then they may need to be updated accordingly.<br /> <br /> *vtkSliceViewInteractorStyle renamed to vtkMRMLSliceDViewInteractorStyle to reflect that it uses MRML classes directly.<br /> *vtkThreeDViewInteractorStyle renamed to vtkMRMLThreeDViewInteractorStyle to reflect that it uses MRML classes directly.<br /> <br /> ====slicer.util functions====<br /> <br /> *slicer.util.loadVolume (and other node load functions) now return the loaded node instead of a True/False flag. In case of an error, a RuntimeError exception is thrown.<br /> **Old way of loading a node and get it in a variable: &lt;code&gt;volumeNode = slicer.util.loadVolume('path/to/volume.nrrd', returnNode=True)[1]&lt;/code&gt;<br /> **New way of loading a node and get it in a variable: &lt;code&gt;volumeNode = slicer.util.loadVolume('path/to/volume.nrrd')&lt;/code&gt;<br /> <br /> ====Markups====<br /> <br /> *&lt;tt&gt;vtkCommand::Modified&lt;/tt&gt; events are no longer invoked when control points are added/removed/modified to improve performance. Modules that need to know If a point position is modified need to add observers to &lt;tt&gt;vtkMRMLMarkupsNode::PointAddedEvent&lt;/tt&gt;, &lt;tt&gt;vtkMRMLMarkupsNode::PointRemovedEvent&lt;/tt&gt;, &lt;tt&gt;vtkMRMLMarkupsNode::PointModifiedEvent&lt;/tt&gt; events. See example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#get-a-notification-if-a-markup-point-position-is-modified Script repository].<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::MarkupAddedEvent&lt;/tt&gt; is renamed to &lt;tt&gt;PointPositionDefinedEvent&lt;/tt&gt;. There is a similar event, &lt;tt&gt;vtkMRMLMarkupsNode::PointAddedEvent&lt;/tt&gt;, which is called even when preview point is created.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::MarkupRemovedEvent&lt;/tt&gt; is renamed to &lt;tt&gt;vtkMRMLMarkupsNode::PointPositionUndefinedEvent&lt;/tt&gt;. There is a similar event, &lt;tt&gt;vtkMRMLMarkupsNode::PointRemovedEvent&lt;/tt&gt;, which is called even when preview point is removed.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::NthMarkupModifiedEvent&lt;/tt&gt; is replaced by &lt;tt&gt;vtkMRMLMarkupsNode::PointModifiedEvent&lt;/tt&gt;<br /> *During placement of markups, a preview markup point is created. If number of already placed markup points needs to be determined then &lt;code&gt;GetNumberOfDefinedControlPoints()&lt;/code&gt; method can be used.<br /> *&lt;tt&gt;GetDefaultMarkups...()&lt;/tt&gt; and &lt;tt&gt;SetDefaultMarkups...()&lt;/tt&gt; methods are removed. Instead default display node can be accessed by &lt;tt&gt;GetDefaultMarkupsDisplayNode()&lt;/tt&gt; method and default values can be get/set in that class.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::GetNthMarkupSelected()&lt;/tt&gt; is replaced by &lt;tt&gt;GetNthControlPointSelected()&lt;/tt&gt;<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::PointPositionDefinedEvent&lt;/tt&gt; event is added. This event is invoked whenever position is defined for a new point.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::PointPositionUndefinedEvent&lt;/tt&gt; event is added. This event is invoked whenever point with defined position is removed (point is deleted or its position gets undefined).<br /> *For more details, see [{{doxygen-class-url|vtkMRMLMarkupsNode}} vtkMRMLMarkupsNode]<br /> <br /> ====Segmentations====<br /> <br /> Binary labelmap segmentations can now be represented as shared labelmaps.<br /> The previous implementation of binary labelmaps was performance intensive as each labelmap was represented using a separate vtkDataObject.<br /> Visualizing and editing segmentations that contained a large number of segments could cause performance issues, due to the large number of vtkActors required, as well as calculating masks and overwriting other segments when editing.<br /> <br /> By default, newly created segments will now be contained on the same layer.<br /> Segments will only be separated into multiple layers if the user creates an overlapping segment when editing.<br /> <br /> Segments are now saved as a 4D volume with shared 3D layers.<br /> For a segmentation that only uses one layer, the resulting image is a 3D volume.<br /> Before saving, the labelmaps will be collapsed into as few layers as possible.<br /> <br /> *seg.nrrd files now contain two additional attributes for each segment: SegmentX_LabelValue and SegmentX_Layer<br /> *The label value of a segment can be found using vtkSegment::GetLabelValue()<br /> *Whether or not a segment is shared can be found using vtkSegmentation::IsSharedBinaryLabelmap()<br /> *The other segments sharing the same labelmap can be found using vtkSegmentation::GetSegmentIDsSharingBinaryLabelmapRepresentation()<br /> *Segment editor effects should generally use modifySelectedSegmentByLabelmap rather than SetBinaryLabelmapToSegment to manage layer separation<br /> *Conversion rules now call PreConvert() and PostConvert() before and after conversion to perform pre and post processing steps on the segmentation as a whole<br /> *The function signature for vtkSegmentationConverterRule::Convert now accepts a vtkSegment rather than two vtkDataObjects<br /> *slicer.util.arrayFromSegment has been deprecated. slicer.util.arrayFromSegmentBinaryLabelmap and slicer.util.arrayFromSegmentInternalBinaryLabelmap can be used instead<br /> <br /> =====Erase the contents of a single segment=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.ClearSegment(segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Set labelmap in a segment=====<br /> <br /> Directly, bypassing masking settings:<br /> <br /> &lt;pre&gt;<br /> slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(orientedImageDataToSet, segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Move a segment from a shared labelmap to a separate layer=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.SeparateSegmentLabelmap(segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Combine all binary labelmaps to as few layers as possible=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.CollapseBinaryLabelmaps(forceToSingleLayer=false)<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Get a read-only labelmap for a single segment:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> labelmap = slicer.vtkOrientedImageData()<br /> segmentationNode.GetBinaryLabelmapRepresentation(segmentId, labelmap)<br /> &lt;/pre&gt;<br /> <br /> (similarly, use GetClosedSurfaceRepresentation with an additional vtk.vtkPolyData parameter to get a read-only surface mesh)<br /> <br /> or<br /> <br /> &lt;pre&gt;<br /> labelmapNumpyArray = slicer.util.arrayFromSegmentBinaryLabelmap(segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Get a modifiable shared labelmap=====<br /> <br /> &lt;pre&gt;<br /> labelmap = slicer.vtkOrientedImageData()<br /> segmentationNode.GetBinaryLabelmapInternalRepresentation(segmentId, labelmap)<br /> &lt;/pre&gt;<br /> <br /> (similarly, use GetClosedSurfaceInternalRepresentation to get a modifiable surface mesh)<br /> <br /> or<br /> <br /> &lt;pre&gt;<br /> labelmapNumpyArray = slicer.util.arrayFromSegmentInternalBinaryLabelmap(segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Export segments to models=====<br /> <br /> Model hierarchies no longer exist in Slicer5, but instead various kinds of hierarchies are now replaced by &quot;subject hierarchy&quot;, which can accommodate any node types in a single hierarchy. Accordingly, `ExportSegmentsToModelHierarchy`, `ExportAllSegmentsToModelHierarchy`, etc. are replaced by `ExportSegmentsToModels`, `ExportAllSegmentsToModels`, which take a subject hierarchy folder item ID as input.<br /> Documentation/Nightly<br /> See code example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#export-model-nodes-from-segmentation-node Script repository].<br /> <br /> =====Smoothing effect=====<br /> <br /> In Slicer-4.11 version before October 29, 2020 (and earlier versions), Gaussian smoothing method's Standard deviation parameter (&quot;GaussianStandardDeviationMm&quot;) was interpreted in pixels, while on the user interface and code it was claimed to be in physical units (millimeter). The problem was fixed and now the parameter is in millimeter.<br /> <br /> ====Volume rendering====<br /> <br /> vtkMRMLVolumeRenderingDisplayNode::SetAndObserveVolumeNodeID method was removed, as display node base class already maintains a pointer to the displayed (volume) node. To associate a volume display node with a volume node, call &lt;pre&gt;volumeNode-&gt;AddAndObserveDisplayNodeID(volumeRenderingDisplayNode-&gt;GetID());&lt;/pre&gt; after both nodes are added to the scene.<br /> <br /> ''vtkSlicerVolumeRenderingLogic::CreateDefaultVolumeRenderingNodes'' method unnecessarily polluted the scene with ROI node even though the user did not need cropping. In Slicer-5.x we fixed the issue by not creating the ROI nodes automatically. To create a ROI node, you can call ''vtkSlicerVolumeRenderingLogic::CreateROINode'' method.<br /> <br /> ====Extract skeleton====<br /> <br /> Command-line arguments of the module have been updated:<br /> - output image is now optional, therefore the output image file name must be specified using &quot;--outputImage&quot; argument<br /> - output image centerline voxel value is set to 255 (instead of 1) to make it easier to apply image processing operations on it (values can be interpolated between 0 and 255, while there are no integer values between 0 and 1)<br /> - &quot;--dontPrune&quot; is renamed to &quot;--fullTree&quot; for clarity<br /> - centerline curve is saved in mrk.json format<br /> <br /> ==== MRML node copy API improvements ====<br /> <br /> Slicer-4.10 and earlier had a single Copy() method, which had limitations:<br /> - usually implemented deep copy (but sometimes bulk data was just shallow-copied): problem, because for quick browsing of sequences, we need shallow-copy (to avoid copying bulk data, such as vtkImageData)<br /> - copied all node properties (except node ID and scene): this required workarounds, whenever we wanted to copy only the content of nodes (but for example keeping node references or node name intact)<br /> <br /> In Slicer-4.11, these limitations are addressed, by implementing a ''CopyContent(vtkMRMLNode* node, bool deepCopy=true)'' method which allows choosing between deep/shallow copy (create an independent copy of bulk data or pass bulk data pointer) and does not copy node ID, Scene, Name, SingletonTag, HideFromEditors, AddToScene, UndoEnabled, and node references.<br /> <br /> To make it easier to introduce this new method into existing classes, helper macros are implemented.<br /> <br /> If a class implements CopyContent method then the developer must make sure that CopyContent and HasCopyContent methods are implemented in all parent classes by adding vtkMRMLCopyContentMacro(ClassName) or vtkMRMLCopyContentDefaultMacro(ClassName) to the class headers. vtkMRMLCopyContentDefaultMacro should be used when the class does not have any additional properties (only those that parent classes already copy). CopyContent must be implemented by calling CopyContent of the parent class, and then copy node properties added in he class (preferable using shallow copy for large data, if deepCopy argument was set to false).<br /> <br /> If HasCopyContent macro is not added to a class then it cannot be recorded or replayed in Sequences module.<br /> <br /> ==== Removed classes ====<br /> <br /> Classes removed due to removing legacy Editor module:<br /> * vtkITKNewOtsuThresholdImageFilter is replaced by vtkITKImageThresholdCalculator<br /> * vtkITKGrowCutSegmentationImageFilter is replaced by vtkImageGrowCutSegment (it will be replaced by the ITK implementation https://github.com/Slicer/Slicer/pull/5807)<br /> * vtkITKTimeSeriesDatabase was removed, it was an incomplete class, not used anywhere<br /> * vtkITKWandImageFilter was removed, vtkImageThresholdConnectivity (in VTK) can be used instead<br /> * vtkImageConnectivity was removed, vtkImageThresholdConnectivity (in VTK) can be used instead<br /> * vtkImageErode was removed, vtkImageDilateErode3D (in VTK) can be used instead<br /> * vtkImageLabelChange was removed, vtkImageThreshold (in VTK) can be used instead<br /> * vtkImageSlicePaint was replaced by logic built into qSlicerSegmentEditorPaintEffect<br /> * vtkImageStash is replaced by vtkSegmentationHistory<br /> * vtkPichonFastMarching moved to SegmentEditorExtraEffects extension (https://github.com/lassoan/SlicerSegmentEditorExtraEffects)<br /> <br /> Classes removed due to removing Charts and DoubleArrays modules:<br /> * vtkMRMLChartNode is replaced by vtkMRMLPlotNode<br /> * vtkMRMLChartViewNode is replaced by vtkMRMLPlotViewNode<br /> * vtkMRMLDoubleArrayNode is replaced by vtkMRMLTableNode (can store any number of columns, not just two)<br /> * vtkMRMLDoubleArrayStorageNode is replaced by vtkMRMLTableStorageNode<br /> * qMRMLChartView is replaced by qMRMLPlotView<br /> * qMRMLChartViewControllerWidget is replaced by qMRMLPlotViewControllerWidget<br /> * qMRMLChartWidget is replaced by qMRMLPlotWidget<br /> <br /> ===Slicer 5.3: Removed Annotation module===<br /> <br /> Annotations module, which provides `vtkMRMLAnnotationROI` and `vtkMRMLAnnotationRuler` nodes have been deprecated since April 2021 and is to be removed in Slicer-4.3.<br /> <br /> When a scene is loaded into Slicer that contains annotation nodes, they are converted to markup nodes: `vtkMRMLAnnotationROI` is converted to `vtkMRMLMarkupsROI`; and `vtkMRMLAnnotationRuler` is converted to `vtkMRMLMarkupsLine`. All Slicer core modules that previously used annotation nodes, now use markup nodes instead.<br /> <br /> All extensions, too, need to be updated to use markup nodes instead of annotation nodes. For backward compatibility (so that the same extension can be used with current Slicer version and Slicer-4.2 and earlier versions), it is useful to keep the modules accept both markup and annotation nodes, but always create markup nodes by default.<br /> <br /> Tips for updating a module to use markups:<br /> <br /> * In node selectors, wherever `vtkMRMLAnnotationROINode` is accepted, add `vtkMRMLMarkupsLineNode` _before_ it (so they are both accepted, but markups are preferred)<br /> * In node selectors, wherever `vtkMRMLAnnotationRuler` is accepted, add `vtkMRMLMarkupsLine` _before_ it (so they are both accepted, but markups are preferred)<br /> * For ROIs:<br /> ** When only non-rotated ROIs are used: you can still use `GetXYZ()` and `GetRadiusXYZ()` methods work the same way for markups ROI<br /> ** When ROIs are rotated, markups ROIs support built-in rotation and scaling, therefore it is recommended to use the `exportRoi.GetObjectToWorldMatrix()` method to get all the transforms (including the transform inside the markup node and any transforms applied using transform nodes) that are applied to the bounding box object (that has its center in the origin and its diameter returned by `GetSize()`).<br /> * For rulers:<br /> ** Use `GetNthControlPointPosition(0)` and `GetNthControlPointPosition(1)` methods to get the endpoints of the line.<br /> ** Use `GetNumberOfDefinedControlPoints()` method to check if both endpoints of the line are defined.<br /> ** Use `GetMeasurement('length').GetValue()` to get the line length (or for the displayed string, with units: `getNode('L').GetMeasurement('length').GetValueWithUnitsAsPrintableString()`)<br /> <br /> ===Slicer 5.0: Fiducial List was renamed to Point List===<br /> <br /> To simplify terms used in Slicer, &quot;Fiducial List&quot; term was renamed to &quot;Point List&quot; on the user interface.<br /> The term in the API has not been changed to preserve backward compatibility.<br /> <br /> See discussion of the topic [https://discourse.slicer.org/t/delete-control-point-delete-fiducial-pop-up-confirm-box/20430/18 here].<br /> <br /> ===Slicer 5.0: SliceIntersectionVisibility was moved from vtkMRMLSliceCompositeNode to vtkMRMLSliceDisplayNode===<br /> <br /> SliceIntersectionVisibility property (that controls if intersections of other slices should be displayed in the slice view) was stored in vtkMRMLSliceCompositeNode. This was not a good choice because the composite node stores what image layers should be displayed in the slice view and how (what opacity, what blending method, etc.). The property was kept in that class for a long time to preserve backward compatibility, but when interactive slice intersection feature was added and additional properties had to be added that control appearance and behavior of slice intersections, this property was moved into the new vtkMRMLSliceDisplayNode node type and renamed to IntersectingSlicesVisibility.<br /> <br /> Scripts that previously used SliceIntersectionVisibility property will now fail with this error:<br /> <br /> AttributeError: 'MRMLCore.vtkMRMLSliceCompositeNode' object has no attribute 'SetSliceIntersectionVisibility'<br /> <br /> Those failing scripts can be updated with this example in the script repository: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#turn-on-slice-intersections<br /> <br /> ===Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead===<br /> <br /> &lt;b&gt;Error message:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> SlicerPython executable is obsolete and will be removed. Use PythonSlicer executable instead.<br /> For more details, see https://github.com/Slicer/Slicer/issues/4843<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Use &lt;tt&gt;PythonSlicer&lt;/tt&gt; instead of &lt;tt&gt;SlicerPython&lt;/tt&gt;<br /> <br /> &lt;b&gt;Background:&lt;/b&gt;<br /> <br /> Python IDEs (specifically PyCharm, but potentially others) only recognize &lt;tt&gt;Python*.exe&lt;/tt&gt; files as Python interpreters.<br /> <br /> To allow using Slicer's Python interpreter in these IDEs, we had to add &lt;tt&gt;PythonSlicer&lt;/tt&gt;, but kept &lt;tt&gt;SlicerPython&lt;/tt&gt; around for not immediately breaking things.<br /> <br /> This redundancy is confusing for users that we could resolve by simply removing SlicerPython for Slicer5.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/issues/4843<br /> <br /> ===Slicer 5.0: Application must be installed in writable location to install extensions===<br /> <br /> Extensions are now installed in the application home folder because Python packages are installed there anyway, so the application home folder has to be writable (or Slicer has to be run as admin when you install extensions). It also allows making Slicer fully portable - see details [https://discourse.slicer.org/t/slicer-is-now-fully-portable/15410 here].<br /> <br /> If you want to allow any user to install extensions without admin rights and you only need to use extensions that don’t install Python packages at runtime then you can specify a custom extension install path folder in Slicer-NNN.ini file or revert to the old behavior of Slicer by specifying &lt;code&gt;Slicer_STORE_SETTINGS_IN_APPLICATION_HOME_DIR:BOOL=OFF&lt;/code&gt; when configuring your Slicer build.<br /> <br /> ===Slicer 5.0: Models are saved in LPS coordinate system by default===<br /> <br /> While Slicer uses RAS coordinate system internally, images, transforms, and markups files are stored in LPS coordinate system, because DICOM and all medical image computing software (maybe except a few very old ones) uses LPS coordinate system in files.<br /> <br /> However, Slicer has been still using its internal RAS coordinate system in mesh files (STL, VTK, VTP, OBJ, PLY), which caused issues when interfacing with third-party software.<br /> <br /> From Slicer-4.11.0-2020-02-26 (revision 28794) models are saved in LPS coordinate system, and mesh files assumed to be in LPS coordinate system by default (if no other coordinate system specified in the file).<br /> <br /> Slicer started embedding coordinate system name in mesh files a few years ago (see &lt;code&gt;SPACE=RAS&lt;/code&gt; in the file header), so all the files that Slicer saved in recent years will load correctly and any scene files created with any version of Slicer will also load the models with correct orientation, too.<br /> <br /> Manual setting of coordinate system (in Add data dialog / Options column) is only needed when loading a mesh file without a scene that were created by Slicer-4.6 (2017-09-27) and earlier; and obj files created by Slicer-4.6 and Slicer-4.8 (between 2016-10-11 and 2018-03-26), or files are created by third-party software in RAS coordinate system.<br /> <br /> If you encounter orientation issues when loading a model file, you have the following options:<br /> <br /> *Option A: Specify the coordinate system when you open the model file. In “Add data” dialog, click “Show Options” and then choose “RAS” as coordinate system.<br /> *Option B: Update the third-party software that generate the mesh to save coordinates in LPS coordinate system instead of RAS coordinate system. Conversion is simple inverting the sign of the first two coordinates.<br /> *Option C: Write &lt;code&gt;SPACE=RAS&lt;/code&gt; in the comment/description field in the mesh file (for STL, OBJ, PLY, VTK file; for VTP files, add in the first value of a vtkStringArray field array named &lt;code&gt;SPACE&lt;/code&gt;) to indicate that the values are stored in RAS coordinate system. This option is useful if coordinates have to be stored in RAS coordinate system (for example, for compatibility with other software). See implementation example [https://github.com/Slicer/SlicerGitSVNArchive/blob/c0829f596f0ea661e0c5484056bd1374a3d22958/Libs/MRML/Core/vtkMRMLModelStorageNode.cxx#L421-L647 here].<br /> <br /> See more information, discussion of this topic on the [https://discourse.slicer.org/t/model-files-are-now-saved-in-lps-coordinate-system/10446 Slicer forum].<br /> <br /> ===Slicer 5.0: CLI module descriptor XML files assume LPS coordinate system by default===<br /> <br /> If [[Documentation/Nightly/Developers/SlicerExecutionModel|SlicerExecutionModel]] descriptor XML file of a CLI module does not specify coordinate system for a point, pointfile, or region element then the coordinate system is assumed to be &quot;lps&quot;. To preserve previous behavior and use &quot;ras&quot; coordinate system instead, add '''coordinateSystem=&quot;ras&quot;''' to the element.<br /> <br /> ===Slicer 5.0: Sequences extension has been merged into Slicer core===<br /> <br /> Sequences extension has been merged into Slicer core, therefore extensions do not need to depend on Sequences extension anymore.<br /> <br /> SequenceBrowser module has been merged into Sequences module, therefore previous code that used SequenceBrowser module now should use Sequences module instead.<br /> <br /> ===Slicer 5.0: FreeSurfer support has been removed from Slicer core===<br /> The loading of FreeSurfer models and scalar overlays, as well as the FreeSurfer-specific color nodes, have been moved to the new [https://github.com/PerkLab/SlicerFreeSurfer SlicerFreeSurfer] extension. Tutorials on how to use the FreeSurfer Importer module to load multiple files at once can be found on the [https://github.com/PerkLab/SlicerFreeSurfer/wiki/Tutorials SlicerFreeSurfer tutorial page].<br /> <br /> ===Slicer 5.0: Removed Editor module===<br /> <br /> The legacy Editor module has been deprecated since about 2017 and got removed in November 2021. It is replaced by the much improved Segment Editor module.<br /> <br /> ===Slicer 5.0: Removed Charts and DoubleArrays module===<br /> <br /> Charts and DoubleArrays module have been deprecated since about 2018 and got removed in November 2021. They are replaced by Plots and Tables modules.<br /> <br /> '''Example of commits'''<br /> * [https://github.com/SlicerRt/SlicerRT/commit/8f9155f94399be71e747d3d45b1f6c4152caa139 SlicerRT@8f9155f94] ENH: Update DVH module to use plots infrastructure instead of charts<br /> <br /> ===Slicer 5.0 : Avoid typedef of anonymous structure===<br /> <br /> Due to a recent (but retroactive) C++ rule change, only sufficiently C-compatible classes are permitted to be given a typedef name for linkage purposes. Add an &lt;tt&gt;enabled-by-default&lt;/tt&gt; warning for these cases, and rephrase our existing error for the case where we encounter the &lt;tt&gt;typedef&lt;/tt&gt; name for linkage after we've already computed and used a wrong linkage in terms of the new rule.<br /> <br /> &lt;b&gt;To fix warning message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:95:17:<br /> warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]<br /> typedef struct<br /> ^<br /> ColumnInfo<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:99:5:<br /> note: type is not C-compatible due to this default member initializer<br /> int ScalarType = VTK_STRING;<br /> ^~~~~~~~~~~~~~<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:102:5:<br /> note: type is given name 'ColumnInfo' for linkage purposes by this typedef declaration<br /> } ColumnInfo;<br /> ^<br /> For consistency, Use 'using' to a named structure definintion for all <br /> structures.<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> typedef struct<br /> {<br /> std::string ColumnName;<br /> std::vector&lt;vtkAbstractArray*&gt; RawComponentArrays;<br /> int ScalarType = VTK_STRING;<br /> std::vector&lt;std::string&gt; ComponentNames;<br /> std::string NullValueString;<br /> } ColumnInfo;<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> struct StructColumnInfo<br /> {<br /> std::string ColumnName;<br /> std::vector&lt;vtkAbstractArray*&gt; RawComponentArrays;<br /> int ScalarType = VTK_STRING;<br /> std::vector&lt;std::string&gt; ComponentNames;<br /> std::string NullValueString;<br /> };<br /> using ColumnInfo = struct StructColumnInfo;<br /> &lt;/pre&gt;<br /> <br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://reviews.llvm.org/D74103<br /> <br /> ===Slicer 5.0 : Temporary path===<br /> <br /> Temporary path was stored redundantly application settings (Slicer.ini) in two keys: &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; and &lt;code&gt;TemporaryPath&lt;/code&gt;. &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; overwrote &lt;code&gt;TemporaryPath&lt;/code&gt; at startup, but when temporary path was set via the &lt;code&gt;slicer.app.temporaryPath&lt;/code&gt; then it was only written to &lt;code&gt;TemporaryPath&lt;/code&gt;.<br /> <br /> Changed behavior so that only &lt;code&gt;TemporaryPath&lt;/code&gt; is used. &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; is ignored.<br /> <br /> To ensure that temporary path is always writable, it as checked at startup that a file can be created in temporary path and if this check fails then temporary path is reset to default (&lt;code&gt;QDir::tempPath()&lt;/code&gt;).<br /> <br /> ===Slicer 5.0 : Always prefer executable CLIs===<br /> <br /> Previously, if a CLI module was available both as an executable and a shared library, then PreferExecutableCLI application setting was used to determine which one is used. Now always CLIs are always executed in an external process (if an executable is available). Reasons are described in this issue: https://github.com/Slicer/Slicer/issues/4893. The application setting is no more displayed in the GUI and any setting specified in earlier Slicer versions is ignored.<br /> <br /> ===Slicer 5.0 : SlicerApp-real is a console application on Windows===<br /> <br /> Previously, the application (SlicerApp-real.exe) was built as a GUI application (without console) on Windows, to avoid displaying a terminal window when starting the application. This had the drawback that the Slicer application did not have standard input/output that could be displayed or redirected (for example, for capturing into a file). SlicerApp-real has always been a console application on Linux and macOS, therefore this change makes the software behavior more consistent across platforms.<br /> <br /> SlicerApp-real.exe is now built as a console application (see [https://github.com/Slicer/Slicer/issues/2934 #2934]). Displaying of a terminal window is prevented by using a launcher (Slicer.exe) that is built as a GUI application and it starts Slicer with the standard input and outputs redirected.<br /> <br /> To display console output: https://slicer.readthedocs.io/en/latest/developer_guide/debugging/overview.html#console-output-on-windows<br /> <br /> To launch a command-line terminal using &lt;code&gt;subprocess.Popen&lt;/code&gt; that shows a new terminal, specify &lt;code&gt;creationflags=subprocess.CREATE_NEW_CONSOLE&lt;/code&gt; argument.<br /> <br /> ===Slicer 4.11: Variable CMAKE_DEFAULT_BUILD_TYPE renamed to Slicer_DEFAULT_BUILD_TYPE===<br /> <br /> Setting the default build type for single config generator may be done setting &lt;tt&gt;Slicer_DEFAULT_BUILD_TYPE&lt;/tt&gt; instead of &lt;tt&gt;CMAKE_DEFAULT_BUILD_TYPE&lt;/tt&gt;.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> CMake Error:<br /> Generator<br /> <br /> Visual Studio 15 2017<br /> <br /> does not support variable<br /> <br /> CMAKE_DEFAULT_BUILD_TYPE<br /> <br /> but it has been specified.<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/pull/4799<br /> <br /> ===Slicer 4.11: teem python module renamed to vtkTeem, explicit import required===<br /> <br /> *Since the module provides VTK classes interfacing with &quot;teem&quot;, the name is now representative of the class it contains.<br /> *&lt;tt&gt;vtkTeem&lt;/tt&gt; classes are expected to be used by explicitly importing the module.<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> import teem<br /> <br /> class CalculateTensorScalars(object):<br /> def __init__(self):<br /> self.dti_math = teem.vtkDiffusionTensorMathematics()<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> import vtkTeem<br /> <br /> class CalculateTensorScalars(object):<br /> def __init__(self):<br /> self.dti_math = vtkTeem.vtkDiffusionTensorMathematics()<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.11: Display window/level (brightness/contrast) adjustment===<br /> <br /> *A new &quot;Window/level&quot; mouse interaction mode was introduced. Volume display window/level can only be changed if this mode is activated by clicking the corresponding button in the toolbar. The new mouse mode prevents accidental modification of volume window/level (when for example the user accidentally clicked too far from a markup) and it also allows more sophisticated window/level adjustments.<br /> *New region-based auto window/level feature added: activate &quot;Window/level&quot; mouse mode and use Ctrl + left-click-and-drag to highlight a region and optimize window/level for that (pressing Escape or right-click cancels the operation).<br /> *Auto window/level reset: activate &quot;Window/level&quot; mouse mode and double-click the left mouse button.<br /> *Improved auto window/level algorithm to prevent too bright display of images. Window/level is set to display values between 0.1th and 99.9th percentile of gray levels. See details here: https://discourse.slicer.org/t/feedback-requested-how-to-improve-mouse-interaction-in-views/6420.<br /> *Removed class &lt;tt&gt;vtkImageBimodalAnalysis&lt;/tt&gt;<br /> <br /> ===Slicer 4.10: Registration of runTest function done in ScriptedLoadableModule base class===<br /> <br /> Following [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27617 r27617]:<br /> <br /> *the &lt;code&gt;ScriptedLoadableModule&lt;/code&gt; class takes care of registering the &lt;code&gt;runTest&lt;/code&gt; function.<br /> *the &lt;code&gt;runTest&lt;/code&gt; function expects &lt;code&gt;msec&lt;/code&gt; keyword argument.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> Traceback (most recent call last):<br /> File &quot;/path/to/Slicer-SuperBuild/Slicer-build/bin/Python/slicer/ScriptedLoadableModule.py&quot;, line 205, in onReloadAndTest<br /> test(msec=int(slicer.app.userSettings().value(&quot;Developer/SelfTestDisplayMessageDelay&quot;)), **kwargs)<br /> TypeError: runTest() got an unexpected keyword argument 'msec'<br /> Reload and Test: Exception!<br /> <br /> runTest() got an unexpected keyword argument 'msec'<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> class sceneImport2428(ScriptedLoadableModule):<br /> [...]<br /> def __init__(self, parent):<br /> ScriptedLoadableModule.__init__(self, parent)<br /> parent.title = &quot;...&quot;<br /> [...]<br /> parent.acknowledgementText = &quot;...&quot;<br /> self.parent = parent <br /> <br /> # Add this test to the SelfTest module's list for discovery when the module <br /> # is created. Since this module may be discovered before SelfTests itself, <br /> # create the list if it doesn't already exist. <br /> try: <br /> slicer.selfTests <br /> except AttributeError: <br /> slicer.selfTests = {} <br /> slicer.selfTests['sceneImport2428'] = self.runTest <br /> <br /> def runTest(self): <br /> tester = sceneImport2428Test() <br /> tester.runTest()<br /> <br /> [...]<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> class sceneImport2428(ScriptedLoadableModule):<br /> [...]<br /> def __init__(self, parent):<br /> ScriptedLoadableModule.__init__(self, parent)<br /> parent.title = &quot;...&quot;<br /> [...]<br /> parent.acknowledgementText = &quot;...&quot;<br /> <br /> [...]<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: Update of VTK version from 9.0 to 8.2===<br /> <br /> Following [https://github.com/Kitware/VTK/commit/b703d78be3ffd8ae69c319afa0230097ff270f26 kitware/VTK@b703d78be], VTK has updated to use version number 8.2 instead of 9.0. This was discussed in on the VTK mailing list in http://vtk.1045678.n5.nabble.com/Discussion-OK-to-change-VTK-s-version-number-from-9-0-to-8-2-tt5748702.html<br /> <br /> At first, this VTK commit and its companion [https://github.com/Kitware/VTK/commit/8a00b357e84eec695bda049216f30f2b76d80855 kitware/VTK@8a00b357e] were both reverted from the [https://github.com/Slicer/VTK/ Slicer/VTK] fork. Then, since having the corresponding changes reverted in VTK was not possible, it was decided to also update Slicer. This was done in the following commits:<br /> <br /> *[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27472 r27472]: COMP: Update c++ classes to support building against VTK &gt;= 9 and VTK &gt;= 8.2<br /> *[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27473 r27473]: COMP: Update VTK to include version change from 9.0 to 8.2. Fixes #4623<br /> <br /> This means that code depending on VTK must also be updated to include similar fixes.<br /> <br /> '''Replace this:'''<br /> #if VTK_MAJOR_VERSION &gt;= 9<br /> <br /> '''By this:'''<br /> #if VTK_MAJOR_VERSION &gt;= 9 || (VTK_MAJOR_VERSION &gt;= 8 &amp;&amp; VTK_MINOR_VERSION &gt;= 2)<br /> <br /> and<br /> <br /> '''Replace this:'''<br /> #if VTK_MAJOR_VERSION &lt; 9<br /> <br /> '''By this:'''<br /> #if VTK_MAJOR_VERSION &lt;= 7 || (VTK_MAJOR_VERSION &lt;= 8 &amp;&amp; VTK_MINOR_VERSION &lt;= 1)<br /> <br /> <br /> ===Slicer 4.9: ITK_LEGACY_REMOVE is now OFF===<br /> In preparation to switch to ITK 5.0, we disable legacy functionality in ITK. This might affect some modules which rely on ITK. Take a look at [https://itk.org/migrationv4 ITK 4 migration guide] before [https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md ITK 5 migration guide].<br /> <br /> ===Slicer 4.9: vtkMRMLPlotDataNode renamed to vtkMRMLPlotSeriesNode===<br /> Plotting was improved in [https://github.com/Slicer/Slicer/commit/082edc40c this commit]<br /> <br /> '''Replace this:'''<br /> <br /> vtkMRMLPlotDataNode<br /> <br /> '''By this:'''<br /> vtkMRMLPlotSeriesNode<br /> <br /> ===Slicer 4.9: CMake: Module MIDAS not available===<br /> <br /> The test infrastructure of your project should be updated to use [https://cmake.org/cmake/help/latest/module/ExternalData.html ExternalData] built-in CMake module<br /> instead of the specific &lt;tt&gt;MIDAS&lt;/tt&gt; module.<br /> <br /> See EMSegment commit [http://viewvc.slicer.org/viewvc.cgi/Slicer3?view=revision&amp;revision=17150 r17150] for an example of transition.<br /> <br /> This means that instead of using &lt;tt&gt;midas_add_test&lt;/tt&gt; with the &lt;tt&gt;MIDAS{path/to/file.ext.md5}&lt;/tt&gt;<br /> syntax for addressing the test data, the function [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_test ExternalData_add_target] is used by<br /> specifying both &lt;tt&gt;DATA{path/to/file.ext}&lt;/tt&gt; and a download target name.<br /> <br /> '''Replace this:'''<br /> <br /> midas_add_test(NAME test1 COMMAND ...)<br /> midas_add_test(NAME test2 COMMAND ...)<br /> <br /> '''By this:'''<br /> <br /> ExternalData_add_test(EMSegmentData NAME test1 COMMAND ...)<br /> ExternalData_add_test(EMSegmentData NAME test2 COMMAND ...)<br /> <br /> [...]<br /> <br /> ExternalData_add_target(EMSegmentData)<br /> <br /> <br /> A key difference with the former approaches is that instead of adding two tests (one named<br /> &lt;tt&gt;&lt;testName&gt;_fetchData&lt;/tt&gt; to downoad the data and one running the test command), only one<br /> test is added but a common download target is added at the end using [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_target ExternalData_add_target]<br /> function.<br /> <br /> This means that test data can now be downloaded in parallel (and cached) at build time instead<br /> of testing time.<br /> <br /> ===Slicer 4.9: CMake: Module SlicerMacroCheckExternalProjectDependency not available===<br /> <br /> Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26992 r26992], consider updating<br /> your build system to use CMake module &lt;code&gt;ExternalProjectDependency&lt;/code&gt;<br /> <br /> ===Slicer 4.9: CMake: Module SlicerMacroEmptyExternalProject not available===<br /> <br /> Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26991 r26991]<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerMacroEmptyExternalProject)<br /> <br /> [...]<br /> <br /> SlicerMacroEmptyExternalProject(&quot;${proj}&quot; &quot;${${proj}_DEPENDENCIES}&quot;)<br /> &lt;/pre&gt;<br /> <br /> '''By this:'''<br /> <br /> &lt;pre&gt;<br /> include(ExternalProjectDependency)<br /> <br /> [...]<br /> <br /> ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDENCIES})<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: CMake: Module SlicerBlockSetCMakeOSXVariables not available===<br /> <br /> Since it was renamed to &lt;tt&gt;SlicerInitializeOSXVariables&lt;/tt&gt; in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26982 r26982]<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerBlockSetCMakeOSXVariables)<br /> &lt;/pre&gt;<br /> <br /> '''By this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerInitializeOSXVariables)<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: Application: isRelease() function not available===<br /> <br /> See [[#Slicer_4.8:_Application:_isRelease.28.29_function_not_available_or_deprecated]]<br /> <br /> ===Slicer 4.9: slicer.util.getNode() raises exception if node not found===<br /> <br /> If slicer.util.getNode() is called and the node is not found then instead of just returning None (Slicer 4.8 behavior), the method now raises a MRMLNodeNotFoundException. This makes code debugging easier (the error is reported when it happens), and in general more consistent with Python conventions.<br /> <br /> How to update existing code:<br /> <br /> It is advisable to only use slicer.util.getNode in tests, or interactively in the Python console, as its behavior is somewhat unpredictable (it may either found a node by name or ID, and result of wildcard search is even less deterministic). In general, it is recommended to use the MRML scene's GetFirstNodeByName and GetNodeByID methods instead.<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> n = slicer.util.getNode(nodeNameOrID)<br /> &lt;/pre&gt;<br /> <br /> '''By one of these:'''<br /> <br /> If node is to be found by name:<br /> &lt;pre&gt;<br /> n = slicer.mrmlScene.GetFirstNodeByName(nodeName)<br /> &lt;/pre&gt;<br /> <br /> If node is to be found by ID:<br /> &lt;pre&gt;<br /> n = slicer.mrmlScene.GetNodeByID(nodeID)<br /> &lt;/pre&gt;<br /> <br /> If node is to be found by name or ID (slower, less predictable, recommended for testing only):<br /> <br /> &lt;pre&gt;<br /> try:<br /> n = slicer.util.getNode(nodeNameOrID)<br /> except slicer.util.MRMLNodeNotFoundException:<br /> n = None<br /> &lt;/pre&gt;<br /> <br /> More information: https://github.com/Slicer/Slicer/commit/b63484af1b1b413f35396f8f7efb73e870448bd4<br /> <br /> ===Slicer 4.8: Application: isRelease() function not available or deprecated===<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> Missing/deprecated qSlicerCoreApplication::isRelease()<br /> <br /> or<br /> <br /> Missing/deprecated slicer.app.isRelease()<br /> <br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Use &lt;tt&gt;qSlicerCoreApplication::releaseType() == &quot;Stable&quot;&lt;/tt&gt;<br /> <br /> &lt;b&gt;Summary:&lt;/b&gt;<br /> <br /> Prior to r26420, the variable &lt;tt&gt;Slicer_VERSION_TWEAK&lt;/tt&gt; was used to check if a &quot;stable release&quot; was built. The variable value<br /> was set by updating the sources and defining the variable to an integer greater or equal to 0. In other word, if the variable<br /> evaluated to an empty string, a nighty or experimental build was being done, if it evaluated to an integer, a stable release build<br /> was being done.<br /> <br /> The approach had few issues:<br /> <br /> *the name of the variable was confusing<br /> *identifying a &quot;stable release&quot; only from a source tree revision was not enough. Indeed the environment defining a &quot;release&quot; is the one found on the build machines used to generate the installer.<br /> *nightly build are also considered as release<br /> <br /> To address this, the CMake variable &lt;tt&gt;Slicer_RELEASE_TYPE&lt;/tt&gt; was introduced. As of 2017-10-04, it can be set to &lt;tt&gt;Experimental&lt;/tt&gt;, &lt;tt&gt;Nightly&lt;/tt&gt;<br /> or &lt;tt&gt;Stable&lt;/tt&gt; with &lt;tt&gt;Experimental&lt;/tt&gt; being the value hard-coded in the source.<br /> <br /> Identifying a build as &quot;stable&quot; is now explicitly done by setting &lt;tt&gt;Slicer_RELEASE_TYPE&lt;/tt&gt; to &lt;tt&gt;Stable&lt;/tt&gt; at configure time.<br /> <br /> Also, since the concept of release types was introduced, the function &lt;tt&gt;isRelease()&lt;/tt&gt; has been removed in favor of &lt;tt&gt;releaseType()&lt;/tt&gt;.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/pull/354<br /> <br /> ===Slicer Python Module: modulewidget and others removed.===<br /> <br /> &lt;b&gt; Summary&lt;/b&gt;<br /> Python classes formerly in &quot;slicer.moduledm&quot;, &quot;slicer.modulelogic&quot;, &quot;slicer.modulemrml&quot;<br /> and &quot;slicer.modulewidget&quot; are now directly available in the slicer module.<br /> <br /> See example of change [https://github.com/QIICR/LongitudinalPETCT/pull/11 here].<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> See comments in commit messages referenced blow.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/commit/628f83fe7a6f4e0710e306bcaf7c04b9e3e5e6bd<br /> <br /> https://github.com/Slicer/Slicer/commit/9cb5668fde1abc8f0430a91ca37fc29277ceeb4e<br /> <br /> ===MRML: Slicer 4.6: Moved up vtkMRMLStorableNode in the MRML node hierarchy.===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> vtkMRMLStorableNode is not a children of vtkMRMLTransformable node anymore,<br /> but directly a children of vtkMRMLNode.<br /> <br /> This allows making a node storable without requiring it to be also<br /> transformable. It is important for several node types (color maps, tables,<br /> etc), which require separate storage node but are not transformable.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *Changed introduced in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=24891 r24891]<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx: In member function ‘void vtkMRMLLongitudinalPETCTStudyNode::ObserveRegistrationTransform(bool)’:<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:478:28: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘GetParentTransformNode’<br /> &amp;&amp; propNode-&gt;GetParentTransformNode()<br /> ^<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:480:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’<br /> propNode-&gt;SetAndObserveTransformNodeID(<br /> ^<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:503:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’<br /> propNode-&gt;SetAndObserveTransformNodeID(NULL);<br /> ^<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Removes lines and/or refactor code<br /> <br /> <br /> ===MRML: Slicer 4.5: Introduction of vtkMRMLLabelMapVolumeNode===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> Before &lt;tt&gt;vtkMRMLScalarVolumeNode&lt;/tt&gt; was used for both scalar and label map<br /> volumes and the LabelMap custom MRML node attribute was used for<br /> distinguishing between them (0=scalar; 1=label map volume).<br /> <br /> This made conversion between labelmap/scalar volumes very easy but made<br /> it difficult to customize behavior, display, processing of segmentation<br /> information.<br /> <br /> Now a new &lt;tt&gt;vtkMRMLLabelMapVolumeNode&lt;/tt&gt; class is used for storing segmentation<br /> information (still using &lt;tt&gt;vtkMRMLScalarVolume&lt;/tt&gt; used as base class for backward<br /> compatibility; but in the future the base class may be changed to reflect<br /> that segmentation can be represented in various ways, not just as volumes).<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> error: ‘class vtkMRMLScalarVolumeNode’ has no member named ‘SetLabelMap’<br /> outputVolumeNode-&gt;SetLabelMap(1);<br /> ^<br /> <br /> &lt;b&gt;Solution (part1: down cast to &lt;tt&gt;vtkMRMLLabelMapVolumeNode&lt;/tt&gt;, remove call to &lt;tt&gt;SetLabelMap&lt;/tt&gt;)&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> vtkMRMLNode* outputNode = d-&gt;OutputLabelVolumeMRMLNodeComboBox-&gt;currentNode();<br /> vtkMRMLScalarVolumeNode* outputVolumeNode = vtkMRMLScalarVolumeNode::SafeDownCast(outputNode);<br /> [...]<br /> outputVolumeNode-&gt;SetLabelMap(1);<br /> <br /> <br /> with:<br /> <br /> vtkMRMLLabelMapVolumeNode* outputVolumeNode =<br /> vtkMRMLLabelMapVolumeNode::SafeDownCast(d-&gt;OutputLabelVolumeMRMLNodeComboBox-&gt;currentNode());<br /> [...]<br /> <br /> <br /> &lt;b&gt;Solution (part2: Update UI file):&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> &lt;widget class=&quot;qMRMLNodeComboBox&quot; name=&quot;InputLabelVolumeMRMLNodeComboBox&quot;&gt;<br /> &lt;property name=&quot;nodeTypes&quot;&gt;<br /> &lt;stringlist&gt;<br /> &lt;string&gt;vtkMRMLScalarVolumeNode&lt;/string&gt;<br /> &lt;/stringlist&gt;<br /> &lt;/property&gt;<br /> [...]<br /> &lt;/widget&gt;<br /> <br /> with:<br /> <br /> &lt;widget class=&quot;qMRMLNodeComboBox&quot; name=&quot;InputLabelVolumeMRMLNodeComboBox&quot;&gt;<br /> &lt;property name=&quot;nodeTypes&quot;&gt;<br /> &lt;stringlist&gt;<br /> &lt;string&gt;vtkMRMLLabelMapVolumeNode&lt;/string&gt; &lt;------------- Update Here<br /> &lt;/stringlist&gt;<br /> &lt;/property&gt;<br /> [...]<br /> &lt;/widget&gt;<br /> <br /> <br /> &lt;b&gt;Solution (part3: Update node selector configuration):&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> nodeSelector.setNodeTypes(QStringList(&quot;vtkMRMLScalarVolumeNode&quot;));<br /> nodeSelector.addAttribute(&quot;vtkMRMLScalarVolumeNode&quot;, &quot;LabelMap&quot;, &quot;1&quot;);<br /> <br /> with:<br /> <br /> nodeSelector.setNodeTypes(QStringList(&quot;vtkMRMLLabelMapVolumeNode&quot;));<br /> <br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *https://www.slicer.org/wiki/Documentation/Labs/Segmentations#vtkMRMLLabelMapVolumeNode_integration* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=24291<br /> <br /> <br /> ===CLI: Slicer 4.3: Add ITKFactoryRegistration library centralizing ITK IO factory registration===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> Linking against &lt;tt&gt;ITKFactoryRegistration&lt;/tt&gt; ensures that ITK IO factory are properly registered on all supported platforms.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> Undefined symbols for architecture x86_64:<br /> &quot;itk::itkFactoryRegistration()&quot;, referenced from:<br /> _main in ImageMakerTest.cxx.o<br /> ld: symbol(s) not found for architecture x86_64<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> target_link_libraries(${CLP}Test ${CLP}Lib)<br /> <br /> with:<br /> <br /> target_link_libraries(${CLP}Test ${CLP}Lib ${SlicerExecutionModel_EXTRA_EXECUTABLE_TARGET_LIBRARIES})<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21592<br /> *https://issues.slicer.org/view.php?id=2813</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Tutorials/MigrationGuide/Slicer&diff=64186 2022-09-14T16:42:19Z

<p>Lasso: /* Slicer 5.0: Fiducial List was renamed to Point List */</p> <hr /> <div>&lt;noinclude&gt;__TOC__&lt;/noinclude&gt;<br /> ==Slicer backward incompatible changes==<br /> <br /> ===Slicer 5.0: API changes since 4.10===<br /> <br /> *Removed protected method &lt;tt&gt;vtkMRMLModelDisplayableManager::FindPickedDisplayNodeFromMesh&lt;/tt&gt;<br /> <br /> ==== Supporting only Python 3.6 and above ====<br /> Slicer python code has been updated to support Python 3.6 and above syntax using [https://github.com/asottile/pyupgrade pyupgrade] to automatically update the syntax.<br /> <br /> Install pyupgrade: &lt;code&gt;PythonSlicer -m pip install pyupgrade&lt;/code&gt;<br /> <br /> * Running:<br /> ** On 1 file: &lt;code&gt;PythonSlicer -m pyupgrade --py36-plus MyPythonFile.py&lt;/code&gt;<br /> ** On multiple files: Here is my pyupgrade-script.py written to automate running pyupgrade across all python files in the Slicer repo. It was run by &lt;code&gt;PythonSlicer pyupgrade-script.py&lt;/code&gt;<br /> &lt;syntaxhighlight lang=&quot;python&quot;&gt;<br /> # pyupgrade-script.py<br /> import os<br /> import subprocess<br /> <br /> search_directory = &quot;C:/Users/MyUserName/Documents/GitHub/Slicer&quot;<br /> for root, _, files in os.walk(search_directory):<br />   for file_item in files:<br />     file_path = os.path.join(root, file_item)<br />       if os.path.isfile(file_path) and file_path.endswith(&quot;.py&quot;):<br />         subprocess.call([&quot;PythonSlicer&quot;, &quot;-m&quot;, &quot;pyupgrade&quot;, &quot;--py36-plus&quot;, file_path])<br /> &lt;/syntaxhighlight&gt;<br /> <br /> ====Python 2 to Python 3====<br /> <br /> Slicer core has been updated to only support Python 3.<br /> <br /> C++ classes and python scripts have been updated to use idioms and constructs only available in Python 3.<br /> <br /> Update to python scripts have been done leveraging the CLI provided by https://python-future.org by (1) iteratively applying each one of the associates &quot;fixes&quot;, (2) reviewing associated changes and (3) updating as needed.<br /> <br /> Updates specific to extensions are discussed in [[Documentation/Nightly/Developers/Tutorials/MigrationGuide#Slicer_5.0:_Python2_to_Python3]]<br /> <br /> ====Interactor styles====<br /> <br /> Limitations of VTK widgets (editable points, lines, curves, etc.) prevented Slicer from having sophisticated user interaction in slice and 3D views. In Slicer5, we replaced VTK widgets with MRML widgets. These widgets are still VTK-based and somewhat similar to VTK widgets, but they operate directly on MRML nodes, they use direct method calls between widgets and their representation, and they use a more efficient and flexible event processing. Instead of hardcoding how viewers behave in response to interaction (mouse move, button click, keyboard, ...) events in an interactor style, all these events are translated to actions and performed in a MRML widget. Most modules are not expected to observe interactor events or styles directly, but if they did, then they may need to be updated accordingly.<br /> <br /> *vtkSliceViewInteractorStyle renamed to vtkMRMLSliceDViewInteractorStyle to reflect that it uses MRML classes directly.<br /> *vtkThreeDViewInteractorStyle renamed to vtkMRMLThreeDViewInteractorStyle to reflect that it uses MRML classes directly.<br /> <br /> ====slicer.util functions====<br /> <br /> *slicer.util.loadVolume (and other node load functions) now return the loaded node instead of a True/False flag. In case of an error, a RuntimeError exception is thrown.<br /> **Old way of loading a node and get it in a variable: &lt;code&gt;volumeNode = slicer.util.loadVolume('path/to/volume.nrrd', returnNode=True)[1]&lt;/code&gt;<br /> **New way of loading a node and get it in a variable: &lt;code&gt;volumeNode = slicer.util.loadVolume('path/to/volume.nrrd')&lt;/code&gt;<br /> <br /> ====Markups====<br /> <br /> *&lt;tt&gt;vtkCommand::Modified&lt;/tt&gt; events are no longer invoked when control points are added/removed/modified to improve performance. Modules that need to know If a point position is modified need to add observers to &lt;tt&gt;vtkMRMLMarkupsNode::PointAddedEvent&lt;/tt&gt;, &lt;tt&gt;vtkMRMLMarkupsNode::PointRemovedEvent&lt;/tt&gt;, &lt;tt&gt;vtkMRMLMarkupsNode::PointModifiedEvent&lt;/tt&gt; events. See example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#get-a-notification-if-a-markup-point-position-is-modified Script repository].<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::MarkupAddedEvent&lt;/tt&gt; is renamed to &lt;tt&gt;PointPositionDefinedEvent&lt;/tt&gt;. There is a similar event, &lt;tt&gt;vtkMRMLMarkupsNode::PointAddedEvent&lt;/tt&gt;, which is called even when preview point is created.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::MarkupRemovedEvent&lt;/tt&gt; is renamed to &lt;tt&gt;vtkMRMLMarkupsNode::PointPositionUndefinedEvent&lt;/tt&gt;. There is a similar event, &lt;tt&gt;vtkMRMLMarkupsNode::PointRemovedEvent&lt;/tt&gt;, which is called even when preview point is removed.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::NthMarkupModifiedEvent&lt;/tt&gt; is replaced by &lt;tt&gt;vtkMRMLMarkupsNode::PointModifiedEvent&lt;/tt&gt;<br /> *During placement of markups, a preview markup point is created. If number of already placed markup points needs to be determined then &lt;code&gt;GetNumberOfDefinedControlPoints()&lt;/code&gt; method can be used.<br /> *&lt;tt&gt;GetDefaultMarkups...()&lt;/tt&gt; and &lt;tt&gt;SetDefaultMarkups...()&lt;/tt&gt; methods are removed. Instead default display node can be accessed by &lt;tt&gt;GetDefaultMarkupsDisplayNode()&lt;/tt&gt; method and default values can be get/set in that class.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::GetNthMarkupSelected()&lt;/tt&gt; is replaced by &lt;tt&gt;GetNthControlPointSelected()&lt;/tt&gt;<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::PointPositionDefinedEvent&lt;/tt&gt; event is added. This event is invoked whenever position is defined for a new point.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::PointPositionUndefinedEvent&lt;/tt&gt; event is added. This event is invoked whenever point with defined position is removed (point is deleted or its position gets undefined).<br /> *For more details, see [{{doxygen-class-url|vtkMRMLMarkupsNode}} vtkMRMLMarkupsNode]<br /> <br /> ====Segmentations====<br /> <br /> Binary labelmap segmentations can now be represented as shared labelmaps.<br /> The previous implementation of binary labelmaps was performance intensive as each labelmap was represented using a separate vtkDataObject.<br /> Visualizing and editing segmentations that contained a large number of segments could cause performance issues, due to the large number of vtkActors required, as well as calculating masks and overwriting other segments when editing.<br /> <br /> By default, newly created segments will now be contained on the same layer.<br /> Segments will only be separated into multiple layers if the user creates an overlapping segment when editing.<br /> <br /> Segments are now saved as a 4D volume with shared 3D layers.<br /> For a segmentation that only uses one layer, the resulting image is a 3D volume.<br /> Before saving, the labelmaps will be collapsed into as few layers as possible.<br /> <br /> *seg.nrrd files now contain two additional attributes for each segment: SegmentX_LabelValue and SegmentX_Layer<br /> *The label value of a segment can be found using vtkSegment::GetLabelValue()<br /> *Whether or not a segment is shared can be found using vtkSegmentation::IsSharedBinaryLabelmap()<br /> *The other segments sharing the same labelmap can be found using vtkSegmentation::GetSegmentIDsSharingBinaryLabelmapRepresentation()<br /> *Segment editor effects should generally use modifySelectedSegmentByLabelmap rather than SetBinaryLabelmapToSegment to manage layer separation<br /> *Conversion rules now call PreConvert() and PostConvert() before and after conversion to perform pre and post processing steps on the segmentation as a whole<br /> *The function signature for vtkSegmentationConverterRule::Convert now accepts a vtkSegment rather than two vtkDataObjects<br /> *slicer.util.arrayFromSegment has been deprecated. slicer.util.arrayFromSegmentBinaryLabelmap and slicer.util.arrayFromSegmentInternalBinaryLabelmap can be used instead<br /> <br /> =====Erase the contents of a single segment=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.ClearSegment(segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Set labelmap in a segment=====<br /> <br /> Directly, bypassing masking settings:<br /> <br /> &lt;pre&gt;<br /> slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(orientedImageDataToSet, segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Move a segment from a shared labelmap to a separate layer=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.SeparateSegmentLabelmap(segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Combine all binary labelmaps to as few layers as possible=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.CollapseBinaryLabelmaps(forceToSingleLayer=false)<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Get a read-only labelmap for a single segment:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> labelmap = slicer.vtkOrientedImageData()<br /> segmentationNode.GetBinaryLabelmapRepresentation(segmentId, labelmap)<br /> &lt;/pre&gt;<br /> <br /> (similarly, use GetClosedSurfaceRepresentation with an additional vtk.vtkPolyData parameter to get a read-only surface mesh)<br /> <br /> or<br /> <br /> &lt;pre&gt;<br /> labelmapNumpyArray = slicer.util.arrayFromSegmentBinaryLabelmap(segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Get a modifiable shared labelmap=====<br /> <br /> &lt;pre&gt;<br /> labelmap = slicer.vtkOrientedImageData()<br /> segmentationNode.GetBinaryLabelmapInternalRepresentation(segmentId, labelmap)<br /> &lt;/pre&gt;<br /> <br /> (similarly, use GetClosedSurfaceInternalRepresentation to get a modifiable surface mesh)<br /> <br /> or<br /> <br /> &lt;pre&gt;<br /> labelmapNumpyArray = slicer.util.arrayFromSegmentInternalBinaryLabelmap(segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Export segments to models=====<br /> <br /> Model hierarchies no longer exist in Slicer5, but instead various kinds of hierarchies are now replaced by &quot;subject hierarchy&quot;, which can accommodate any node types in a single hierarchy. Accordingly, `ExportSegmentsToModelHierarchy`, `ExportAllSegmentsToModelHierarchy`, etc. are replaced by `ExportSegmentsToModels`, `ExportAllSegmentsToModels`, which take a subject hierarchy folder item ID as input.<br /> Documentation/Nightly<br /> See code example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#export-model-nodes-from-segmentation-node Script repository].<br /> <br /> =====Smoothing effect=====<br /> <br /> In Slicer-4.11 version before October 29, 2020 (and earlier versions), Gaussian smoothing method's Standard deviation parameter (&quot;GaussianStandardDeviationMm&quot;) was interpreted in pixels, while on the user interface and code it was claimed to be in physical units (millimeter). The problem was fixed and now the parameter is in millimeter.<br /> <br /> ====Volume rendering====<br /> <br /> vtkMRMLVolumeRenderingDisplayNode::SetAndObserveVolumeNodeID method was removed, as display node base class already maintains a pointer to the displayed (volume) node. To associate a volume display node with a volume node, call &lt;pre&gt;volumeNode-&gt;AddAndObserveDisplayNodeID(volumeRenderingDisplayNode-&gt;GetID());&lt;/pre&gt; after both nodes are added to the scene.<br /> <br /> ''vtkSlicerVolumeRenderingLogic::CreateDefaultVolumeRenderingNodes'' method unnecessarily polluted the scene with ROI node even though the user did not need cropping. In Slicer-5.x we fixed the issue by not creating the ROI nodes automatically. To create a ROI node, you can call ''vtkSlicerVolumeRenderingLogic::CreateROINode'' method.<br /> <br /> ====Extract skeleton====<br /> <br /> Command-line arguments of the module have been updated:<br /> - output image is now optional, therefore the output image file name must be specified using &quot;--outputImage&quot; argument<br /> - output image centerline voxel value is set to 255 (instead of 1) to make it easier to apply image processing operations on it (values can be interpolated between 0 and 255, while there are no integer values between 0 and 1)<br /> - &quot;--dontPrune&quot; is renamed to &quot;--fullTree&quot; for clarity<br /> - centerline curve is saved in mrk.json format<br /> <br /> ==== MRML node copy API improvements ====<br /> <br /> Slicer-4.10 and earlier had a single Copy() method, which had limitations:<br /> - usually implemented deep copy (but sometimes bulk data was just shallow-copied): problem, because for quick browsing of sequences, we need shallow-copy (to avoid copying bulk data, such as vtkImageData)<br /> - copied all node properties (except node ID and scene): this required workarounds, whenever we wanted to copy only the content of nodes (but for example keeping node references or node name intact)<br /> <br /> In Slicer-4.11, these limitations are addressed, by implementing a ''CopyContent(vtkMRMLNode* node, bool deepCopy=true)'' method which allows choosing between deep/shallow copy (create an independent copy of bulk data or pass bulk data pointer) and does not copy node ID, Scene, Name, SingletonTag, HideFromEditors, AddToScene, UndoEnabled, and node references.<br /> <br /> To make it easier to introduce this new method into existing classes, helper macros are implemented.<br /> <br /> If a class implements CopyContent method then the developer must make sure that CopyContent and HasCopyContent methods are implemented in all parent classes by adding vtkMRMLCopyContentMacro(ClassName) or vtkMRMLCopyContentDefaultMacro(ClassName) to the class headers. vtkMRMLCopyContentDefaultMacro should be used when the class does not have any additional properties (only those that parent classes already copy). CopyContent must be implemented by calling CopyContent of the parent class, and then copy node properties added in he class (preferable using shallow copy for large data, if deepCopy argument was set to false).<br /> <br /> If HasCopyContent macro is not added to a class then it cannot be recorded or replayed in Sequences module.<br /> <br /> ==== Removed classes ====<br /> <br /> Classes removed due to removing legacy Editor module:<br /> * vtkITKNewOtsuThresholdImageFilter is replaced by vtkITKImageThresholdCalculator<br /> * vtkITKGrowCutSegmentationImageFilter is replaced by vtkImageGrowCutSegment (it will be replaced by the ITK implementation https://github.com/Slicer/Slicer/pull/5807)<br /> * vtkITKTimeSeriesDatabase was removed, it was an incomplete class, not used anywhere<br /> * vtkITKWandImageFilter was removed, vtkImageThresholdConnectivity (in VTK) can be used instead<br /> * vtkImageConnectivity was removed, vtkImageThresholdConnectivity (in VTK) can be used instead<br /> * vtkImageErode was removed, vtkImageDilateErode3D (in VTK) can be used instead<br /> * vtkImageLabelChange was removed, vtkImageThreshold (in VTK) can be used instead<br /> * vtkImageSlicePaint was replaced by logic built into qSlicerSegmentEditorPaintEffect<br /> * vtkImageStash is replaced by vtkSegmentationHistory<br /> * vtkPichonFastMarching moved to SegmentEditorExtraEffects extension (https://github.com/lassoan/SlicerSegmentEditorExtraEffects)<br /> <br /> Classes removed due to removing Charts and DoubleArrays modules:<br /> * vtkMRMLChartNode is replaced by vtkMRMLPlotNode<br /> * vtkMRMLChartViewNode is replaced by vtkMRMLPlotViewNode<br /> * vtkMRMLDoubleArrayNode is replaced by vtkMRMLTableNode (can store any number of columns, not just two)<br /> * vtkMRMLDoubleArrayStorageNode is replaced by vtkMRMLTableStorageNode<br /> * qMRMLChartView is replaced by qMRMLPlotView<br /> * qMRMLChartViewControllerWidget is replaced by qMRMLPlotViewControllerWidget<br /> * qMRMLChartWidget is replaced by qMRMLPlotWidget<br /> <br /> ===Slicer 5.3: Removed Annotation module===<br /> <br /> Annotations module, which provides `vtkMRMLAnnotationROI` and `vtkMRMLAnnotationRuler` nodes have been deprecated since April 2021 and is to be removed in Slicer-4.3.<br /> <br /> When a scene is loaded into Slicer that contains annotation nodes, they are converted to markup nodes: `vtkMRMLAnnotationROI` is converted to `vtkMRMLMarkupsROI`; and `vtkMRMLAnnotationRuler` is converted to `vtkMRMLMarkupsLine`. All Slicer core modules that previously used annotation nodes, now use markup nodes instead.<br /> <br /> All extensions, too, need to be updated to use markup nodes instead of annotation nodes. For backward compatibility (so that the same extension can be used with current Slicer version and Slicer-4.2 and earlier versions), it is useful to keep the modules accept both markup and annotation nodes, but always create markup nodes by default.<br /> <br /> Tips for updating a module to use markups:<br /> <br /> - In node selectors, wherever `vtkMRMLAnnotationROINode` is accepted, add `vtkMRMLMarkupsLineNode` _before_ it (so they are both accepted, but markups are preferred)<br /> - In node selectors, wherever `vtkMRMLAnnotationRuler` is accepted, add `vtkMRMLMarkupsLine` _before_ it (so they are both accepted, but markups are preferred)<br /> - For ROIs:<br /> - When only non-rotated ROIs are used: you can still use `GetXYZ()` and `GetRadiusXYZ()` methods work the same way for markups ROI<br /> - When ROIs are rotated, markups ROIs support built-in rotation and scaling, therefore it is recommended to use the `exportRoi.GetObjectToWorldMatrix()` method to get all the transforms (including the transform inside the markup node and any transforms applied using transform nodes) that are applied to the bounding box object (that has its center in the origin and its diameter returned by `GetSize()`).<br /> - For rulers:<br /> - Use `GetNthControlPointPosition(0)` and `GetNthControlPointPosition(1)` methods to get the endpoints of the line.<br /> - Use `GetNumberOfDefinedControlPoints()` method to check if both endpoints of the line are defined.<br /> - Use `GetMeasurement('length').GetValue()` to get the line length (or for the displayed string, with units: `getNode('L').GetMeasurement('length').GetValueWithUnitsAsPrintableString()`)<br /> <br /> ===Slicer 5.0: Fiducial List was renamed to Point List===<br /> <br /> To simplify terms used in Slicer, &quot;Fiducial List&quot; term was renamed to &quot;Point List&quot; on the user interface.<br /> The term in the API has not been changed to preserve backward compatibility.<br /> <br /> See discussion of the topic [https://discourse.slicer.org/t/delete-control-point-delete-fiducial-pop-up-confirm-box/20430/18 here].<br /> <br /> ===Slicer 5.0: SliceIntersectionVisibility was moved from vtkMRMLSliceCompositeNode to vtkMRMLSliceDisplayNode===<br /> <br /> SliceIntersectionVisibility property (that controls if intersections of other slices should be displayed in the slice view) was stored in vtkMRMLSliceCompositeNode. This was not a good choice because the composite node stores what image layers should be displayed in the slice view and how (what opacity, what blending method, etc.). The property was kept in that class for a long time to preserve backward compatibility, but when interactive slice intersection feature was added and additional properties had to be added that control appearance and behavior of slice intersections, this property was moved into the new vtkMRMLSliceDisplayNode node type and renamed to IntersectingSlicesVisibility.<br /> <br /> Scripts that previously used SliceIntersectionVisibility property will now fail with this error:<br /> <br /> AttributeError: 'MRMLCore.vtkMRMLSliceCompositeNode' object has no attribute 'SetSliceIntersectionVisibility'<br /> <br /> Those failing scripts can be updated with this example in the script repository: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#turn-on-slice-intersections<br /> <br /> ===Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead===<br /> <br /> &lt;b&gt;Error message:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> SlicerPython executable is obsolete and will be removed. Use PythonSlicer executable instead.<br /> For more details, see https://github.com/Slicer/Slicer/issues/4843<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Use &lt;tt&gt;PythonSlicer&lt;/tt&gt; instead of &lt;tt&gt;SlicerPython&lt;/tt&gt;<br /> <br /> &lt;b&gt;Background:&lt;/b&gt;<br /> <br /> Python IDEs (specifically PyCharm, but potentially others) only recognize &lt;tt&gt;Python*.exe&lt;/tt&gt; files as Python interpreters.<br /> <br /> To allow using Slicer's Python interpreter in these IDEs, we had to add &lt;tt&gt;PythonSlicer&lt;/tt&gt;, but kept &lt;tt&gt;SlicerPython&lt;/tt&gt; around for not immediately breaking things.<br /> <br /> This redundancy is confusing for users that we could resolve by simply removing SlicerPython for Slicer5.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/issues/4843<br /> <br /> ===Slicer 5.0: Application must be installed in writable location to install extensions===<br /> <br /> Extensions are now installed in the application home folder because Python packages are installed there anyway, so the application home folder has to be writable (or Slicer has to be run as admin when you install extensions). It also allows making Slicer fully portable - see details [https://discourse.slicer.org/t/slicer-is-now-fully-portable/15410 here].<br /> <br /> If you want to allow any user to install extensions without admin rights and you only need to use extensions that don’t install Python packages at runtime then you can specify a custom extension install path folder in Slicer-NNN.ini file or revert to the old behavior of Slicer by specifying &lt;code&gt;Slicer_STORE_SETTINGS_IN_APPLICATION_HOME_DIR:BOOL=OFF&lt;/code&gt; when configuring your Slicer build.<br /> <br /> ===Slicer 5.0: Models are saved in LPS coordinate system by default===<br /> <br /> While Slicer uses RAS coordinate system internally, images, transforms, and markups files are stored in LPS coordinate system, because DICOM and all medical image computing software (maybe except a few very old ones) uses LPS coordinate system in files.<br /> <br /> However, Slicer has been still using its internal RAS coordinate system in mesh files (STL, VTK, VTP, OBJ, PLY), which caused issues when interfacing with third-party software.<br /> <br /> From Slicer-4.11.0-2020-02-26 (revision 28794) models are saved in LPS coordinate system, and mesh files assumed to be in LPS coordinate system by default (if no other coordinate system specified in the file).<br /> <br /> Slicer started embedding coordinate system name in mesh files a few years ago (see &lt;code&gt;SPACE=RAS&lt;/code&gt; in the file header), so all the files that Slicer saved in recent years will load correctly and any scene files created with any version of Slicer will also load the models with correct orientation, too.<br /> <br /> Manual setting of coordinate system (in Add data dialog / Options column) is only needed when loading a mesh file without a scene that were created by Slicer-4.6 (2017-09-27) and earlier; and obj files created by Slicer-4.6 and Slicer-4.8 (between 2016-10-11 and 2018-03-26), or files are created by third-party software in RAS coordinate system.<br /> <br /> If you encounter orientation issues when loading a model file, you have the following options:<br /> <br /> *Option A: Specify the coordinate system when you open the model file. In “Add data” dialog, click “Show Options” and then choose “RAS” as coordinate system.<br /> *Option B: Update the third-party software that generate the mesh to save coordinates in LPS coordinate system instead of RAS coordinate system. Conversion is simple inverting the sign of the first two coordinates.<br /> *Option C: Write &lt;code&gt;SPACE=RAS&lt;/code&gt; in the comment/description field in the mesh file (for STL, OBJ, PLY, VTK file; for VTP files, add in the first value of a vtkStringArray field array named &lt;code&gt;SPACE&lt;/code&gt;) to indicate that the values are stored in RAS coordinate system. This option is useful if coordinates have to be stored in RAS coordinate system (for example, for compatibility with other software). See implementation example [https://github.com/Slicer/SlicerGitSVNArchive/blob/c0829f596f0ea661e0c5484056bd1374a3d22958/Libs/MRML/Core/vtkMRMLModelStorageNode.cxx#L421-L647 here].<br /> <br /> See more information, discussion of this topic on the [https://discourse.slicer.org/t/model-files-are-now-saved-in-lps-coordinate-system/10446 Slicer forum].<br /> <br /> ===Slicer 5.0: CLI module descriptor XML files assume LPS coordinate system by default===<br /> <br /> If [[Documentation/Nightly/Developers/SlicerExecutionModel|SlicerExecutionModel]] descriptor XML file of a CLI module does not specify coordinate system for a point, pointfile, or region element then the coordinate system is assumed to be &quot;lps&quot;. To preserve previous behavior and use &quot;ras&quot; coordinate system instead, add '''coordinateSystem=&quot;ras&quot;''' to the element.<br /> <br /> ===Slicer 5.0: Sequences extension has been merged into Slicer core===<br /> <br /> Sequences extension has been merged into Slicer core, therefore extensions do not need to depend on Sequences extension anymore.<br /> <br /> SequenceBrowser module has been merged into Sequences module, therefore previous code that used SequenceBrowser module now should use Sequences module instead.<br /> <br /> ===Slicer 5.0: FreeSurfer support has been removed from Slicer core===<br /> The loading of FreeSurfer models and scalar overlays, as well as the FreeSurfer-specific color nodes, have been moved to the new [https://github.com/PerkLab/SlicerFreeSurfer SlicerFreeSurfer] extension. Tutorials on how to use the FreeSurfer Importer module to load multiple files at once can be found on the [https://github.com/PerkLab/SlicerFreeSurfer/wiki/Tutorials SlicerFreeSurfer tutorial page].<br /> <br /> ===Slicer 5.0: Removed Editor module===<br /> <br /> The legacy Editor module has been deprecated since about 2017 and got removed in November 2021. It is replaced by the much improved Segment Editor module.<br /> <br /> ===Slicer 5.0: Removed Charts and DoubleArrays module===<br /> <br /> Charts and DoubleArrays module have been deprecated since about 2018 and got removed in November 2021. They are replaced by Plots and Tables modules.<br /> <br /> '''Example of commits'''<br /> * [https://github.com/SlicerRt/SlicerRT/commit/8f9155f94399be71e747d3d45b1f6c4152caa139 SlicerRT@8f9155f94] ENH: Update DVH module to use plots infrastructure instead of charts<br /> <br /> ===Slicer 5.0 : Avoid typedef of anonymous structure===<br /> <br /> Due to a recent (but retroactive) C++ rule change, only sufficiently C-compatible classes are permitted to be given a typedef name for linkage purposes. Add an &lt;tt&gt;enabled-by-default&lt;/tt&gt; warning for these cases, and rephrase our existing error for the case where we encounter the &lt;tt&gt;typedef&lt;/tt&gt; name for linkage after we've already computed and used a wrong linkage in terms of the new rule.<br /> <br /> &lt;b&gt;To fix warning message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:95:17:<br /> warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]<br /> typedef struct<br /> ^<br /> ColumnInfo<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:99:5:<br /> note: type is not C-compatible due to this default member initializer<br /> int ScalarType = VTK_STRING;<br /> ^~~~~~~~~~~~~~<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:102:5:<br /> note: type is given name 'ColumnInfo' for linkage purposes by this typedef declaration<br /> } ColumnInfo;<br /> ^<br /> For consistency, Use 'using' to a named structure definintion for all <br /> structures.<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> typedef struct<br /> {<br /> std::string ColumnName;<br /> std::vector&lt;vtkAbstractArray*&gt; RawComponentArrays;<br /> int ScalarType = VTK_STRING;<br /> std::vector&lt;std::string&gt; ComponentNames;<br /> std::string NullValueString;<br /> } ColumnInfo;<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> struct StructColumnInfo<br /> {<br /> std::string ColumnName;<br /> std::vector&lt;vtkAbstractArray*&gt; RawComponentArrays;<br /> int ScalarType = VTK_STRING;<br /> std::vector&lt;std::string&gt; ComponentNames;<br /> std::string NullValueString;<br /> };<br /> using ColumnInfo = struct StructColumnInfo;<br /> &lt;/pre&gt;<br /> <br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://reviews.llvm.org/D74103<br /> <br /> ===Slicer 5.0 : Temporary path===<br /> <br /> Temporary path was stored redundantly application settings (Slicer.ini) in two keys: &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; and &lt;code&gt;TemporaryPath&lt;/code&gt;. &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; overwrote &lt;code&gt;TemporaryPath&lt;/code&gt; at startup, but when temporary path was set via the &lt;code&gt;slicer.app.temporaryPath&lt;/code&gt; then it was only written to &lt;code&gt;TemporaryPath&lt;/code&gt;.<br /> <br /> Changed behavior so that only &lt;code&gt;TemporaryPath&lt;/code&gt; is used. &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; is ignored.<br /> <br /> To ensure that temporary path is always writable, it as checked at startup that a file can be created in temporary path and if this check fails then temporary path is reset to default (&lt;code&gt;QDir::tempPath()&lt;/code&gt;).<br /> <br /> ===Slicer 5.0 : Always prefer executable CLIs===<br /> <br /> Previously, if a CLI module was available both as an executable and a shared library, then PreferExecutableCLI application setting was used to determine which one is used. Now always CLIs are always executed in an external process (if an executable is available). Reasons are described in this issue: https://github.com/Slicer/Slicer/issues/4893. The application setting is no more displayed in the GUI and any setting specified in earlier Slicer versions is ignored.<br /> <br /> ===Slicer 5.0 : SlicerApp-real is a console application on Windows===<br /> <br /> Previously, the application (SlicerApp-real.exe) was built as a GUI application (without console) on Windows, to avoid displaying a terminal window when starting the application. This had the drawback that the Slicer application did not have standard input/output that could be displayed or redirected (for example, for capturing into a file). SlicerApp-real has always been a console application on Linux and macOS, therefore this change makes the software behavior more consistent across platforms.<br /> <br /> SlicerApp-real.exe is now built as a console application (see [https://github.com/Slicer/Slicer/issues/2934 #2934]). Displaying of a terminal window is prevented by using a launcher (Slicer.exe) that is built as a GUI application and it starts Slicer with the standard input and outputs redirected.<br /> <br /> To display console output: https://slicer.readthedocs.io/en/latest/developer_guide/debugging/overview.html#console-output-on-windows<br /> <br /> To launch a command-line terminal using &lt;code&gt;subprocess.Popen&lt;/code&gt; that shows a new terminal, specify &lt;code&gt;creationflags=subprocess.CREATE_NEW_CONSOLE&lt;/code&gt; argument.<br /> <br /> ===Slicer 4.11: Variable CMAKE_DEFAULT_BUILD_TYPE renamed to Slicer_DEFAULT_BUILD_TYPE===<br /> <br /> Setting the default build type for single config generator may be done setting &lt;tt&gt;Slicer_DEFAULT_BUILD_TYPE&lt;/tt&gt; instead of &lt;tt&gt;CMAKE_DEFAULT_BUILD_TYPE&lt;/tt&gt;.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> CMake Error:<br /> Generator<br /> <br /> Visual Studio 15 2017<br /> <br /> does not support variable<br /> <br /> CMAKE_DEFAULT_BUILD_TYPE<br /> <br /> but it has been specified.<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/pull/4799<br /> <br /> ===Slicer 4.11: teem python module renamed to vtkTeem, explicit import required===<br /> <br /> *Since the module provides VTK classes interfacing with &quot;teem&quot;, the name is now representative of the class it contains.<br /> *&lt;tt&gt;vtkTeem&lt;/tt&gt; classes are expected to be used by explicitly importing the module.<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> import teem<br /> <br /> class CalculateTensorScalars(object):<br /> def __init__(self):<br /> self.dti_math = teem.vtkDiffusionTensorMathematics()<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> import vtkTeem<br /> <br /> class CalculateTensorScalars(object):<br /> def __init__(self):<br /> self.dti_math = vtkTeem.vtkDiffusionTensorMathematics()<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.11: Display window/level (brightness/contrast) adjustment===<br /> <br /> *A new &quot;Window/level&quot; mouse interaction mode was introduced. Volume display window/level can only be changed if this mode is activated by clicking the corresponding button in the toolbar. The new mouse mode prevents accidental modification of volume window/level (when for example the user accidentally clicked too far from a markup) and it also allows more sophisticated window/level adjustments.<br /> *New region-based auto window/level feature added: activate &quot;Window/level&quot; mouse mode and use Ctrl + left-click-and-drag to highlight a region and optimize window/level for that (pressing Escape or right-click cancels the operation).<br /> *Auto window/level reset: activate &quot;Window/level&quot; mouse mode and double-click the left mouse button.<br /> *Improved auto window/level algorithm to prevent too bright display of images. Window/level is set to display values between 0.1th and 99.9th percentile of gray levels. See details here: https://discourse.slicer.org/t/feedback-requested-how-to-improve-mouse-interaction-in-views/6420.<br /> *Removed class &lt;tt&gt;vtkImageBimodalAnalysis&lt;/tt&gt;<br /> <br /> ===Slicer 4.10: Registration of runTest function done in ScriptedLoadableModule base class===<br /> <br /> Following [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27617 r27617]:<br /> <br /> *the &lt;code&gt;ScriptedLoadableModule&lt;/code&gt; class takes care of registering the &lt;code&gt;runTest&lt;/code&gt; function.<br /> *the &lt;code&gt;runTest&lt;/code&gt; function expects &lt;code&gt;msec&lt;/code&gt; keyword argument.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> Traceback (most recent call last):<br /> File &quot;/path/to/Slicer-SuperBuild/Slicer-build/bin/Python/slicer/ScriptedLoadableModule.py&quot;, line 205, in onReloadAndTest<br /> test(msec=int(slicer.app.userSettings().value(&quot;Developer/SelfTestDisplayMessageDelay&quot;)), **kwargs)<br /> TypeError: runTest() got an unexpected keyword argument 'msec'<br /> Reload and Test: Exception!<br /> <br /> runTest() got an unexpected keyword argument 'msec'<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> class sceneImport2428(ScriptedLoadableModule):<br /> [...]<br /> def __init__(self, parent):<br /> ScriptedLoadableModule.__init__(self, parent)<br /> parent.title = &quot;...&quot;<br /> [...]<br /> parent.acknowledgementText = &quot;...&quot;<br /> self.parent = parent <br /> <br /> # Add this test to the SelfTest module's list for discovery when the module <br /> # is created. Since this module may be discovered before SelfTests itself, <br /> # create the list if it doesn't already exist. <br /> try: <br /> slicer.selfTests <br /> except AttributeError: <br /> slicer.selfTests = {} <br /> slicer.selfTests['sceneImport2428'] = self.runTest <br /> <br /> def runTest(self): <br /> tester = sceneImport2428Test() <br /> tester.runTest()<br /> <br /> [...]<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> class sceneImport2428(ScriptedLoadableModule):<br /> [...]<br /> def __init__(self, parent):<br /> ScriptedLoadableModule.__init__(self, parent)<br /> parent.title = &quot;...&quot;<br /> [...]<br /> parent.acknowledgementText = &quot;...&quot;<br /> <br /> [...]<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: Update of VTK version from 9.0 to 8.2===<br /> <br /> Following [https://github.com/Kitware/VTK/commit/b703d78be3ffd8ae69c319afa0230097ff270f26 kitware/VTK@b703d78be], VTK has updated to use version number 8.2 instead of 9.0. This was discussed in on the VTK mailing list in http://vtk.1045678.n5.nabble.com/Discussion-OK-to-change-VTK-s-version-number-from-9-0-to-8-2-tt5748702.html<br /> <br /> At first, this VTK commit and its companion [https://github.com/Kitware/VTK/commit/8a00b357e84eec695bda049216f30f2b76d80855 kitware/VTK@8a00b357e] were both reverted from the [https://github.com/Slicer/VTK/ Slicer/VTK] fork. Then, since having the corresponding changes reverted in VTK was not possible, it was decided to also update Slicer. This was done in the following commits:<br /> <br /> *[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27472 r27472]: COMP: Update c++ classes to support building against VTK &gt;= 9 and VTK &gt;= 8.2<br /> *[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27473 r27473]: COMP: Update VTK to include version change from 9.0 to 8.2. Fixes #4623<br /> <br /> This means that code depending on VTK must also be updated to include similar fixes.<br /> <br /> '''Replace this:'''<br /> #if VTK_MAJOR_VERSION &gt;= 9<br /> <br /> '''By this:'''<br /> #if VTK_MAJOR_VERSION &gt;= 9 || (VTK_MAJOR_VERSION &gt;= 8 &amp;&amp; VTK_MINOR_VERSION &gt;= 2)<br /> <br /> and<br /> <br /> '''Replace this:'''<br /> #if VTK_MAJOR_VERSION &lt; 9<br /> <br /> '''By this:'''<br /> #if VTK_MAJOR_VERSION &lt;= 7 || (VTK_MAJOR_VERSION &lt;= 8 &amp;&amp; VTK_MINOR_VERSION &lt;= 1)<br /> <br /> <br /> ===Slicer 4.9: ITK_LEGACY_REMOVE is now OFF===<br /> In preparation to switch to ITK 5.0, we disable legacy functionality in ITK. This might affect some modules which rely on ITK. Take a look at [https://itk.org/migrationv4 ITK 4 migration guide] before [https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md ITK 5 migration guide].<br /> <br /> ===Slicer 4.9: vtkMRMLPlotDataNode renamed to vtkMRMLPlotSeriesNode===<br /> Plotting was improved in [https://github.com/Slicer/Slicer/commit/082edc40c this commit]<br /> <br /> '''Replace this:'''<br /> <br /> vtkMRMLPlotDataNode<br /> <br /> '''By this:'''<br /> vtkMRMLPlotSeriesNode<br /> <br /> ===Slicer 4.9: CMake: Module MIDAS not available===<br /> <br /> The test infrastructure of your project should be updated to use [https://cmake.org/cmake/help/latest/module/ExternalData.html ExternalData] built-in CMake module<br /> instead of the specific &lt;tt&gt;MIDAS&lt;/tt&gt; module.<br /> <br /> See EMSegment commit [http://viewvc.slicer.org/viewvc.cgi/Slicer3?view=revision&amp;revision=17150 r17150] for an example of transition.<br /> <br /> This means that instead of using &lt;tt&gt;midas_add_test&lt;/tt&gt; with the &lt;tt&gt;MIDAS{path/to/file.ext.md5}&lt;/tt&gt;<br /> syntax for addressing the test data, the function [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_test ExternalData_add_target] is used by<br /> specifying both &lt;tt&gt;DATA{path/to/file.ext}&lt;/tt&gt; and a download target name.<br /> <br /> '''Replace this:'''<br /> <br /> midas_add_test(NAME test1 COMMAND ...)<br /> midas_add_test(NAME test2 COMMAND ...)<br /> <br /> '''By this:'''<br /> <br /> ExternalData_add_test(EMSegmentData NAME test1 COMMAND ...)<br /> ExternalData_add_test(EMSegmentData NAME test2 COMMAND ...)<br /> <br /> [...]<br /> <br /> ExternalData_add_target(EMSegmentData)<br /> <br /> <br /> A key difference with the former approaches is that instead of adding two tests (one named<br /> &lt;tt&gt;&lt;testName&gt;_fetchData&lt;/tt&gt; to downoad the data and one running the test command), only one<br /> test is added but a common download target is added at the end using [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_target ExternalData_add_target]<br /> function.<br /> <br /> This means that test data can now be downloaded in parallel (and cached) at build time instead<br /> of testing time.<br /> <br /> ===Slicer 4.9: CMake: Module SlicerMacroCheckExternalProjectDependency not available===<br /> <br /> Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26992 r26992], consider updating<br /> your build system to use CMake module &lt;code&gt;ExternalProjectDependency&lt;/code&gt;<br /> <br /> ===Slicer 4.9: CMake: Module SlicerMacroEmptyExternalProject not available===<br /> <br /> Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26991 r26991]<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerMacroEmptyExternalProject)<br /> <br /> [...]<br /> <br /> SlicerMacroEmptyExternalProject(&quot;${proj}&quot; &quot;${${proj}_DEPENDENCIES}&quot;)<br /> &lt;/pre&gt;<br /> <br /> '''By this:'''<br /> <br /> &lt;pre&gt;<br /> include(ExternalProjectDependency)<br /> <br /> [...]<br /> <br /> ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDENCIES})<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: CMake: Module SlicerBlockSetCMakeOSXVariables not available===<br /> <br /> Since it was renamed to &lt;tt&gt;SlicerInitializeOSXVariables&lt;/tt&gt; in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26982 r26982]<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerBlockSetCMakeOSXVariables)<br /> &lt;/pre&gt;<br /> <br /> '''By this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerInitializeOSXVariables)<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: Application: isRelease() function not available===<br /> <br /> See [[#Slicer_4.8:_Application:_isRelease.28.29_function_not_available_or_deprecated]]<br /> <br /> ===Slicer 4.9: slicer.util.getNode() raises exception if node not found===<br /> <br /> If slicer.util.getNode() is called and the node is not found then instead of just returning None (Slicer 4.8 behavior), the method now raises a MRMLNodeNotFoundException. This makes code debugging easier (the error is reported when it happens), and in general more consistent with Python conventions.<br /> <br /> How to update existing code:<br /> <br /> It is advisable to only use slicer.util.getNode in tests, or interactively in the Python console, as its behavior is somewhat unpredictable (it may either found a node by name or ID, and result of wildcard search is even less deterministic). In general, it is recommended to use the MRML scene's GetFirstNodeByName and GetNodeByID methods instead.<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> n = slicer.util.getNode(nodeNameOrID)<br /> &lt;/pre&gt;<br /> <br /> '''By one of these:'''<br /> <br /> If node is to be found by name:<br /> &lt;pre&gt;<br /> n = slicer.mrmlScene.GetFirstNodeByName(nodeName)<br /> &lt;/pre&gt;<br /> <br /> If node is to be found by ID:<br /> &lt;pre&gt;<br /> n = slicer.mrmlScene.GetNodeByID(nodeID)<br /> &lt;/pre&gt;<br /> <br /> If node is to be found by name or ID (slower, less predictable, recommended for testing only):<br /> <br /> &lt;pre&gt;<br /> try:<br /> n = slicer.util.getNode(nodeNameOrID)<br /> except slicer.util.MRMLNodeNotFoundException:<br /> n = None<br /> &lt;/pre&gt;<br /> <br /> More information: https://github.com/Slicer/Slicer/commit/b63484af1b1b413f35396f8f7efb73e870448bd4<br /> <br /> ===Slicer 4.8: Application: isRelease() function not available or deprecated===<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> Missing/deprecated qSlicerCoreApplication::isRelease()<br /> <br /> or<br /> <br /> Missing/deprecated slicer.app.isRelease()<br /> <br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Use &lt;tt&gt;qSlicerCoreApplication::releaseType() == &quot;Stable&quot;&lt;/tt&gt;<br /> <br /> &lt;b&gt;Summary:&lt;/b&gt;<br /> <br /> Prior to r26420, the variable &lt;tt&gt;Slicer_VERSION_TWEAK&lt;/tt&gt; was used to check if a &quot;stable release&quot; was built. The variable value<br /> was set by updating the sources and defining the variable to an integer greater or equal to 0. In other word, if the variable<br /> evaluated to an empty string, a nighty or experimental build was being done, if it evaluated to an integer, a stable release build<br /> was being done.<br /> <br /> The approach had few issues:<br /> <br /> *the name of the variable was confusing<br /> *identifying a &quot;stable release&quot; only from a source tree revision was not enough. Indeed the environment defining a &quot;release&quot; is the one found on the build machines used to generate the installer.<br /> *nightly build are also considered as release<br /> <br /> To address this, the CMake variable &lt;tt&gt;Slicer_RELEASE_TYPE&lt;/tt&gt; was introduced. As of 2017-10-04, it can be set to &lt;tt&gt;Experimental&lt;/tt&gt;, &lt;tt&gt;Nightly&lt;/tt&gt;<br /> or &lt;tt&gt;Stable&lt;/tt&gt; with &lt;tt&gt;Experimental&lt;/tt&gt; being the value hard-coded in the source.<br /> <br /> Identifying a build as &quot;stable&quot; is now explicitly done by setting &lt;tt&gt;Slicer_RELEASE_TYPE&lt;/tt&gt; to &lt;tt&gt;Stable&lt;/tt&gt; at configure time.<br /> <br /> Also, since the concept of release types was introduced, the function &lt;tt&gt;isRelease()&lt;/tt&gt; has been removed in favor of &lt;tt&gt;releaseType()&lt;/tt&gt;.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/pull/354<br /> <br /> ===Slicer Python Module: modulewidget and others removed.===<br /> <br /> &lt;b&gt; Summary&lt;/b&gt;<br /> Python classes formerly in &quot;slicer.moduledm&quot;, &quot;slicer.modulelogic&quot;, &quot;slicer.modulemrml&quot;<br /> and &quot;slicer.modulewidget&quot; are now directly available in the slicer module.<br /> <br /> See example of change [https://github.com/QIICR/LongitudinalPETCT/pull/11 here].<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> See comments in commit messages referenced blow.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/commit/628f83fe7a6f4e0710e306bcaf7c04b9e3e5e6bd<br /> <br /> https://github.com/Slicer/Slicer/commit/9cb5668fde1abc8f0430a91ca37fc29277ceeb4e<br /> <br /> ===MRML: Slicer 4.6: Moved up vtkMRMLStorableNode in the MRML node hierarchy.===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> vtkMRMLStorableNode is not a children of vtkMRMLTransformable node anymore,<br /> but directly a children of vtkMRMLNode.<br /> <br /> This allows making a node storable without requiring it to be also<br /> transformable. It is important for several node types (color maps, tables,<br /> etc), which require separate storage node but are not transformable.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *Changed introduced in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=24891 r24891]<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx: In member function ‘void vtkMRMLLongitudinalPETCTStudyNode::ObserveRegistrationTransform(bool)’:<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:478:28: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘GetParentTransformNode’<br /> &amp;&amp; propNode-&gt;GetParentTransformNode()<br /> ^<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:480:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’<br /> propNode-&gt;SetAndObserveTransformNodeID(<br /> ^<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:503:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’<br /> propNode-&gt;SetAndObserveTransformNodeID(NULL);<br /> ^<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Removes lines and/or refactor code<br /> <br /> <br /> ===MRML: Slicer 4.5: Introduction of vtkMRMLLabelMapVolumeNode===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> Before &lt;tt&gt;vtkMRMLScalarVolumeNode&lt;/tt&gt; was used for both scalar and label map<br /> volumes and the LabelMap custom MRML node attribute was used for<br /> distinguishing between them (0=scalar; 1=label map volume).<br /> <br /> This made conversion between labelmap/scalar volumes very easy but made<br /> it difficult to customize behavior, display, processing of segmentation<br /> information.<br /> <br /> Now a new &lt;tt&gt;vtkMRMLLabelMapVolumeNode&lt;/tt&gt; class is used for storing segmentation<br /> information (still using &lt;tt&gt;vtkMRMLScalarVolume&lt;/tt&gt; used as base class for backward<br /> compatibility; but in the future the base class may be changed to reflect<br /> that segmentation can be represented in various ways, not just as volumes).<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> error: ‘class vtkMRMLScalarVolumeNode’ has no member named ‘SetLabelMap’<br /> outputVolumeNode-&gt;SetLabelMap(1);<br /> ^<br /> <br /> &lt;b&gt;Solution (part1: down cast to &lt;tt&gt;vtkMRMLLabelMapVolumeNode&lt;/tt&gt;, remove call to &lt;tt&gt;SetLabelMap&lt;/tt&gt;)&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> vtkMRMLNode* outputNode = d-&gt;OutputLabelVolumeMRMLNodeComboBox-&gt;currentNode();<br /> vtkMRMLScalarVolumeNode* outputVolumeNode = vtkMRMLScalarVolumeNode::SafeDownCast(outputNode);<br /> [...]<br /> outputVolumeNode-&gt;SetLabelMap(1);<br /> <br /> <br /> with:<br /> <br /> vtkMRMLLabelMapVolumeNode* outputVolumeNode =<br /> vtkMRMLLabelMapVolumeNode::SafeDownCast(d-&gt;OutputLabelVolumeMRMLNodeComboBox-&gt;currentNode());<br /> [...]<br /> <br /> <br /> &lt;b&gt;Solution (part2: Update UI file):&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> &lt;widget class=&quot;qMRMLNodeComboBox&quot; name=&quot;InputLabelVolumeMRMLNodeComboBox&quot;&gt;<br /> &lt;property name=&quot;nodeTypes&quot;&gt;<br /> &lt;stringlist&gt;<br /> &lt;string&gt;vtkMRMLScalarVolumeNode&lt;/string&gt;<br /> &lt;/stringlist&gt;<br /> &lt;/property&gt;<br /> [...]<br /> &lt;/widget&gt;<br /> <br /> with:<br /> <br /> &lt;widget class=&quot;qMRMLNodeComboBox&quot; name=&quot;InputLabelVolumeMRMLNodeComboBox&quot;&gt;<br /> &lt;property name=&quot;nodeTypes&quot;&gt;<br /> &lt;stringlist&gt;<br /> &lt;string&gt;vtkMRMLLabelMapVolumeNode&lt;/string&gt; &lt;------------- Update Here<br /> &lt;/stringlist&gt;<br /> &lt;/property&gt;<br /> [...]<br /> &lt;/widget&gt;<br /> <br /> <br /> &lt;b&gt;Solution (part3: Update node selector configuration):&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> nodeSelector.setNodeTypes(QStringList(&quot;vtkMRMLScalarVolumeNode&quot;));<br /> nodeSelector.addAttribute(&quot;vtkMRMLScalarVolumeNode&quot;, &quot;LabelMap&quot;, &quot;1&quot;);<br /> <br /> with:<br /> <br /> nodeSelector.setNodeTypes(QStringList(&quot;vtkMRMLLabelMapVolumeNode&quot;));<br /> <br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *https://www.slicer.org/wiki/Documentation/Labs/Segmentations#vtkMRMLLabelMapVolumeNode_integration* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=24291<br /> <br /> <br /> ===CLI: Slicer 4.3: Add ITKFactoryRegistration library centralizing ITK IO factory registration===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> Linking against &lt;tt&gt;ITKFactoryRegistration&lt;/tt&gt; ensures that ITK IO factory are properly registered on all supported platforms.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> Undefined symbols for architecture x86_64:<br /> &quot;itk::itkFactoryRegistration()&quot;, referenced from:<br /> _main in ImageMakerTest.cxx.o<br /> ld: symbol(s) not found for architecture x86_64<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> target_link_libraries(${CLP}Test ${CLP}Lib)<br /> <br /> with:<br /> <br /> target_link_libraries(${CLP}Test ${CLP}Lib ${SlicerExecutionModel_EXTRA_EXECUTABLE_TARGET_LIBRARIES})<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21592<br /> *https://issues.slicer.org/view.php?id=2813</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Tutorials/MigrationGuide/Slicer&diff=64185 2022-08-27T22:51:21Z

<p>Lasso: /* Volume rendering */</p> <hr /> <div>&lt;noinclude&gt;__TOC__&lt;/noinclude&gt;<br /> ==Slicer backward incompatible changes==<br /> <br /> ===Slicer 5.0: API changes since 4.10===<br /> <br /> *Removed protected method &lt;tt&gt;vtkMRMLModelDisplayableManager::FindPickedDisplayNodeFromMesh&lt;/tt&gt;<br /> <br /> ==== Supporting only Python 3.6 and above ====<br /> Slicer python code has been updated to support Python 3.6 and above syntax using [https://github.com/asottile/pyupgrade pyupgrade] to automatically update the syntax.<br /> <br /> Install pyupgrade: &lt;code&gt;PythonSlicer -m pip install pyupgrade&lt;/code&gt;<br /> <br /> * Running:<br /> ** On 1 file: &lt;code&gt;PythonSlicer -m pyupgrade --py36-plus MyPythonFile.py&lt;/code&gt;<br /> ** On multiple files: Here is my pyupgrade-script.py written to automate running pyupgrade across all python files in the Slicer repo. It was run by &lt;code&gt;PythonSlicer pyupgrade-script.py&lt;/code&gt;<br /> &lt;syntaxhighlight lang=&quot;python&quot;&gt;<br /> # pyupgrade-script.py<br /> import os<br /> import subprocess<br /> <br /> search_directory = &quot;C:/Users/MyUserName/Documents/GitHub/Slicer&quot;<br /> for root, _, files in os.walk(search_directory):<br />   for file_item in files:<br />     file_path = os.path.join(root, file_item)<br />       if os.path.isfile(file_path) and file_path.endswith(&quot;.py&quot;):<br />         subprocess.call([&quot;PythonSlicer&quot;, &quot;-m&quot;, &quot;pyupgrade&quot;, &quot;--py36-plus&quot;, file_path])<br /> &lt;/syntaxhighlight&gt;<br /> <br /> ====Python 2 to Python 3====<br /> <br /> Slicer core has been updated to only support Python 3.<br /> <br /> C++ classes and python scripts have been updated to use idioms and constructs only available in Python 3.<br /> <br /> Update to python scripts have been done leveraging the CLI provided by https://python-future.org by (1) iteratively applying each one of the associates &quot;fixes&quot;, (2) reviewing associated changes and (3) updating as needed.<br /> <br /> Updates specific to extensions are discussed in [[Documentation/Nightly/Developers/Tutorials/MigrationGuide#Slicer_5.0:_Python2_to_Python3]]<br /> <br /> ====Interactor styles====<br /> <br /> Limitations of VTK widgets (editable points, lines, curves, etc.) prevented Slicer from having sophisticated user interaction in slice and 3D views. In Slicer5, we replaced VTK widgets with MRML widgets. These widgets are still VTK-based and somewhat similar to VTK widgets, but they operate directly on MRML nodes, they use direct method calls between widgets and their representation, and they use a more efficient and flexible event processing. Instead of hardcoding how viewers behave in response to interaction (mouse move, button click, keyboard, ...) events in an interactor style, all these events are translated to actions and performed in a MRML widget. Most modules are not expected to observe interactor events or styles directly, but if they did, then they may need to be updated accordingly.<br /> <br /> *vtkSliceViewInteractorStyle renamed to vtkMRMLSliceDViewInteractorStyle to reflect that it uses MRML classes directly.<br /> *vtkThreeDViewInteractorStyle renamed to vtkMRMLThreeDViewInteractorStyle to reflect that it uses MRML classes directly.<br /> <br /> ====slicer.util functions====<br /> <br /> *slicer.util.loadVolume (and other node load functions) now return the loaded node instead of a True/False flag. In case of an error, a RuntimeError exception is thrown.<br /> **Old way of loading a node and get it in a variable: &lt;code&gt;volumeNode = slicer.util.loadVolume('path/to/volume.nrrd', returnNode=True)[1]&lt;/code&gt;<br /> **New way of loading a node and get it in a variable: &lt;code&gt;volumeNode = slicer.util.loadVolume('path/to/volume.nrrd')&lt;/code&gt;<br /> <br /> ====Markups====<br /> <br /> *&lt;tt&gt;vtkCommand::Modified&lt;/tt&gt; events are no longer invoked when control points are added/removed/modified to improve performance. Modules that need to know If a point position is modified need to add observers to &lt;tt&gt;vtkMRMLMarkupsNode::PointAddedEvent&lt;/tt&gt;, &lt;tt&gt;vtkMRMLMarkupsNode::PointRemovedEvent&lt;/tt&gt;, &lt;tt&gt;vtkMRMLMarkupsNode::PointModifiedEvent&lt;/tt&gt; events. See example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#get-a-notification-if-a-markup-point-position-is-modified Script repository].<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::MarkupAddedEvent&lt;/tt&gt; is renamed to &lt;tt&gt;PointPositionDefinedEvent&lt;/tt&gt;. There is a similar event, &lt;tt&gt;vtkMRMLMarkupsNode::PointAddedEvent&lt;/tt&gt;, which is called even when preview point is created.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::MarkupRemovedEvent&lt;/tt&gt; is renamed to &lt;tt&gt;vtkMRMLMarkupsNode::PointPositionUndefinedEvent&lt;/tt&gt;. There is a similar event, &lt;tt&gt;vtkMRMLMarkupsNode::PointRemovedEvent&lt;/tt&gt;, which is called even when preview point is removed.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::NthMarkupModifiedEvent&lt;/tt&gt; is replaced by &lt;tt&gt;vtkMRMLMarkupsNode::PointModifiedEvent&lt;/tt&gt;<br /> *During placement of markups, a preview markup point is created. If number of already placed markup points needs to be determined then &lt;code&gt;GetNumberOfDefinedControlPoints()&lt;/code&gt; method can be used.<br /> *&lt;tt&gt;GetDefaultMarkups...()&lt;/tt&gt; and &lt;tt&gt;SetDefaultMarkups...()&lt;/tt&gt; methods are removed. Instead default display node can be accessed by &lt;tt&gt;GetDefaultMarkupsDisplayNode()&lt;/tt&gt; method and default values can be get/set in that class.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::GetNthMarkupSelected()&lt;/tt&gt; is replaced by &lt;tt&gt;GetNthControlPointSelected()&lt;/tt&gt;<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::PointPositionDefinedEvent&lt;/tt&gt; event is added. This event is invoked whenever position is defined for a new point.<br /> *&lt;tt&gt;vtkMRMLMarkupsNode::PointPositionUndefinedEvent&lt;/tt&gt; event is added. This event is invoked whenever point with defined position is removed (point is deleted or its position gets undefined).<br /> *For more details, see [{{doxygen-class-url|vtkMRMLMarkupsNode}} vtkMRMLMarkupsNode]<br /> <br /> ====Segmentations====<br /> <br /> Binary labelmap segmentations can now be represented as shared labelmaps.<br /> The previous implementation of binary labelmaps was performance intensive as each labelmap was represented using a separate vtkDataObject.<br /> Visualizing and editing segmentations that contained a large number of segments could cause performance issues, due to the large number of vtkActors required, as well as calculating masks and overwriting other segments when editing.<br /> <br /> By default, newly created segments will now be contained on the same layer.<br /> Segments will only be separated into multiple layers if the user creates an overlapping segment when editing.<br /> <br /> Segments are now saved as a 4D volume with shared 3D layers.<br /> For a segmentation that only uses one layer, the resulting image is a 3D volume.<br /> Before saving, the labelmaps will be collapsed into as few layers as possible.<br /> <br /> *seg.nrrd files now contain two additional attributes for each segment: SegmentX_LabelValue and SegmentX_Layer<br /> *The label value of a segment can be found using vtkSegment::GetLabelValue()<br /> *Whether or not a segment is shared can be found using vtkSegmentation::IsSharedBinaryLabelmap()<br /> *The other segments sharing the same labelmap can be found using vtkSegmentation::GetSegmentIDsSharingBinaryLabelmapRepresentation()<br /> *Segment editor effects should generally use modifySelectedSegmentByLabelmap rather than SetBinaryLabelmapToSegment to manage layer separation<br /> *Conversion rules now call PreConvert() and PostConvert() before and after conversion to perform pre and post processing steps on the segmentation as a whole<br /> *The function signature for vtkSegmentationConverterRule::Convert now accepts a vtkSegment rather than two vtkDataObjects<br /> *slicer.util.arrayFromSegment has been deprecated. slicer.util.arrayFromSegmentBinaryLabelmap and slicer.util.arrayFromSegmentInternalBinaryLabelmap can be used instead<br /> <br /> =====Erase the contents of a single segment=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.ClearSegment(segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Set labelmap in a segment=====<br /> <br /> Directly, bypassing masking settings:<br /> <br /> &lt;pre&gt;<br /> slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(orientedImageDataToSet, segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Move a segment from a shared labelmap to a separate layer=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.SeparateSegmentLabelmap(segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Combine all binary labelmaps to as few layers as possible=====<br /> <br /> &lt;pre&gt;<br /> segmentation = segmentationNode.GetSegmentation()<br /> segmentation.CollapseBinaryLabelmaps(forceToSingleLayer=false)<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Get a read-only labelmap for a single segment:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> labelmap = slicer.vtkOrientedImageData()<br /> segmentationNode.GetBinaryLabelmapRepresentation(segmentId, labelmap)<br /> &lt;/pre&gt;<br /> <br /> (similarly, use GetClosedSurfaceRepresentation with an additional vtk.vtkPolyData parameter to get a read-only surface mesh)<br /> <br /> or<br /> <br /> &lt;pre&gt;<br /> labelmapNumpyArray = slicer.util.arrayFromSegmentBinaryLabelmap(segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Get a modifiable shared labelmap=====<br /> <br /> &lt;pre&gt;<br /> labelmap = slicer.vtkOrientedImageData()<br /> segmentationNode.GetBinaryLabelmapInternalRepresentation(segmentId, labelmap)<br /> &lt;/pre&gt;<br /> <br /> (similarly, use GetClosedSurfaceInternalRepresentation to get a modifiable surface mesh)<br /> <br /> or<br /> <br /> &lt;pre&gt;<br /> labelmapNumpyArray = slicer.util.arrayFromSegmentInternalBinaryLabelmap(segmentationNode, segmentId)<br /> &lt;/pre&gt;<br /> <br /> =====Export segments to models=====<br /> <br /> Model hierarchies no longer exist in Slicer5, but instead various kinds of hierarchies are now replaced by &quot;subject hierarchy&quot;, which can accommodate any node types in a single hierarchy. Accordingly, `ExportSegmentsToModelHierarchy`, `ExportAllSegmentsToModelHierarchy`, etc. are replaced by `ExportSegmentsToModels`, `ExportAllSegmentsToModels`, which take a subject hierarchy folder item ID as input.<br /> Documentation/Nightly<br /> See code example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#export-model-nodes-from-segmentation-node Script repository].<br /> <br /> =====Smoothing effect=====<br /> <br /> In Slicer-4.11 version before October 29, 2020 (and earlier versions), Gaussian smoothing method's Standard deviation parameter (&quot;GaussianStandardDeviationMm&quot;) was interpreted in pixels, while on the user interface and code it was claimed to be in physical units (millimeter). The problem was fixed and now the parameter is in millimeter.<br /> <br /> ====Volume rendering====<br /> <br /> vtkMRMLVolumeRenderingDisplayNode::SetAndObserveVolumeNodeID method was removed, as display node base class already maintains a pointer to the displayed (volume) node. To associate a volume display node with a volume node, call &lt;pre&gt;volumeNode-&gt;AddAndObserveDisplayNodeID(volumeRenderingDisplayNode-&gt;GetID());&lt;/pre&gt; after both nodes are added to the scene.<br /> <br /> ''vtkSlicerVolumeRenderingLogic::CreateDefaultVolumeRenderingNodes'' method unnecessarily polluted the scene with ROI node even though the user did not need cropping. In Slicer-5.x we fixed the issue by not creating the ROI nodes automatically. To create a ROI node, you can call ''vtkSlicerVolumeRenderingLogic::CreateROINode'' method.<br /> <br /> ====Extract skeleton====<br /> <br /> Command-line arguments of the module have been updated:<br /> - output image is now optional, therefore the output image file name must be specified using &quot;--outputImage&quot; argument<br /> - output image centerline voxel value is set to 255 (instead of 1) to make it easier to apply image processing operations on it (values can be interpolated between 0 and 255, while there are no integer values between 0 and 1)<br /> - &quot;--dontPrune&quot; is renamed to &quot;--fullTree&quot; for clarity<br /> - centerline curve is saved in mrk.json format<br /> <br /> ==== MRML node copy API improvements ====<br /> <br /> Slicer-4.10 and earlier had a single Copy() method, which had limitations:<br /> - usually implemented deep copy (but sometimes bulk data was just shallow-copied): problem, because for quick browsing of sequences, we need shallow-copy (to avoid copying bulk data, such as vtkImageData)<br /> - copied all node properties (except node ID and scene): this required workarounds, whenever we wanted to copy only the content of nodes (but for example keeping node references or node name intact)<br /> <br /> In Slicer-4.11, these limitations are addressed, by implementing a ''CopyContent(vtkMRMLNode* node, bool deepCopy=true)'' method which allows choosing between deep/shallow copy (create an independent copy of bulk data or pass bulk data pointer) and does not copy node ID, Scene, Name, SingletonTag, HideFromEditors, AddToScene, UndoEnabled, and node references.<br /> <br /> To make it easier to introduce this new method into existing classes, helper macros are implemented.<br /> <br /> If a class implements CopyContent method then the developer must make sure that CopyContent and HasCopyContent methods are implemented in all parent classes by adding vtkMRMLCopyContentMacro(ClassName) or vtkMRMLCopyContentDefaultMacro(ClassName) to the class headers. vtkMRMLCopyContentDefaultMacro should be used when the class does not have any additional properties (only those that parent classes already copy). CopyContent must be implemented by calling CopyContent of the parent class, and then copy node properties added in he class (preferable using shallow copy for large data, if deepCopy argument was set to false).<br /> <br /> If HasCopyContent macro is not added to a class then it cannot be recorded or replayed in Sequences module.<br /> <br /> ==== Removed classes ====<br /> <br /> Classes removed due to removing legacy Editor module:<br /> * vtkITKNewOtsuThresholdImageFilter is replaced by vtkITKImageThresholdCalculator<br /> * vtkITKGrowCutSegmentationImageFilter is replaced by vtkImageGrowCutSegment (it will be replaced by the ITK implementation https://github.com/Slicer/Slicer/pull/5807)<br /> * vtkITKTimeSeriesDatabase was removed, it was an incomplete class, not used anywhere<br /> * vtkITKWandImageFilter was removed, vtkImageThresholdConnectivity (in VTK) can be used instead<br /> * vtkImageConnectivity was removed, vtkImageThresholdConnectivity (in VTK) can be used instead<br /> * vtkImageErode was removed, vtkImageDilateErode3D (in VTK) can be used instead<br /> * vtkImageLabelChange was removed, vtkImageThreshold (in VTK) can be used instead<br /> * vtkImageSlicePaint was replaced by logic built into qSlicerSegmentEditorPaintEffect<br /> * vtkImageStash is replaced by vtkSegmentationHistory<br /> * vtkPichonFastMarching moved to SegmentEditorExtraEffects extension (https://github.com/lassoan/SlicerSegmentEditorExtraEffects)<br /> <br /> Classes removed due to removing Charts and DoubleArrays modules:<br /> * vtkMRMLChartNode is replaced by vtkMRMLPlotNode<br /> * vtkMRMLChartViewNode is replaced by vtkMRMLPlotViewNode<br /> * vtkMRMLDoubleArrayNode is replaced by vtkMRMLTableNode (can store any number of columns, not just two)<br /> * vtkMRMLDoubleArrayStorageNode is replaced by vtkMRMLTableStorageNode<br /> * qMRMLChartView is replaced by qMRMLPlotView<br /> * qMRMLChartViewControllerWidget is replaced by qMRMLPlotViewControllerWidget<br /> * qMRMLChartWidget is replaced by qMRMLPlotWidget<br /> <br /> ===Slicer 5.0: Fiducial List was renamed to Point List===<br /> <br /> To simplify terms used in Slicer, &quot;Fiducial List&quot; term was renamed to &quot;Point List&quot; on the user interface.<br /> The term in the API has not been changed to preserve backward compatibility.<br /> <br /> See discussion of the topic [https://discourse.slicer.org/t/delete-control-point-delete-fiducial-pop-up-confirm-box/20430/18 here].<br /> <br /> ===Slicer 5.0: SliceIntersectionVisibility was moved from vtkMRMLSliceCompositeNode to vtkMRMLSliceDisplayNode===<br /> <br /> SliceIntersectionVisibility property (that controls if intersections of other slices should be displayed in the slice view) was stored in vtkMRMLSliceCompositeNode. This was not a good choice because the composite node stores what image layers should be displayed in the slice view and how (what opacity, what blending method, etc.). The property was kept in that class for a long time to preserve backward compatibility, but when interactive slice intersection feature was added and additional properties had to be added that control appearance and behavior of slice intersections, this property was moved into the new vtkMRMLSliceDisplayNode node type and renamed to IntersectingSlicesVisibility.<br /> <br /> Scripts that previously used SliceIntersectionVisibility property will now fail with this error:<br /> <br /> AttributeError: 'MRMLCore.vtkMRMLSliceCompositeNode' object has no attribute 'SetSliceIntersectionVisibility'<br /> <br /> Those failing scripts can be updated with this example in the script repository: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#turn-on-slice-intersections<br /> <br /> ===Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead===<br /> <br /> &lt;b&gt;Error message:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> SlicerPython executable is obsolete and will be removed. Use PythonSlicer executable instead.<br /> For more details, see https://github.com/Slicer/Slicer/issues/4843<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Use &lt;tt&gt;PythonSlicer&lt;/tt&gt; instead of &lt;tt&gt;SlicerPython&lt;/tt&gt;<br /> <br /> &lt;b&gt;Background:&lt;/b&gt;<br /> <br /> Python IDEs (specifically PyCharm, but potentially others) only recognize &lt;tt&gt;Python*.exe&lt;/tt&gt; files as Python interpreters.<br /> <br /> To allow using Slicer's Python interpreter in these IDEs, we had to add &lt;tt&gt;PythonSlicer&lt;/tt&gt;, but kept &lt;tt&gt;SlicerPython&lt;/tt&gt; around for not immediately breaking things.<br /> <br /> This redundancy is confusing for users that we could resolve by simply removing SlicerPython for Slicer5.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/issues/4843<br /> <br /> ===Slicer 5.0: Application must be installed in writable location to install extensions===<br /> <br /> Extensions are now installed in the application home folder because Python packages are installed there anyway, so the application home folder has to be writable (or Slicer has to be run as admin when you install extensions). It also allows making Slicer fully portable - see details [https://discourse.slicer.org/t/slicer-is-now-fully-portable/15410 here].<br /> <br /> If you want to allow any user to install extensions without admin rights and you only need to use extensions that don’t install Python packages at runtime then you can specify a custom extension install path folder in Slicer-NNN.ini file or revert to the old behavior of Slicer by specifying &lt;code&gt;Slicer_STORE_SETTINGS_IN_APPLICATION_HOME_DIR:BOOL=OFF&lt;/code&gt; when configuring your Slicer build.<br /> <br /> ===Slicer 5.0: Models are saved in LPS coordinate system by default===<br /> <br /> While Slicer uses RAS coordinate system internally, images, transforms, and markups files are stored in LPS coordinate system, because DICOM and all medical image computing software (maybe except a few very old ones) uses LPS coordinate system in files.<br /> <br /> However, Slicer has been still using its internal RAS coordinate system in mesh files (STL, VTK, VTP, OBJ, PLY), which caused issues when interfacing with third-party software.<br /> <br /> From Slicer-4.11.0-2020-02-26 (revision 28794) models are saved in LPS coordinate system, and mesh files assumed to be in LPS coordinate system by default (if no other coordinate system specified in the file).<br /> <br /> Slicer started embedding coordinate system name in mesh files a few years ago (see &lt;code&gt;SPACE=RAS&lt;/code&gt; in the file header), so all the files that Slicer saved in recent years will load correctly and any scene files created with any version of Slicer will also load the models with correct orientation, too.<br /> <br /> Manual setting of coordinate system (in Add data dialog / Options column) is only needed when loading a mesh file without a scene that were created by Slicer-4.6 (2017-09-27) and earlier; and obj files created by Slicer-4.6 and Slicer-4.8 (between 2016-10-11 and 2018-03-26), or files are created by third-party software in RAS coordinate system.<br /> <br /> If you encounter orientation issues when loading a model file, you have the following options:<br /> <br /> *Option A: Specify the coordinate system when you open the model file. In “Add data” dialog, click “Show Options” and then choose “RAS” as coordinate system.<br /> *Option B: Update the third-party software that generate the mesh to save coordinates in LPS coordinate system instead of RAS coordinate system. Conversion is simple inverting the sign of the first two coordinates.<br /> *Option C: Write &lt;code&gt;SPACE=RAS&lt;/code&gt; in the comment/description field in the mesh file (for STL, OBJ, PLY, VTK file; for VTP files, add in the first value of a vtkStringArray field array named &lt;code&gt;SPACE&lt;/code&gt;) to indicate that the values are stored in RAS coordinate system. This option is useful if coordinates have to be stored in RAS coordinate system (for example, for compatibility with other software). See implementation example [https://github.com/Slicer/SlicerGitSVNArchive/blob/c0829f596f0ea661e0c5484056bd1374a3d22958/Libs/MRML/Core/vtkMRMLModelStorageNode.cxx#L421-L647 here].<br /> <br /> See more information, discussion of this topic on the [https://discourse.slicer.org/t/model-files-are-now-saved-in-lps-coordinate-system/10446 Slicer forum].<br /> <br /> ===Slicer 5.0: CLI module descriptor XML files assume LPS coordinate system by default===<br /> <br /> If [[Documentation/Nightly/Developers/SlicerExecutionModel|SlicerExecutionModel]] descriptor XML file of a CLI module does not specify coordinate system for a point, pointfile, or region element then the coordinate system is assumed to be &quot;lps&quot;. To preserve previous behavior and use &quot;ras&quot; coordinate system instead, add '''coordinateSystem=&quot;ras&quot;''' to the element.<br /> <br /> ===Slicer 5.0: Sequences extension has been merged into Slicer core===<br /> <br /> Sequences extension has been merged into Slicer core, therefore extensions do not need to depend on Sequences extension anymore.<br /> <br /> SequenceBrowser module has been merged into Sequences module, therefore previous code that used SequenceBrowser module now should use Sequences module instead.<br /> <br /> ===Slicer 5.0: FreeSurfer support has been removed from Slicer core===<br /> The loading of FreeSurfer models and scalar overlays, as well as the FreeSurfer-specific color nodes, have been moved to the new [https://github.com/PerkLab/SlicerFreeSurfer SlicerFreeSurfer] extension. Tutorials on how to use the FreeSurfer Importer module to load multiple files at once can be found on the [https://github.com/PerkLab/SlicerFreeSurfer/wiki/Tutorials SlicerFreeSurfer tutorial page].<br /> <br /> ===Slicer 5.0: Removed Editor module===<br /> <br /> The legacy Editor module has been deprecated since about 2017 and got removed in November 2021. It is replaced by the much improved Segment Editor module.<br /> <br /> ===Slicer 5.0: Removed Charts and DoubleArrays module===<br /> <br /> Charts and DoubleArrays module have been deprecated since about 2018 and got removed in November 2021. They are replaced by Plots and Tables modules.<br /> <br /> '''Example of commits'''<br /> * [https://github.com/SlicerRt/SlicerRT/commit/8f9155f94399be71e747d3d45b1f6c4152caa139 SlicerRT@8f9155f94] ENH: Update DVH module to use plots infrastructure instead of charts<br /> <br /> ===Slicer 5.0 : Avoid typedef of anonymous structure===<br /> <br /> Due to a recent (but retroactive) C++ rule change, only sufficiently C-compatible classes are permitted to be given a typedef name for linkage purposes. Add an &lt;tt&gt;enabled-by-default&lt;/tt&gt; warning for these cases, and rephrase our existing error for the case where we encounter the &lt;tt&gt;typedef&lt;/tt&gt; name for linkage after we've already computed and used a wrong linkage in terms of the new rule.<br /> <br /> &lt;b&gt;To fix warning message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:95:17:<br /> warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]<br /> typedef struct<br /> ^<br /> ColumnInfo<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:99:5:<br /> note: type is not C-compatible due to this default member initializer<br /> int ScalarType = VTK_STRING;<br /> ^~~~~~~~~~~~~~<br /> Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:102:5:<br /> note: type is given name 'ColumnInfo' for linkage purposes by this typedef declaration<br /> } ColumnInfo;<br /> ^<br /> For consistency, Use 'using' to a named structure definintion for all <br /> structures.<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> typedef struct<br /> {<br /> std::string ColumnName;<br /> std::vector&lt;vtkAbstractArray*&gt; RawComponentArrays;<br /> int ScalarType = VTK_STRING;<br /> std::vector&lt;std::string&gt; ComponentNames;<br /> std::string NullValueString;<br /> } ColumnInfo;<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> struct StructColumnInfo<br /> {<br /> std::string ColumnName;<br /> std::vector&lt;vtkAbstractArray*&gt; RawComponentArrays;<br /> int ScalarType = VTK_STRING;<br /> std::vector&lt;std::string&gt; ComponentNames;<br /> std::string NullValueString;<br /> };<br /> using ColumnInfo = struct StructColumnInfo;<br /> &lt;/pre&gt;<br /> <br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://reviews.llvm.org/D74103<br /> <br /> ===Slicer 5.0 : Temporary path===<br /> <br /> Temporary path was stored redundantly application settings (Slicer.ini) in two keys: &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; and &lt;code&gt;TemporaryPath&lt;/code&gt;. &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; overwrote &lt;code&gt;TemporaryPath&lt;/code&gt; at startup, but when temporary path was set via the &lt;code&gt;slicer.app.temporaryPath&lt;/code&gt; then it was only written to &lt;code&gt;TemporaryPath&lt;/code&gt;.<br /> <br /> Changed behavior so that only &lt;code&gt;TemporaryPath&lt;/code&gt; is used. &lt;code&gt;Modules/TemporaryDirectory&lt;/code&gt; is ignored.<br /> <br /> To ensure that temporary path is always writable, it as checked at startup that a file can be created in temporary path and if this check fails then temporary path is reset to default (&lt;code&gt;QDir::tempPath()&lt;/code&gt;).<br /> <br /> ===Slicer 5.0 : Always prefer executable CLIs===<br /> <br /> Previously, if a CLI module was available both as an executable and a shared library, then PreferExecutableCLI application setting was used to determine which one is used. Now always CLIs are always executed in an external process (if an executable is available). Reasons are described in this issue: https://github.com/Slicer/Slicer/issues/4893. The application setting is no more displayed in the GUI and any setting specified in earlier Slicer versions is ignored.<br /> <br /> ===Slicer 5.0 : SlicerApp-real is a console application on Windows===<br /> <br /> Previously, the application (SlicerApp-real.exe) was built as a GUI application (without console) on Windows, to avoid displaying a terminal window when starting the application. This had the drawback that the Slicer application did not have standard input/output that could be displayed or redirected (for example, for capturing into a file). SlicerApp-real has always been a console application on Linux and macOS, therefore this change makes the software behavior more consistent across platforms.<br /> <br /> SlicerApp-real.exe is now built as a console application (see [https://github.com/Slicer/Slicer/issues/2934 #2934]). Displaying of a terminal window is prevented by using a launcher (Slicer.exe) that is built as a GUI application and it starts Slicer with the standard input and outputs redirected.<br /> <br /> To display console output: https://slicer.readthedocs.io/en/latest/developer_guide/debugging/overview.html#console-output-on-windows<br /> <br /> To launch a command-line terminal using &lt;code&gt;subprocess.Popen&lt;/code&gt; that shows a new terminal, specify &lt;code&gt;creationflags=subprocess.CREATE_NEW_CONSOLE&lt;/code&gt; argument.<br /> <br /> ===Slicer 4.11: Variable CMAKE_DEFAULT_BUILD_TYPE renamed to Slicer_DEFAULT_BUILD_TYPE===<br /> <br /> Setting the default build type for single config generator may be done setting &lt;tt&gt;Slicer_DEFAULT_BUILD_TYPE&lt;/tt&gt; instead of &lt;tt&gt;CMAKE_DEFAULT_BUILD_TYPE&lt;/tt&gt;.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> CMake Error:<br /> Generator<br /> <br /> Visual Studio 15 2017<br /> <br /> does not support variable<br /> <br /> CMAKE_DEFAULT_BUILD_TYPE<br /> <br /> but it has been specified.<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/pull/4799<br /> <br /> ===Slicer 4.11: teem python module renamed to vtkTeem, explicit import required===<br /> <br /> *Since the module provides VTK classes interfacing with &quot;teem&quot;, the name is now representative of the class it contains.<br /> *&lt;tt&gt;vtkTeem&lt;/tt&gt; classes are expected to be used by explicitly importing the module.<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> import teem<br /> <br /> class CalculateTensorScalars(object):<br /> def __init__(self):<br /> self.dti_math = teem.vtkDiffusionTensorMathematics()<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> import vtkTeem<br /> <br /> class CalculateTensorScalars(object):<br /> def __init__(self):<br /> self.dti_math = vtkTeem.vtkDiffusionTensorMathematics()<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.11: Display window/level (brightness/contrast) adjustment===<br /> <br /> *A new &quot;Window/level&quot; mouse interaction mode was introduced. Volume display window/level can only be changed if this mode is activated by clicking the corresponding button in the toolbar. The new mouse mode prevents accidental modification of volume window/level (when for example the user accidentally clicked too far from a markup) and it also allows more sophisticated window/level adjustments.<br /> *New region-based auto window/level feature added: activate &quot;Window/level&quot; mouse mode and use Ctrl + left-click-and-drag to highlight a region and optimize window/level for that (pressing Escape or right-click cancels the operation).<br /> *Auto window/level reset: activate &quot;Window/level&quot; mouse mode and double-click the left mouse button.<br /> *Improved auto window/level algorithm to prevent too bright display of images. Window/level is set to display values between 0.1th and 99.9th percentile of gray levels. See details here: https://discourse.slicer.org/t/feedback-requested-how-to-improve-mouse-interaction-in-views/6420.<br /> *Removed class &lt;tt&gt;vtkImageBimodalAnalysis&lt;/tt&gt;<br /> <br /> ===Slicer 4.10: Registration of runTest function done in ScriptedLoadableModule base class===<br /> <br /> Following [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27617 r27617]:<br /> <br /> *the &lt;code&gt;ScriptedLoadableModule&lt;/code&gt; class takes care of registering the &lt;code&gt;runTest&lt;/code&gt; function.<br /> *the &lt;code&gt;runTest&lt;/code&gt; function expects &lt;code&gt;msec&lt;/code&gt; keyword argument.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> Traceback (most recent call last):<br /> File &quot;/path/to/Slicer-SuperBuild/Slicer-build/bin/Python/slicer/ScriptedLoadableModule.py&quot;, line 205, in onReloadAndTest<br /> test(msec=int(slicer.app.userSettings().value(&quot;Developer/SelfTestDisplayMessageDelay&quot;)), **kwargs)<br /> TypeError: runTest() got an unexpected keyword argument 'msec'<br /> Reload and Test: Exception!<br /> <br /> runTest() got an unexpected keyword argument 'msec'<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;Replace code like this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> class sceneImport2428(ScriptedLoadableModule):<br /> [...]<br /> def __init__(self, parent):<br /> ScriptedLoadableModule.__init__(self, parent)<br /> parent.title = &quot;...&quot;<br /> [...]<br /> parent.acknowledgementText = &quot;...&quot;<br /> self.parent = parent <br /> <br /> # Add this test to the SelfTest module's list for discovery when the module <br /> # is created. Since this module may be discovered before SelfTests itself, <br /> # create the list if it doesn't already exist. <br /> try: <br /> slicer.selfTests <br /> except AttributeError: <br /> slicer.selfTests = {} <br /> slicer.selfTests['sceneImport2428'] = self.runTest <br /> <br /> def runTest(self): <br /> tester = sceneImport2428Test() <br /> tester.runTest()<br /> <br /> [...]<br /> &lt;/pre&gt;<br /> <br /> &lt;b&gt;By this:&lt;/b&gt;<br /> <br /> &lt;pre&gt;<br /> class sceneImport2428(ScriptedLoadableModule):<br /> [...]<br /> def __init__(self, parent):<br /> ScriptedLoadableModule.__init__(self, parent)<br /> parent.title = &quot;...&quot;<br /> [...]<br /> parent.acknowledgementText = &quot;...&quot;<br /> <br /> [...]<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: Update of VTK version from 9.0 to 8.2===<br /> <br /> Following [https://github.com/Kitware/VTK/commit/b703d78be3ffd8ae69c319afa0230097ff270f26 kitware/VTK@b703d78be], VTK has updated to use version number 8.2 instead of 9.0. This was discussed in on the VTK mailing list in http://vtk.1045678.n5.nabble.com/Discussion-OK-to-change-VTK-s-version-number-from-9-0-to-8-2-tt5748702.html<br /> <br /> At first, this VTK commit and its companion [https://github.com/Kitware/VTK/commit/8a00b357e84eec695bda049216f30f2b76d80855 kitware/VTK@8a00b357e] were both reverted from the [https://github.com/Slicer/VTK/ Slicer/VTK] fork. Then, since having the corresponding changes reverted in VTK was not possible, it was decided to also update Slicer. This was done in the following commits:<br /> <br /> *[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27472 r27472]: COMP: Update c++ classes to support building against VTK &gt;= 9 and VTK &gt;= 8.2<br /> *[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27473 r27473]: COMP: Update VTK to include version change from 9.0 to 8.2. Fixes #4623<br /> <br /> This means that code depending on VTK must also be updated to include similar fixes.<br /> <br /> '''Replace this:'''<br /> #if VTK_MAJOR_VERSION &gt;= 9<br /> <br /> '''By this:'''<br /> #if VTK_MAJOR_VERSION &gt;= 9 || (VTK_MAJOR_VERSION &gt;= 8 &amp;&amp; VTK_MINOR_VERSION &gt;= 2)<br /> <br /> and<br /> <br /> '''Replace this:'''<br /> #if VTK_MAJOR_VERSION &lt; 9<br /> <br /> '''By this:'''<br /> #if VTK_MAJOR_VERSION &lt;= 7 || (VTK_MAJOR_VERSION &lt;= 8 &amp;&amp; VTK_MINOR_VERSION &lt;= 1)<br /> <br /> <br /> ===Slicer 4.9: ITK_LEGACY_REMOVE is now OFF===<br /> In preparation to switch to ITK 5.0, we disable legacy functionality in ITK. This might affect some modules which rely on ITK. Take a look at [https://itk.org/migrationv4 ITK 4 migration guide] before [https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md ITK 5 migration guide].<br /> <br /> ===Slicer 4.9: vtkMRMLPlotDataNode renamed to vtkMRMLPlotSeriesNode===<br /> Plotting was improved in [https://github.com/Slicer/Slicer/commit/082edc40c this commit]<br /> <br /> '''Replace this:'''<br /> <br /> vtkMRMLPlotDataNode<br /> <br /> '''By this:'''<br /> vtkMRMLPlotSeriesNode<br /> <br /> ===Slicer 4.9: CMake: Module MIDAS not available===<br /> <br /> The test infrastructure of your project should be updated to use [https://cmake.org/cmake/help/latest/module/ExternalData.html ExternalData] built-in CMake module<br /> instead of the specific &lt;tt&gt;MIDAS&lt;/tt&gt; module.<br /> <br /> See EMSegment commit [http://viewvc.slicer.org/viewvc.cgi/Slicer3?view=revision&amp;revision=17150 r17150] for an example of transition.<br /> <br /> This means that instead of using &lt;tt&gt;midas_add_test&lt;/tt&gt; with the &lt;tt&gt;MIDAS{path/to/file.ext.md5}&lt;/tt&gt;<br /> syntax for addressing the test data, the function [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_test ExternalData_add_target] is used by<br /> specifying both &lt;tt&gt;DATA{path/to/file.ext}&lt;/tt&gt; and a download target name.<br /> <br /> '''Replace this:'''<br /> <br /> midas_add_test(NAME test1 COMMAND ...)<br /> midas_add_test(NAME test2 COMMAND ...)<br /> <br /> '''By this:'''<br /> <br /> ExternalData_add_test(EMSegmentData NAME test1 COMMAND ...)<br /> ExternalData_add_test(EMSegmentData NAME test2 COMMAND ...)<br /> <br /> [...]<br /> <br /> ExternalData_add_target(EMSegmentData)<br /> <br /> <br /> A key difference with the former approaches is that instead of adding two tests (one named<br /> &lt;tt&gt;&lt;testName&gt;_fetchData&lt;/tt&gt; to downoad the data and one running the test command), only one<br /> test is added but a common download target is added at the end using [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_target ExternalData_add_target]<br /> function.<br /> <br /> This means that test data can now be downloaded in parallel (and cached) at build time instead<br /> of testing time.<br /> <br /> ===Slicer 4.9: CMake: Module SlicerMacroCheckExternalProjectDependency not available===<br /> <br /> Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26992 r26992], consider updating<br /> your build system to use CMake module &lt;code&gt;ExternalProjectDependency&lt;/code&gt;<br /> <br /> ===Slicer 4.9: CMake: Module SlicerMacroEmptyExternalProject not available===<br /> <br /> Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26991 r26991]<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerMacroEmptyExternalProject)<br /> <br /> [...]<br /> <br /> SlicerMacroEmptyExternalProject(&quot;${proj}&quot; &quot;${${proj}_DEPENDENCIES}&quot;)<br /> &lt;/pre&gt;<br /> <br /> '''By this:'''<br /> <br /> &lt;pre&gt;<br /> include(ExternalProjectDependency)<br /> <br /> [...]<br /> <br /> ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDENCIES})<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: CMake: Module SlicerBlockSetCMakeOSXVariables not available===<br /> <br /> Since it was renamed to &lt;tt&gt;SlicerInitializeOSXVariables&lt;/tt&gt; in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=26982 r26982]<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerBlockSetCMakeOSXVariables)<br /> &lt;/pre&gt;<br /> <br /> '''By this:'''<br /> <br /> &lt;pre&gt;<br /> include(SlicerInitializeOSXVariables)<br /> &lt;/pre&gt;<br /> <br /> ===Slicer 4.9: Application: isRelease() function not available===<br /> <br /> See [[#Slicer_4.8:_Application:_isRelease.28.29_function_not_available_or_deprecated]]<br /> <br /> ===Slicer 4.9: slicer.util.getNode() raises exception if node not found===<br /> <br /> If slicer.util.getNode() is called and the node is not found then instead of just returning None (Slicer 4.8 behavior), the method now raises a MRMLNodeNotFoundException. This makes code debugging easier (the error is reported when it happens), and in general more consistent with Python conventions.<br /> <br /> How to update existing code:<br /> <br /> It is advisable to only use slicer.util.getNode in tests, or interactively in the Python console, as its behavior is somewhat unpredictable (it may either found a node by name or ID, and result of wildcard search is even less deterministic). In general, it is recommended to use the MRML scene's GetFirstNodeByName and GetNodeByID methods instead.<br /> <br /> '''Replace this:'''<br /> <br /> &lt;pre&gt;<br /> n = slicer.util.getNode(nodeNameOrID)<br /> &lt;/pre&gt;<br /> <br /> '''By one of these:'''<br /> <br /> If node is to be found by name:<br /> &lt;pre&gt;<br /> n = slicer.mrmlScene.GetFirstNodeByName(nodeName)<br /> &lt;/pre&gt;<br /> <br /> If node is to be found by ID:<br /> &lt;pre&gt;<br /> n = slicer.mrmlScene.GetNodeByID(nodeID)<br /> &lt;/pre&gt;<br /> <br /> If node is to be found by name or ID (slower, less predictable, recommended for testing only):<br /> <br /> &lt;pre&gt;<br /> try:<br /> n = slicer.util.getNode(nodeNameOrID)<br /> except slicer.util.MRMLNodeNotFoundException:<br /> n = None<br /> &lt;/pre&gt;<br /> <br /> More information: https://github.com/Slicer/Slicer/commit/b63484af1b1b413f35396f8f7efb73e870448bd4<br /> <br /> ===Slicer 4.8: Application: isRelease() function not available or deprecated===<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> Missing/deprecated qSlicerCoreApplication::isRelease()<br /> <br /> or<br /> <br /> Missing/deprecated slicer.app.isRelease()<br /> <br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Use &lt;tt&gt;qSlicerCoreApplication::releaseType() == &quot;Stable&quot;&lt;/tt&gt;<br /> <br /> &lt;b&gt;Summary:&lt;/b&gt;<br /> <br /> Prior to r26420, the variable &lt;tt&gt;Slicer_VERSION_TWEAK&lt;/tt&gt; was used to check if a &quot;stable release&quot; was built. The variable value<br /> was set by updating the sources and defining the variable to an integer greater or equal to 0. In other word, if the variable<br /> evaluated to an empty string, a nighty or experimental build was being done, if it evaluated to an integer, a stable release build<br /> was being done.<br /> <br /> The approach had few issues:<br /> <br /> *the name of the variable was confusing<br /> *identifying a &quot;stable release&quot; only from a source tree revision was not enough. Indeed the environment defining a &quot;release&quot; is the one found on the build machines used to generate the installer.<br /> *nightly build are also considered as release<br /> <br /> To address this, the CMake variable &lt;tt&gt;Slicer_RELEASE_TYPE&lt;/tt&gt; was introduced. As of 2017-10-04, it can be set to &lt;tt&gt;Experimental&lt;/tt&gt;, &lt;tt&gt;Nightly&lt;/tt&gt;<br /> or &lt;tt&gt;Stable&lt;/tt&gt; with &lt;tt&gt;Experimental&lt;/tt&gt; being the value hard-coded in the source.<br /> <br /> Identifying a build as &quot;stable&quot; is now explicitly done by setting &lt;tt&gt;Slicer_RELEASE_TYPE&lt;/tt&gt; to &lt;tt&gt;Stable&lt;/tt&gt; at configure time.<br /> <br /> Also, since the concept of release types was introduced, the function &lt;tt&gt;isRelease()&lt;/tt&gt; has been removed in favor of &lt;tt&gt;releaseType()&lt;/tt&gt;.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/pull/354<br /> <br /> ===Slicer Python Module: modulewidget and others removed.===<br /> <br /> &lt;b&gt; Summary&lt;/b&gt;<br /> Python classes formerly in &quot;slicer.moduledm&quot;, &quot;slicer.modulelogic&quot;, &quot;slicer.modulemrml&quot;<br /> and &quot;slicer.modulewidget&quot; are now directly available in the slicer module.<br /> <br /> See example of change [https://github.com/QIICR/LongitudinalPETCT/pull/11 here].<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> See comments in commit messages referenced blow.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> https://github.com/Slicer/Slicer/commit/628f83fe7a6f4e0710e306bcaf7c04b9e3e5e6bd<br /> <br /> https://github.com/Slicer/Slicer/commit/9cb5668fde1abc8f0430a91ca37fc29277ceeb4e<br /> <br /> ===MRML: Slicer 4.6: Moved up vtkMRMLStorableNode in the MRML node hierarchy.===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> vtkMRMLStorableNode is not a children of vtkMRMLTransformable node anymore,<br /> but directly a children of vtkMRMLNode.<br /> <br /> This allows making a node storable without requiring it to be also<br /> transformable. It is important for several node types (color maps, tables,<br /> etc), which require separate storage node but are not transformable.<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *Changed introduced in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=24891 r24891]<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx: In member function ‘void vtkMRMLLongitudinalPETCTStudyNode::ObserveRegistrationTransform(bool)’:<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:478:28: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘GetParentTransformNode’<br /> &amp;&amp; propNode-&gt;GetParentTransformNode()<br /> ^<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:480:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’<br /> propNode-&gt;SetAndObserveTransformNodeID(<br /> ^<br /> /tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:503:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’<br /> propNode-&gt;SetAndObserveTransformNodeID(NULL);<br /> ^<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Removes lines and/or refactor code<br /> <br /> <br /> ===MRML: Slicer 4.5: Introduction of vtkMRMLLabelMapVolumeNode===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> Before &lt;tt&gt;vtkMRMLScalarVolumeNode&lt;/tt&gt; was used for both scalar and label map<br /> volumes and the LabelMap custom MRML node attribute was used for<br /> distinguishing between them (0=scalar; 1=label map volume).<br /> <br /> This made conversion between labelmap/scalar volumes very easy but made<br /> it difficult to customize behavior, display, processing of segmentation<br /> information.<br /> <br /> Now a new &lt;tt&gt;vtkMRMLLabelMapVolumeNode&lt;/tt&gt; class is used for storing segmentation<br /> information (still using &lt;tt&gt;vtkMRMLScalarVolume&lt;/tt&gt; used as base class for backward<br /> compatibility; but in the future the base class may be changed to reflect<br /> that segmentation can be represented in various ways, not just as volumes).<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> error: ‘class vtkMRMLScalarVolumeNode’ has no member named ‘SetLabelMap’<br /> outputVolumeNode-&gt;SetLabelMap(1);<br /> ^<br /> <br /> &lt;b&gt;Solution (part1: down cast to &lt;tt&gt;vtkMRMLLabelMapVolumeNode&lt;/tt&gt;, remove call to &lt;tt&gt;SetLabelMap&lt;/tt&gt;)&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> vtkMRMLNode* outputNode = d-&gt;OutputLabelVolumeMRMLNodeComboBox-&gt;currentNode();<br /> vtkMRMLScalarVolumeNode* outputVolumeNode = vtkMRMLScalarVolumeNode::SafeDownCast(outputNode);<br /> [...]<br /> outputVolumeNode-&gt;SetLabelMap(1);<br /> <br /> <br /> with:<br /> <br /> vtkMRMLLabelMapVolumeNode* outputVolumeNode =<br /> vtkMRMLLabelMapVolumeNode::SafeDownCast(d-&gt;OutputLabelVolumeMRMLNodeComboBox-&gt;currentNode());<br /> [...]<br /> <br /> <br /> &lt;b&gt;Solution (part2: Update UI file):&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> &lt;widget class=&quot;qMRMLNodeComboBox&quot; name=&quot;InputLabelVolumeMRMLNodeComboBox&quot;&gt;<br /> &lt;property name=&quot;nodeTypes&quot;&gt;<br /> &lt;stringlist&gt;<br /> &lt;string&gt;vtkMRMLScalarVolumeNode&lt;/string&gt;<br /> &lt;/stringlist&gt;<br /> &lt;/property&gt;<br /> [...]<br /> &lt;/widget&gt;<br /> <br /> with:<br /> <br /> &lt;widget class=&quot;qMRMLNodeComboBox&quot; name=&quot;InputLabelVolumeMRMLNodeComboBox&quot;&gt;<br /> &lt;property name=&quot;nodeTypes&quot;&gt;<br /> &lt;stringlist&gt;<br /> &lt;string&gt;vtkMRMLLabelMapVolumeNode&lt;/string&gt; &lt;------------- Update Here<br /> &lt;/stringlist&gt;<br /> &lt;/property&gt;<br /> [...]<br /> &lt;/widget&gt;<br /> <br /> <br /> &lt;b&gt;Solution (part3: Update node selector configuration):&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> nodeSelector.setNodeTypes(QStringList(&quot;vtkMRMLScalarVolumeNode&quot;));<br /> nodeSelector.addAttribute(&quot;vtkMRMLScalarVolumeNode&quot;, &quot;LabelMap&quot;, &quot;1&quot;);<br /> <br /> with:<br /> <br /> nodeSelector.setNodeTypes(QStringList(&quot;vtkMRMLLabelMapVolumeNode&quot;));<br /> <br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *https://www.slicer.org/wiki/Documentation/Labs/Segmentations#vtkMRMLLabelMapVolumeNode_integration* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=24291<br /> <br /> <br /> ===CLI: Slicer 4.3: Add ITKFactoryRegistration library centralizing ITK IO factory registration===<br /> <br /> &lt;b&gt;Rational:&lt;/b&gt;<br /> <br /> Linking against &lt;tt&gt;ITKFactoryRegistration&lt;/tt&gt; ensures that ITK IO factory are properly registered on all supported platforms.<br /> <br /> &lt;b&gt;Error message similar to:&lt;/b&gt;<br /> <br /> Undefined symbols for architecture x86_64:<br /> &quot;itk::itkFactoryRegistration()&quot;, referenced from:<br /> _main in ImageMakerTest.cxx.o<br /> ld: symbol(s) not found for architecture x86_64<br /> <br /> &lt;b&gt;Solution:&lt;/b&gt;<br /> <br /> Replace lines like:<br /> <br /> target_link_libraries(${CLP}Test ${CLP}Lib)<br /> <br /> with:<br /> <br /> target_link_libraries(${CLP}Test ${CLP}Lib ${SlicerExecutionModel_EXTRA_EXECUTABLE_TARGET_LIBRARIES})<br /> <br /> &lt;b&gt;References:&lt;/b&gt;<br /> <br /> *http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21592<br /> *https://issues.slicer.org/view.php?id=2813</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/FAQ/General&diff=64136 2022-06-21T23:52:17Z

<p>Lasso: /* Where can I download older release of Slicer ? */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;__TOC__<br /> ={{#titleparts: {{PAGENAME}} | | -1 }}=&lt;/noinclude&gt;&lt;includeonly&gt;<br /> {{#ifeq: {{#titleparts: {{PAGENAME}} | 3 }} | Documentation/{{documentation/version}}/Developers | | ='''User FAQ: {{{1}}}'''=}}<br /> &lt;/includeonly&gt;<br /> == What is Slicer ? ==<br /> {{:Documentation/{{documentation/version}}/Slicer}}<br /> <br /> <br /> == Where can I download Slicer? ==<br /> 3DSlicer is available for download by visiting the following link: '''http://download.slicer.org'''<br /> <br /> You can also get older releases by using the offset parameter in the download page. For example, download page from 7 days ago: http://download.slicer.org/?offset=-7<br /> <br /> To get a direct download link of previous revision on a selected operating system: http://download.slicer.org/download?os=macosx&amp;stability=any&amp;offset=-1<br /> <br /> Always include these parameters:<br /> * ''stability'', which can be ''release'', ''nightly'', or ''any''<br /> * ''os'', which can be ''win'', ''macosx'', or ''linux''<br /> <br /> Additional options:<br /> * revision built before or on the date: ''date=2015-01-01''<br /> * same but checkout date: ''checkout-date=2015-02-01''<br /> * exact revision: ''revision=27000''<br /> * revision less than of equal: ''closest-revision=26000''<br /> * latest revision of 4.3 branch, can include patch as well: ''version=4.3''<br /> <br /> Any of these queries can be combined with the offset param, which will step forward or backward a given number of revisions. So,<br /> ''stability=release&amp;version=4.5.0&amp;offset=-1'' should give you the revision just before the first 4.5 release.<br /> <br /> == Where can I download older release of Slicer ? ==<br /> <br /> Older releases of 3DSlicer are available here: https://slicer-packages.kitware.com/#collection/5f4474d0e1d8c75dfc70547e/folder/5f4474d0e1d8c75dfc705482<br /> <br /> Extensions can be downloaded for old Slicer releases manually from the Extensions Catalog at the URL: &lt;code&gt;https://extensions.slicer.org/catalog/All/(revision_number)/(operating_system)&lt;/code&gt;. Revision number is available in Slicer menu: Help / About Slicer (or in the [https://www.slicer.org/wiki/Release_Details#Slicer_4.8 Slicer Releases page]). Operating system can be: &lt;code&gt;win&lt;/code&gt;, &lt;code&gt;linux&lt;/code&gt;, or &lt;code&gt;macosx&lt;/code&gt;. For example for Slicer-4.8.0 on Windows extensions are available at: https://extensions.slicer.org/catalog/All/26489/win<br /> <br /> == Does Slicer work for non-English computing? ==<br /> <br /> At this point no, Slicer uses US English conventions. Specifically this means that directory paths should use ASCII characters only.<br /> <br /> There has been some discussion and planning about internationalization but it is not yet available:<br /> * https://www.slicer.org/wiki/Documentation/Labs/I18N<br /> * https://discourse.slicer.org/t/slicer-internationalization/579<br /> <br /> == How to install Slicer ? ==<br /> <br /> {{:Documentation/{{documentation/version}}/Slicer/Install}}<br /> <br /> <br /> ==Is Slicer really free?==<br /> <br /> Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).<br /> <br /> See [http://www.slicer.org/pages/LicenseText the Slicer License page] for the legal version of this.<br /> <br /> ==Where can I find someone to help me use Slicer?==<br /> <br /> We rely on the community of users and developers to share their expertise. Slicer Community support and development discussions are hosted on Discourse, which provides a modern web forum as well as email-only interaction:<br /> <br /> https://discourse.slicer.org<br /> <br /> If you post to any public forum, be sure not to include any [http://en.wikipedia.org/wiki/Protected_health_information Protected Health Information (PHI)] or any other data that would get you or anyone else in trouble. However, posting example data can be very important to people who are interested in helping you solve your problems. If you can replicate your question using data from the [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] or [[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] modules that's the first choice.<br /> <br /> The [[Documentation/Nightly | Users Manual]] gives descriptions for using each module, and you can check out the [[Documentation/Nightly/Training | Training pages]] for in depth tutorials about workflows.<br /> <br /> Mailing list discussions before 2017 April are [https://www.slicer.org/wiki/Help#Mailing_List_.28discontinued.29_Archives archived]<br /> <br /> ==Can I use slicer for patient care?==<br /> <br /> Slicer is intended for research work and ''has no FDA clearances or approvals of any kind''. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.<br /> <br /> <br /> ==How to cite Slicer?==<br /> {{:CitingSlicer}}<br /> <br /> == How do I create an account for the Slicer wiki? ==<br /> <br /> Current content of this wiki will be moved to https://slicer.readthedocs.io, https://www.slicer.org, and https://github.com/Slicer/Slicer/wiki websites and legacy content will be archived. New user accounts are no longer offered for this wiki.<br /> <br /> ==Can I install Slicer without administrator rights?==<br /> <br /> The most convenient way to install Slicer is to run the installer package (Slicer-{{documentation/currentversion}}....exe) as administrator. However, installation is not necessary, you just need to unpack the files in the installer package and copy them to your user directory or a USB drive and start it by running ''Slicer.exe''.<br /> <br /> You can unpack the installation package by one of the following methods:<br /> * Install Slicer on any computer where you have administrator access. All the files that you need to run Slicer are in the C:\Program Files\Slicer... directory.<br /> * Unpack the installation package by using 7zip or using the InstallExplorer plugin in Total commander or FAR manager (http://nsis.sourceforge.net/Can_I_decompile_an_existing_installer). All the Slicer files will be in the $_OUTDIR directory, except Slicer.exe, so you have to copy Slicer.exe into $_OUTDIR and run it from there. You can rename the $_OUTDIR directory and discard all the other directories ($COMMONFILES, $PLUGINSDIR, etc).<br /> <br /> <br /> ==What if I have problems with Slicer installation?==<br /> You can read our guide explaining [https://slicer.readthedocs.io/en/latest/user_guide/get_help.html#i-want-to-report-a-problem how to report a problem].<br /> <br /> ==Slicer does not start==<br /> <br /> === &quot;Insufficient graphics capability&quot; popup is displayed ===<br /> <br /> In Slicer-4.9, minimum graphics requirements have been increased compared to earlier versions. Computers running Slicer must support OpenGL 3.2. This OpenGL version was released in 2009 and so all desktop and laptop computers should already support it. However, on virtual machines or when connecting to a computer via remote desktop, this minimum requirements may not be met.<br /> <br /> * If you are trying to connect through Windows remote desktop (RDP):<br /> ** Recent Intel integrated GPUs and some NVidia GPUs (Quadro series) running on Windows 10 now support running current OpenGL versions. You may consider upgrading your hardware and operating system.<br /> ** You can use other remote desktop applications, such as [https://www.realvnc.com/ RealVNC], [https://anydesk.com/ AnyDesk], or [https://remotedesktop.google.com/ Google remote desktop] (all free, or free for personal use)<br /> ** If your computer can normally run Slicer but when started through remote desktop it displays &quot;Insufficient graphics capability&quot; popup: You need to start Slicer in normal desktop mode and then establish remote connection. You can achieve this by following these steps:<br /> *** Connect to the remote computer using remote desktop<br /> *** Start Slicer on the remote computer<br /> *** Click &quot;Retry&quot; when &quot;Insufficient graphics capability&quot; popup appears<br /> *** Grant administrator access in the displayed user account control popup (administrator access is needed for termination of the current remote desktop session), this will close the remote desktop connection<br /> *** Reconnect to the remote computer using remote desktop - you should see Slicer application started up successfully<br /> <br /> === Any other issues ===<br /> <br /> See [https://slicer.readthedocs.io/en/latest/user_guide/get_help.html#slicer-application-does-not-start debugging application startup issues].<br /> <br /> ==How to uninstall Slicer?==<br /> *On Windows, choose &quot;Uninstall&quot; option from the Start menu.<br /> *On the Mac, remove the Slicer.app file. To clean up settings, remove &quot;~/.config/www.na-mic.org/&quot;<br /> *On Linux, remove the directory where the application is located. To clean up settings, remove &quot;~/.config/NA-MIC/&quot;<br /> <br /> See the information about the location of [[Documentation/{{documentation/version}}/SlicerApplication/Settings|Settings]] for all platforms. If the uninstaller is not working on windows you may need to remove the settings manually.<br /> <br /> == Where can I find Slicer tutorials? ==<br /> Slicer tutorials associated with the latest {{documentation/currentversion}} stable release are available by visiting the following link: [[Documentation/Nightly/Training|Click Here]].<br /> <br /> <br /> ==I read errors in the logs complaining about memory==<br /> <br /> Errors such as “Description: Failed to allocate memory for image.” indicate that you don’t have enough memory space.<br /> This can be a common issue if you run a 32-bit version of Slicer. You cannot expect a 32-bit executable to deal with any moderately complex problem. The [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration#32_bit_versus_64_bit|recommended solution]] is to download/build/use Slicer in 64-bit mode.<br /> <br /> Possible workarounds:<br /> * Use a 64-bit version of Slicer <br /> * You have somewhat more memory if you run the module in a separate process. To do that open [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Modules|Edit / Application Settings / Modules]] and check the “Prefer Executable CLIs” option, then restart Slicer.<br /> * Decrease the size and/or resolution of the input and output images<br /> ** Consider [[Documentation/{{documentation/version}}/Modules/Crop_Volume|Crop Volume]] to focus on just your area of interest.<br /> ** Consider [[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] or [[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|ResampleScalarVolume]] increase the sample spacing (decrease the resolution) of your data.<br /> <br /> <br /> == Which Slicer version should I use: 3.X or 4.X ? ==<br /> <br /> In general slicer3 and slicer4 have roughly similar functionality with respect to registration basics. Probably the most important thing to keep in mind is that slicer3 is no longer actively maintained.<br /> <br /> Slicer4, on the other hand, has benefited from literally hundreds of bug fixes over the past several years, and typically has better features and much better performance. Also, the nightly builds of slicer4 are now using ITKv4, which has significantly improved registration code. I am told by active users/developers of ITK that ITKv4 should provide significantly better results in many cases. Also, several new registration techniques are being actively developed for slicer4.<br /> <br /> Source: http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006190.html<br /> <br /> <br /> == What is my HOME folder ? ==<br /> <br /> {|width = &quot;100%&quot;<br /> ! width=&quot;50%&quot; style=&quot;border-bottom: 1px solid darkgrey;font-size: 75%;&quot;| Linux or MacOSX<br /> ! width=&quot;50%&quot; style=&quot;border-bottom: 1px solid darkgrey;font-size: 75%;&quot;| Windows<br /> |-<br /> | valign=&quot;top&quot; |<br /> Start a terminal.<br /> {{pre2|&lt;nowiki&gt;<br /> $ echo ~<br /> /home/jchris<br /> &lt;/nowiki&gt;}}<br /> | valign=&quot;top&quot; |<br /> <br /> Start Command Prompt (Start Menu -&gt; All Programs -&gt; Accessories -&gt; Command Prompt)<br /> {{pre2|&lt;nowiki&gt;<br /> &gt; echo %userprofile%<br /> C:\Users\jcfr<br /> &lt;/nowiki&gt;}}<br /> |}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/Sequences&diff=64135 2022-06-17T16:10:07Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://github.com/SNRLab/SNRMeasurement This page has been moved to GitHub.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SkullStripper&diff=64060 2022-04-24T18:58:43Z

<p>Lasso: </p> <hr /> <div>{{documentation/banner<br /> | text = [https://github.com/lassoan/SlicerSwissSkullStripper This page has been moved to the extension's repository.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SkullStripper&diff=64059 2022-04-24T18:58:32Z

<p>Lasso: moved documentation to https://github.com/lassoan/SlicerSwissSkullStripper</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://github.com/lassoan/SlicerSwissSkullStripper This page has been moved to the extension's repository.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Labs/Slicer5-roadmap&diff=64056 2022-04-17T22:19:39Z

<p>Lasso: /* Removal of Charts based infrastructure */</p> <hr /> <div>The major version number upgrade to 5 provides an opportunity to make changes that affect the<br /> application, the API, or the code in a way that was not possible in the past seven or so years.<br /> <br /> This page collects community suggestions related to the transition plan for Slicer 4.10 and major changes for Slicer 5.x<br /> <br /> Related forum post: https://discourse.slicer.org/t/slicer-5-0-deprecation-discussion-wiki/2377<br /> <br /> ==Overall Goals==<br /> <br /> *Improve user experience<br /> **More logical interface<br /> **Perform most common tasks easily<br /> **Easier to discover advanced features<br /> **Improve asynchronous behavior (like loading data in a background thread)<br /> *Defining core and extensions<br /> **Core functionality is:<br /> ***DICOM and other format I/O, Subject management<br /> ***Visualization 2D/3D/4D<br /> ***Segmentation<br /> ***Transforms and Registration<br /> ***Annotations and Markups<br /> ***Programmability and Extensibility<br /> **Move some extensions to core (Sequences, DICOMPlugins...)<br /> **Move some core to extensions (SimpleITK, Editor...)<br /> *Simplify maintenance<br /> **Remove legacy code that adds more complexity than value<br /> **Deprecate support for older build options and platforms (old libs, old compilers, etc)<br /> **Simplify documentation creation and use<br /> **Streamline the build and release process<br /> **Use unmodified upstream libraries<br /> *Developer experience<br /> **Improve API / Scripting documentation organization / search engine optimization<br /> **Simplify/accelerate build process on all platforms (options to use prebuilt sdk for example)<br /> **Use standard packages (Qt, Python, VTK, ITK)<br /> <br /> &lt;hr /&gt;<br /> <br /> ==Specific Change Proposals==<br /> <br /> ===Slicer 5.0: Backward incompatible changes===<br /> <br /> ====Third-party library updates====<br /> <br /> *Update to latest VTK: may fix issues in rendering (Virtual Reality Qt widget, [https://discourse.slicer.org/t/setting-of-markerstyle-does-not-work/9073/6 plot line markers])<br /> *Update to latest Qt: May fix [https://discourse.slicer.org/t/extension-wizard-file-open-dialogs-hang-ui-for-several-seconds/7881/9 Qt temporary hang] on startup and when showing file dialog<br /> <br /> ====Python3====<br /> <br /> Switch to Python3 and use the same compiler as official Python distribution. This would allow installation of any Python package inside Slicer's Python environment.<br /> <br /> Tasks:<br /> <br /> *Update of CTK: Build system, CTK Python console and [https://github.com/commontk/CTK/blob/master/CMake/ctkWrapPythonQt.py ctkWrapPythonQt.py] - '''DONE''' {{done}}<br /> *Update [https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_python.cmake External_python.cmake] - '''DONE''' {{done}}<br /> *Update of &quot;C++ to python bridge&quot; classes ([https://github.com/Slicer/Slicer/blob/master/Base/QTCore/qSlicerScriptedUtils_p.h qSlicerScriptedUtils_p.h], [https://github.com/Slicer/Slicer/blob/master/Base/QTGUI/qSlicerScriptedLoadableModule.h qSlicerScriptedLoadableModule.h], [https://github.com/Slicer/Slicer/blob/master/Base/QTGUI/qSlicerScriptedFileDialog.h qSlicerScriptedFileDialog.h], [https://github.com/Slicer/Slicer/blob/master/Base/QTGUI/qSlicerScriptedLoadableModuleWidget.h qSlicerScriptedLoadableModuleWidget.h], [https://github.com/Slicer/Slicer/blob/master/Base/QTCore/qSlicerScriptedFileWriter.h qSlicerScriptedFileWriter.h], ...) - '''DONE''' {{done}}<br /> *Update of install rules and macos fixup - '''DONE''' {{done}}<br /> *Update of python scripts to be compliant with python 3 - '''DONE''' {{done}}<br /> <br /> Some of the issues discovered after integration of Python 3:<br /> <br /> *Fix iomodule.c build error with VS2017. See https://github.com/Slicer/Slicer/pull/1118#issuecomment-482436689. Fixed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=28138 r28138] - '''DONE''' {{done}}<br /> *Fix crash in Debug build. See https://github.com/lassoan/Slicer/tree/python-startup-hang-in-debug-mode. Fixed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=28141 r28141] - '''DONE''' {{done}}<br /> *&lt;tt&gt;restart()&lt;/tt&gt; Python function does not work. Fixed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=28143 r28143] - '''DONE''' {{done}}<br /> <br /> References:<br /> <br /> *discourse post: https://discourse.slicer.org/t/updating-slicer-to-work-with-python-3/4662/14<br /> *GitHub PR: https://github.com/Slicer/Slicer/pull/1118<br /> <br /> <br /> ====Revisit MRML Copy API====<br /> <br /> Copy method does not perform complete deep-copy in some classes. For Sequences, we need both DeepCopy (for node modifications) and ShallowCopy (for fast replay possible).<br /> <br /> There are also too many variants of node copy methods, which makes it difficult to use them correctly.<br /> <br /> See also https://issues.slicer.org/view.php?id=2608.<br /> <br /> Assign to Andras Lasso. - '''DONE''' {{done}}<br /> <br /> ====Coordinate system in files====<br /> <br /> To be consistent with the rest of the world: Save models and markups in LPS coordinate system by default. If no coordinate system is specified in input file, assume LPS. See https://issues.slicer.org/view.php?id=4445<br /> <br /> ====Acquisition transform====<br /> <br /> Enable acquisition transform by default, to show correct loading of tilted gantry images. It has proven to work well. See https://github.com/Slicer/Slicer/commit/b7650af3c27f34fc894bfdd587f2a4c02ba62a8b<br /> <br /> ====Model Hierarchies====<br /> <br /> Remove Model Hierarchy feature and make sure that Subject Hierarchy covers all use cases. This will impact ModelMaker, which should be converted to a simpler version that only returns models and not semantics. Need to check extensions, especially SlicerDMRI, for any dependencies on Model Hierarchy. - '''DONE''' {{done}}<br /> <br /> ====Extension description file format====<br /> <br /> Transition from [[Documentation/Nightly/Developers/Extensions/DescriptionFile|`.s4ext` text file]] to a json or yaml.<br /> <br /> ===Remove deprecated modules and/or Migrate to extension===<br /> <br /> ====Editor====<br /> The module already directs users to Segment Editor, which provides all the functionality of Editor and more, and<br /> is the successor module that will be improved and maintained. Removing it would decrease confusion of both old<br /> and new Slicer users<br /> <br /> *Potentially the hack about modules with names ending with the string &quot;Lib&quot; can also be removed after the Editor module will not require it. It is [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Base/QTCore/qSlicerUtils.cxx?r1=26891&amp;r2=26890&amp;pathrev=26891 around here].<br /> <br /> *'''Make Editor hidden in 4.10, advertise its removal (some extensions still use it), then remove it in 5.0'''. Remove it from toolbar, move Editor to legacy category in 4.10<br /> <br /> *Investigate if the module could easily be moved to an extension<br /> <br /> ====VectorToScalarVolume====<br /> <br /> The plan would be to improve the Volume module so that vector volume could be converted to scalar volume, similarly to scalar to labelmap conversion option. Then, this module could be removed.<br /> <br /> ====Unused module code====<br /> <br /> *&lt;s&gt;MultiVolumeRendering: A [https://github.com/Slicer/Slicer/tree/master/Modules/Loadable/MultiVolumeRendering module] that was effectively not developed since 2012, and is not currently compiled with Slicer.&lt;/s&gt; - Removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27087 r27087]<br /> *&lt;s&gt;Measurements: Same argument as MultiVolumeRendering&lt;/s&gt; - Removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27087 r27087]<br /> *&lt;s&gt;AtlasCreator Loadable module logic&lt;/s&gt; - Removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27088 r27088]<br /> <br /> ====CLI modules====<br /> <br /> *Model to Label Map: Has too many limitations and bugs (cannot handle concave structures, can cause Slicer to hang or crash, etc.), and is not maintained any more. It might be better to remove it than to fix it, especially that there is an algorithm for the same thing in Slicer that works much better<br /> **The model node to labelmap node conversion feature could be added as a subject hierarchy plugin, if the route via segmentation node is not convenient enough<br /> <br /> *Review CLI modules<br /> **BlobDetection<br /> **ConnectedComponent<br /> **GrayscaleModelMaker, ModelMaker: The modules are too different to combine them. Each have specific use cases.<br /> **DiffusionTensorTest, ROITest, TestGridTransformRegistration: Already excluded from package by specifying &lt;tt&gt;NO_INSTALL&lt;/tt&gt;<br /> **Resample Scalar Volume: Resample Scalar/Vector/DWI Volume module (which Crop Volume uses as well) can do everything it does already, except for four extra interpolation options. Probably can be removed<br /> <br /> ====Migrate to extension====<br /> <br /> Existing [https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/DMRIInstall/DMRIInstall.py DMRIInstall] scripted module will be re-factored and moved into a &lt;tt&gt;Modules/Scripted/InstallSuggestions&lt;/tt&gt; directory.<br /> <br /> Then, after transitioning them to extension, the following module will be added to the &quot;InstallSuggestions&quot; so that the user knows how to install them:<br /> <br /> *BRAINSTools (also add SlicerElastix to the suggestions)<br /> *SimpleITK: Only used in the editor<br /> *EMSegment: already disabled in Slicer-4.10, so it may be completely removed from build scripts instead of moving it to an extension<br /> <br /> Notes:<br /> <br /> *2018-12-13: Jc: Following discussion with Ron, we need to make sure to have at least one non-rigid registration method and one ICP based method (e.g Landmark Registration) available in the main distribution.<br /> <br /> ====PETStandardUptakeValueComputation====<br /> <br /> Remove PETStandardUptakeValueComputation from Slicer core, as a more advanced version of this is available in an extension: https://github.com/QIICR/Slicer-PETDICOMExtension. See details here: https://github.com/Slicer/Slicer/pull/1068#issuecomment-450905887<br /> <br /> ===Coding Style===<br /> <br /> ====Slicer 5.0: Indentation of curly braces====<br /> In Slicer the curly braces have a two-space indentation everywhere within functions. As this was inherited from VTK, but VTK changed its convention to align the braces with the statements (if etc.), it could make sense to make the change in Slicer too. This is considered a major change because it affects almost all cxx files.<br /> <br /> ====Simpler VTK smart pointer usage====<br /> Use &lt;code&gt;vtkNew&lt;type&gt; var;&lt;/code&gt; instead of &lt;code&gt;vtkSmartPointer&lt;type&gt; var = vtkSmartPointer&lt;type&gt;::New();&lt;/code&gt; and remove now unnecessary &lt;code&gt;.GetPointer()&lt;/code&gt; calls.<br /> <br /> ===Usability===<br /> <br /> ====Volume Rendering Activation Method====<br /> <br /> We have had lots of issues with people finding the eye icon.<br /> <br /> ===Miscellaneous===<br /> <br /> ====Tcl codes====<br /> &lt;s&gt;Most of the TCL code seems to be a heritage from Slicer3. Can they be removed?&lt;/s&gt; - Done in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=27091 r27091]<br /> <br /> ====Remove self-test modules from the All modules list====<br /> Users already find the all modules list very long, and as the self tests are for developers only (and can be found in the modules list under the Testing category), they could be removed from the list. Make sure they are available in Developer mode.<br /> <br /> ====Remove BTX/ETX pairs====<br /> Once VTK7 is no longer supported, the old way for disabling python wrapping is no longer needed. According to my tests (Csaba), wrapping works fine in all of those cases, so the new way (#ifndef __VTK_WRAP__) is not needed either.<br /> <br /> ===Slicer 5.2: Backward incompatible changes===<br /> <br /> ====Build System Simplification====<br /> <br /> *Pick the most recent reasonable CMake version and remove any complexities in the build system are only there to work around limitations of old CMake versions.<br /> <br /> *Consider any ways to streamline/simplify the configure and build process, even it if may require changing extensions.<br /> <br /> *Look for ways to minimize the effect of long directory path-related build issues. Currently on mac and windows we are pushing the limit of path length unless very short paths are used (e.g. /s5 or d:\s5). Reorganizing the build tree might give us more headroom.<br /> <br /> ====Remove remote data support from MRML====<br /> <br /> MRML theoretically supports downloading files through http, but this feature has not seen much use. This will not likely to change in the future because there is a wide range of data access and authentication protocols, which would not be practical at MRML level.<br /> <br /> It would be better to remove remote data support from MRML to simplify data storage. We can keep useful utility classes, such as cache manager for keeping track of local temporary files (downloaded using SampleData or other modules that download significant amount of temporary data).<br /> <br /> See also https://discourse.slicer.org/t/improving-testing-data-management-for-self-test/5014/4.<br /> <br /> ====Improve layout manager====<br /> <br /> *Support multiple displays: Currently, it is very hard to leverage multiple displays (need to stretch the Slicer window over multiple screens and align splitter manually to the screen boundary). Allow defining single-display and multi-display layouts. Single-display layouts could be selected for each display independently, while multi-monitor layouts would set views on several displays at once. Keeping a single layout manager (and enhance it with to allow creation of multiple widgets) would make it easier to maintain backward compatibility for existing modules.<br /> *View layout IDs: View layout IDs are currently integer values, which makes it difficult to ensure that modules always choose unique IDs. We should switch to using string IDs. String IDs can may be prefixed with modulename+&quot;.&quot; as we do it for singleton tags and node attributes. We may remain somewhat backward compatible by having SetLayoutID(int) method that maps known layout integer IDs to the new string IDs. See discussion here: https://github.com/Slicer/Slicer/pull/1061#discussion_r241825827<br /> <br /> ====SceneViews====<br /> <br /> The scene views feature does not work well for a long time now, and there is no consensus about what should be the scope it supports.<br /> <br /> Suggestion:<br /> <br /> *Do not save the state of all nodes: Support only display, view and hierarchy nodes.<br /> *Make SceneViews as stable as possible for these cases and remove support for data notes etc.<br /> *If a node is removed, update associated scene views<br /> <br /> Notes:<br /> <br /> *2018-12-13: Jc: Following discussion with Ron, we should keep the SceneView functionality. All data should be associated with the &quot;master&quot; view, and scene view should be different combination of viewing parameters (layout, camera, visibility, etc ...). A mrb to consider for testing is the [http://slicer.kitware.com/midas3/slicerdatastore/view?itemId=126553&amp;layout=layout LungSegments_scene.mrb]<br /> *Another suggestion from Sonia is that SceneViews could be read-only for certain classes of nodes. It's not clear how that would be implemented, but it could address the instability problems while enabling the use of SceneViews for training.<br /> <br /> ====Undo/Redo====<br /> Similarly to SceneViews, it is a great feature but in time it started breaking.<br /> Need to decide if we want to keep it, and if yes fix it.<br /> <br /> Potential fix (currently being tested by Kyle Sunderland and Andras Lasso): Add an &quot;undo enabled&quot; flag to vtkMRMLNode, disable it by default, only enable it for nodes that undo/redo has tested to work correctly. Preliminary tests show that the feature largely works, but there are complications with undo/redo of node add/remove actions and node references.<br /> <br /> Notes:<br /> <br /> *2018-12-13: Jc: Following discussion with Ron, would be nice to also have undo/redo for camera settings, field of view, etc ... within a given view. It is easy to inadvertently modify settings ... (e.g when trying to pan using a trackpad with shift+left click but inadvertently using only left click)<br /> <br /> ====Removal of Charts based infrastructure====<br /> <br /> With Slicer 5.0, the idea is to remove the [[Documentation/Nightly/Developers/Charts|Charts]] infrastructure based on jqPlot, and only keep<br /> the [https://slicer.readthedocs.io/en/latest/user_guide/modules/plots.html Plots] infrastructure based on VTK Charts.<br /> Ron's request: enable anti-aliasing (MSAA or FXAA) and use less subtle default colors (https://www.slicer.org/wiki/Slicer4:2012_GenericChartColors) to improve appearance.<br /> <br /> ==Additional proposed changes to be discussed==<br /> <br /> *Bundle IPython package in Slicer installer - Slicer Jupyter extension has been added, do we need more?<br /> **Do we want history across sessions?<br /> **Quick access to script repository<br /> *[https://discourse.slicer.org/t/add-slicer-nightly-to-homebrew-macos/811 Install using brew]<br /> *Add opt-in collection of usage statistics for various features (e.g. could be triggered when a module is entered).<br /> *Enable geometry correction by default (e.g. gantry tilt as [https://discourse.slicer.org/t/actual-size-of-stl-models/5005/21 discussed here]).<br /> *Remove legacy 1.0 pydicom and only bundle latest (see https://pydicom.github.io/pydicom/stable/transition_to_pydicom1.html#). Import name changed from 'dicom' to 'pydicom' (See also: https://github.com/Slicer/Slicer/pull/1231)<br /> *Remove DICOM Networking (DIMSE) code https://discourse.slicer.org/t/dicom-retrieve-on-windows-10-there-is-no-service-listening-dicom-communications-no-telnet-connection-to-ports<br /> *Update the logo along [https://discourse.slicer.org/t/slicer-module-panel-icon-in-dark-mode/8353/3 as discussed here].</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/FAQ/General&diff=64055 2022-04-17T22:18:33Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;__TOC__<br /> ={{#titleparts: {{PAGENAME}} | | -1 }}=&lt;/noinclude&gt;&lt;includeonly&gt;<br /> ='''Developer FAQ: {{{1}}}'''=<br /> &lt;/includeonly&gt;<br /> <br /> == What is Slicer ? ==<br /> <br /> {{:Documentation/{{documentation/version}}/Developers/Slicer}}<br /> <br /> == How can I get help debugging my code? ==<br /> <br /> You can post questions to the [[Help|developer mailing list]]. <br /> <br /> Please consider:<br /> * Review the mailing list archives for similar questions<br /> * If you ask a coding question, try to use a [http://sscce.org/ Short Self-Contained Correct Example]<br /> * It's a friendly community but people are busy so if you get a terse response don't take it personally :-)<br /> <br /> == How to setup for Git development ? ==<br /> See [[Documentation/{{documentation/version}}/Developers/DevelopmentWithGit#Slicer Setup | Slicer Setup ]]<br /> <br /> == How to contribute a patch ? ==<br /> {{:Documentation/{{documentation/version}}/Developers/Tutorials/ContributePatch}}<br /> <br /> <br /> == What is our bug / feature request workflow ? ==<br /> <br /> {{:Documentation/{{documentation/version}}/Developers/IssueWorkflow}}<br /> <br /> <br /> == How to schedule a Developer Hangout ? ==<br /> See instruction [[Developer_Meetings/OrganizerInstruction|here]]<br /> <br /> <br /> == Should core feature be implemented in C++ or Python ? ==<br /> <br /> There is no one-size-fits-all answer to this. There are many examples of &quot;core' features of Slicer implemented using a variety of programming languages and techniques.<br /> <br /> * MRML and most Logic operations are in C++, implemented as VTK subclasses<br /> * the Application and most GUI functionality is in C++, implemented as QWidget subclasses<br /> * most bundled modules are implemented as &quot;loadable&quot; modules, combining VTK and Qt parent classes<br /> * many important modules bundled with Slicer are implemented as python scripted modules (LabelStatistics, ExtensionWizard...) or with hybrid C++ and Python solutions (Editor, DICOM, DataProbe...)<br /> * other &quot;core&quot; features rely on JavaScript and web technologies (Charts, SceneViews, Extension Manager....)<br /> <br /> The implementation choice depends heavily on the use case and the best judgement of the people who commit to maintain the code. If you are contributing an extension that you will maintain, you have a lot of flexibility. If you are hoping to pass off your code to others and you expect them to maintain it, then you should carefully follow the example of similar code that is already being maintained so that your code will be a pleasure to work with and not a misfit that causes trouble.<br /> <br /> <br /> Original comment from Andras Lasso copied from [https://github.com/Slicer/Slicer/pull/373#issuecomment-146894971 PR#373] discussion.<br /> <br /> <br /> There are many reasons for implementing Slicer core in C++, we just list here few reasons:<br /> <br /> * C++ rigor and extensive compile-time checks increases the chance of catching errors earlier. C++ enforces many things that in Python are managed by good programming practices (that are not enforced and in general not followed by Slicer developers).<br /> <br /> * C++ memory management is much more explicit, which is more difficult to learn than Python, but allows much better efficiency (you can prevent memory fragmentation, optimize memory reallocations, etc), which is useful for code that may run hundreds of times per second (this code does).<br /> <br /> * There are lots of good examples of solid, fast C++ displayable managers. Python displayable managers are more at the experimental level.<br /> <br /> * Accessibility of Python classes from C++ modules is cumbersome. Accessibility of C++ classes is very convenient from both Python and C++ modules.<br /> <br /> * Some projects don't use Python and don't want to use it (Python brings in huge amount of additional code, which is a problem if you want to minimize the amount of code that goes through regulatory approval)<br /> <br /> * Profiling and optimization of mixed C++/Python code is very difficult (both C++ and Python profilers treat the &quot;other side&quot; as black hole). Since all the rest of the Slicer core is implemented in C++ (with a few small exceptions), it is much easier to implement this in C++, too.<br /> <br /> <br /> That said, we love Python programming, do it extensively, but implementing Slicer core features in Python has just too many disadvantages.<br /> <br /> == How to convert between ITK images and Slicer scalar volume nodes? ==<br /> <br /> See discussion and relevant links at http://slicer-devel.65872.n3.nabble.com/Converting-ITK-image-to-Slicer-ScalarVolumeNode-td4035458.html<br /> <br /> Steve Pieper's suggested architecture for using ITK code to process Slicer MRML data is as follows:<br /> <br /> 1) develop an ITK pipeline that implements the desired behavior<br /> <br /> 2) wrap the pipeline in a high level pure C++ ITK class that exposes the key inputs, output, parameters, and events<br /> <br /> 3) write a thin CLI wrapper around (2) using the Slicer Execution mode<br /> <br /> 4a) use the CLI in Slicer as-is<br /> <br /> 4b) write a scripted module that presents a higher level interface and calls the CLI<br /> <br /> 4c) if you need more interactivity, write a vtkITK wrapper around (2) that exposes the high level ITK class aspects using VTK conventions; expose this via a scripted or loadable module.<br /> <br /> A nice thing about this approach is that (1) through (3) are all highly reusable in different contexts both in and out of Slicer.<br /> <br /> Also this path, steps (1) through (4b) all the data types and orientation mappings between itk::Image and vtkMRMLScalarVolumeNode are handled automatically with existing mechanisms. Since the CLI is built as a shared library by default there is no file system overhead, just a few memcpys which is not much different than using the ITK pipeline directly.<br /> <br /> Another option is to implement the pipeline in SimpleITK, but adding custom C++ code into the SimpleITK is more complex and I don't think it's even possible to do this as an extension, whereas the path described above is completely compatible with our extension process.<br /> <br /> Note that the use case for the code that Raul points to is the opposite case, using a VTK class inside of an ITK pipeline. In this case ITKVtkGlue is very appropriate. The IJKToRAS transforms are not relevant since vtkImageData class does not support orientation and all the operations need to be performed in pixel space.<br /> <br /> If CLI route is not suitable for some reason, helper classes are available in SlicerRT that do conversion between itkImage and vtkMRMLScalarVolumeNode initializing IJKtoRAS matrix, see https://github.com/SlicerRt/SlicerRT/blob/master/SlicerRtCommon/SlicerRtCommon.h<br /> <br /> == What is the difference between Slicer Plot and Chart ? ==<br /> <br /> Slicer currently has two ways of displaying plots: Plot and Chart:<br /> * [https://slicer.readthedocs.io/en/latest/user_guide/modules/plots.html Plots]: C++ environment based on VTK plots.<br /> ** Advantages:<br /> *** Plots display data stored in [https://slicer.readthedocs.io/en/latest/user_guide/modules/tables.html tables]. Data is synchronized, therefore any data change in a table updates corresponding plots immediately.<br /> *** Interactive capabilities, such as data selection, point editing by click-and-drag.<br /> *** Faster plotting for many points (number of points &gt; 10^5 is not a problem, it is useful for data exploration).<br /> * [[Documentation/{{documentation/version}}/Developers/Charts | Charts]]: uses a JavaScript library, jqPlot, for the rendering.<br /> ** Advantages: slightly better quality rendering.<br /> <br /> Chart infrastructure will be probably deprecated and removed from future versions of Slicer.</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/FAQ/General&diff=64054 2022-04-17T22:17:02Z

<p>Lasso: moved Plots documentation to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;__TOC__<br /> ={{#titleparts: {{PAGENAME}} | | -1 }}=&lt;/noinclude&gt;&lt;includeonly&gt;<br /> ='''Developer FAQ: {{{1}}}'''=<br /> &lt;/includeonly&gt;<br /> <br /> == What is Slicer ? ==<br /> <br /> {{:Documentation/{{documentation/version}}/Developers/Slicer}}<br /> <br /> == How can I get help debugging my code? ==<br /> <br /> You can post questions to the [[Help|developer mailing list]]. <br /> <br /> Please consider:<br /> * Review the mailing list archives for similar questions<br /> * If you ask a coding question, try to use a [http://sscce.org/ Short Self-Contained Correct Example]<br /> * It's a friendly community but people are busy so if you get a terse response don't take it personally :-)<br /> <br /> == How to setup for Git development ? ==<br /> See [[Documentation/{{documentation/version}}/Developers/DevelopmentWithGit#Slicer Setup | Slicer Setup ]]<br /> <br /> == How to contribute a patch ? ==<br /> {{:Documentation/{{documentation/version}}/Developers/Tutorials/ContributePatch}}<br /> <br /> <br /> == What is our bug / feature request workflow ? ==<br /> <br /> {{:Documentation/{{documentation/version}}/Developers/IssueWorkflow}}<br /> <br /> <br /> == How to schedule a Developer Hangout ? ==<br /> See instruction [[Developer_Meetings/OrganizerInstruction|here]]<br /> <br /> <br /> == Should core feature be implemented in C++ or Python ? ==<br /> <br /> There is no one-size-fits-all answer to this. There are many examples of &quot;core' features of Slicer implemented using a variety of programming languages and techniques.<br /> <br /> * MRML and most Logic operations are in C++, implemented as VTK subclasses<br /> * the Application and most GUI functionality is in C++, implemented as QWidget subclasses<br /> * most bundled modules are implemented as &quot;loadable&quot; modules, combining VTK and Qt parent classes<br /> * many important modules bundled with Slicer are implemented as python scripted modules (LabelStatistics, ExtensionWizard...) or with hybrid C++ and Python solutions (Editor, DICOM, DataProbe...)<br /> * other &quot;core&quot; features rely on JavaScript and web technologies (Charts, SceneViews, Extension Manager....)<br /> <br /> The implementation choice depends heavily on the use case and the best judgement of the people who commit to maintain the code. If you are contributing an extension that you will maintain, you have a lot of flexibility. If you are hoping to pass off your code to others and you expect them to maintain it, then you should carefully follow the example of similar code that is already being maintained so that your code will be a pleasure to work with and not a misfit that causes trouble.<br /> <br /> <br /> Original comment from Andras Lasso copied from [https://github.com/Slicer/Slicer/pull/373#issuecomment-146894971 PR#373] discussion.<br /> <br /> <br /> There are many reasons for implementing Slicer core in C++, we just list here few reasons:<br /> <br /> * C++ rigor and extensive compile-time checks increases the chance of catching errors earlier. C++ enforces many things that in Python are managed by good programming practices (that are not enforced and in general not followed by Slicer developers).<br /> <br /> * C++ memory management is much more explicit, which is more difficult to learn than Python, but allows much better efficiency (you can prevent memory fragmentation, optimize memory reallocations, etc), which is useful for code that may run hundreds of times per second (this code does).<br /> <br /> * There are lots of good examples of solid, fast C++ displayable managers. Python displayable managers are more at the experimental level.<br /> <br /> * Accessibility of Python classes from C++ modules is cumbersome. Accessibility of C++ classes is very convenient from both Python and C++ modules.<br /> <br /> * Some projects don't use Python and don't want to use it (Python brings in huge amount of additional code, which is a problem if you want to minimize the amount of code that goes through regulatory approval)<br /> <br /> * Profiling and optimization of mixed C++/Python code is very difficult (both C++ and Python profilers treat the &quot;other side&quot; as black hole). Since all the rest of the Slicer core is implemented in C++ (with a few small exceptions), it is much easier to implement this in C++, too.<br /> <br /> <br /> That said, we love Python programming, do it extensively, but implementing Slicer core features in Python has just too many disadvantages.<br /> <br /> == How to convert between ITK images and Slicer scalar volume nodes? ==<br /> <br /> See discussion and relevant links at http://slicer-devel.65872.n3.nabble.com/Converting-ITK-image-to-Slicer-ScalarVolumeNode-td4035458.html<br /> <br /> Steve Pieper's suggested architecture for using ITK code to process Slicer MRML data is as follows:<br /> <br /> 1) develop an ITK pipeline that implements the desired behavior<br /> <br /> 2) wrap the pipeline in a high level pure C++ ITK class that exposes the key inputs, output, parameters, and events<br /> <br /> 3) write a thin CLI wrapper around (2) using the Slicer Execution mode<br /> <br /> 4a) use the CLI in Slicer as-is<br /> <br /> 4b) write a scripted module that presents a higher level interface and calls the CLI<br /> <br /> 4c) if you need more interactivity, write a vtkITK wrapper around (2) that exposes the high level ITK class aspects using VTK conventions; expose this via a scripted or loadable module.<br /> <br /> A nice thing about this approach is that (1) through (3) are all highly reusable in different contexts both in and out of Slicer.<br /> <br /> Also this path, steps (1) through (4b) all the data types and orientation mappings between itk::Image and vtkMRMLScalarVolumeNode are handled automatically with existing mechanisms. Since the CLI is built as a shared library by default there is no file system overhead, just a few memcpys which is not much different than using the ITK pipeline directly.<br /> <br /> Another option is to implement the pipeline in SimpleITK, but adding custom C++ code into the SimpleITK is more complex and I don't think it's even possible to do this as an extension, whereas the path described above is completely compatible with our extension process.<br /> <br /> Note that the use case for the code that Raul points to is the opposite case, using a VTK class inside of an ITK pipeline. In this case ITKVtkGlue is very appropriate. The IJKToRAS transforms are not relevant since vtkImageData class does not support orientation and all the operations need to be performed in pixel space.<br /> <br /> If CLI route is not suitable for some reason, helper classes are available in SlicerRT that do conversion between itkImage and vtkMRMLScalarVolumeNode initializing IJKtoRAS matrix, see https://github.com/SlicerRt/SlicerRT/blob/master/SlicerRtCommon/SlicerRtCommon.h<br /> <br /> == What is the difference between Slicer Plot and Chart ? ==<br /> <br /> Slicer currently has two ways of displaying plots: Plot and Chart:<br /> * [https://slicer.readthedocs.io/en/latest/user_guide/modules/plots.html Plots]: C++ environment based on VTK plots.<br /> ** Advantages:<br /> *** Plots display data stored in [[Documentation/{{documentation/version}}/Modules/Tables | Tables]]. Data is synchronized, therefore any data change in a table updates corresponding plots immediately.<br /> *** Interactive capabilities, such as data selection, point editing by click-and-drag.<br /> *** Faster plotting for many points (number of points &gt; 10^5 is not a problem, it is useful for data exploration).<br /> * [[Documentation/{{documentation/version}}/Developers/Charts | Charts]]: uses a JavaScript library, jqPlot, for the rendering.<br /> ** Advantages: slightly better quality rendering.<br /> <br /> Chart infrastructure will be probably deprecated and removed from future versions of Slicer.</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers&diff=64053 2022-04-17T22:15:37Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> __NOTOC__<br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;98%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> |-<br /> |&lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;New Developers&lt;/span&gt;:&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;big&gt;&lt;big&gt;Welcome ! Check these '''[[{{FULLPAGENAME}}/StartHere|instructions]]''' !&lt;/big&gt;&lt;/big&gt;<br /> |}<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;98%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> |-<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> |- <br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Getting involved&lt;/span&gt;<br /> ----<br /> <br /> [[Documentation/{{documentation/version}}/Developers/StartHere|Start here]]<br /> <br /> :New community member checklist<br /> <br /> [[{{FULLPAGENAME}}/Meetings|Developer meetings]]<br /> <br /> :It is open to everyone, feel free to join.<br /> <br /> [https://discourse.slicer.org Discussion Forum]<br /> <br /> :The most effective way to get help from the community<br /> &lt;!--<br /> [http://slicer-devel.65872.n3.nabble.com/ Search developers mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel Sign-up]<br /> : Intended for discussion of programming related questions<br /> --&gt;<br /> <br /> [[Documentation/{{documentation/version}}/Developers/FAQ|FAQ]]<br /> <br /> :Set of common development questions/answers<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Resources&lt;/span&gt;<br /> ----<br /> [[Roadmap|Roadmap]]{{updated}}<br /> <br /> :What's next ? What's the plan ?<br /> <br /> [[Documentation/Labs|Labs]] {{new}}<br /> <br /> :Keep track of on-going experiments.<br /> <br /> [http://apidocs.slicer.org/master/annotated.html Doxygen]<br /> <br /> :Source code API documentation.<br /> <br /> Source code repository<br /> <br /> :[https://github.com/Slicer/Slicer Github] or [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk SVN]<br /> <br /> CDash Quality Dashboard: [http://slicer.cdash.org/index.php?project=Slicer4 SlicerStable], [http://slicer.cdash.org/index.php?project=SlicerPreview SlicerPreview]<br /> <br /> :Nightly, continuous and experimental dashboards. - &lt;small&gt;[[{{FULLPAGENAME}}/Tutorials/DashboardSetup|Setup a dashboard]]&lt;/small&gt;<br /> <br /> [https://issues.slicer.org Bug tracker] / [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem]] / [[Documentation/{{documentation/version}}/Developers/Tutorials/ContributePatch|Contribute a patch]]<br /> <br /> :Web-based bug tracking system - &lt;small&gt;[[Documentation/{{documentation/version}}/Developers/BugTrackerConfiguration|Configuration]]&lt;/small&gt;<br /> <br /> [[{{FULLPAGENAME}}/Style Guide|Slicer Style Guidelines]]<br /> <br /> :Consistency and Readability for a manageable code base<br /> <br /> [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html Script repository]<br /> <br /> :Collection of python scripts manipulating various Slicer components.<br /> <br /> [[Release Details|Change logs and release details]]<br /> <br /> :Informations about Slicer releases<br /> <br /> [[Resources]]<br /> <br /> :List Slicer resources and who to contact in case of problem.<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Build instructions&lt;/span&gt;<br /> ----<br /> <br /> [https://slicer.readthedocs.io/en/latest/developer_guide/extensions.html Create Slicer extensions]<br /> <br /> :Build, test, package and distribute extensions<br /> <br /> [https://slicer.readthedocs.io/en/latest/developer_guide/build_instructions Build Slicer application]<br /> <br /> :Compiling and installing Slicer from source.<br /> <br /> [[Documentation/{{documentation/version}}/Developers/Build Module|Build Module]]<br /> <br /> :Compiling slicer modules outside of the slicer source tree.<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How-tos&lt;/span&gt;&amp;nbsp;&amp;nbsp;<br /> ----<br /> {{:{{FULLPAGENAME}}/Tutorials}}<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Quick links&lt;/span&gt;&amp;nbsp;&amp;nbsp;<br /> ----<br /> {{:{{FULLPAGENAME}}/Quicklinks}}<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Design &amp; Implementation&lt;/span&gt;<br /> ----<br /> <br /> [[{{FULLPAGENAME}}/Modules | Modules]]<br /> <br /> :Comparison between the different supported module types<br /> <br /> [https://slicer.readthedocs.io/en/latest/developer_guide/mrml_overview.html Data Model / MRML]<br /> <br /> :Objects and their organization. MRML Library provides API for managing medical image data type<br /> <br /> [[{{FULLPAGENAME}}/Logics | Logics]]<br /> <br /> :Details the role of MRML/Slicer/Application/Modules logics and Displayable managers<br /> <br /> [[{{FULLPAGENAME}}/Layouts | Layouts]] {{updated}}<br /> <br /> :How to control the layout of the views<br /> <br /> [[{{FULLPAGENAME}}/Slice Orientation Presets | Slice Orientation Presets]] {{new}}<br /> <br /> :How to manage slice orientation presets<br /> <br /> [[{{FULLPAGENAME}}/Slicelets | Slicelets]]<br /> <br /> :Create simple standalone applications (slicelets)<br /> <br /> [[{{FULLPAGENAME}}/IO | IO Mechanism]]<br /> <br /> :How to read or write nodes from file<br /> <br /> [[{{FULLPAGENAME}}/Python scripting | Python scripting]]<br /> <br /> :Presents the underlying infrastructure.<br /> <br /> [[{{FULLPAGENAME}}/Charts | Charts]]<br /> <br /> :Description of the Charting (jqPlot) architecture.<br /> <br /> [https://slicer.readthedocs.io/en/latest/developer_guide/modules/plots.html Plots]<br /> <br /> :Description of the Plotting (VTK) architecture.<br /> <br /> [[{{FULLPAGENAME}}/CompressedVideo | Compressed Video]] {{new}}<br /> <br /> :Description of the compressed video architecture.<br /> <br /> [[{{FULLPAGENAME}}/DirectoryStructure | Directory Structure]]<br /> <br /> :Files location in the build and install tree.<br /> <br /> [[{{FULLPAGENAME}}/QtPlugins|Qt Plugins]]<br /> <br /> :How to build and load Qt plugins.<br /> <br /> [[{{FULLPAGENAME}}/Build system | Build system / Release process / Factory description]]<br /> <br /> :Details how Slicer is built and packaged.<br /> <br /> [[{{FULLPAGENAME}}/QtTesting | QtTesting]]<br /> <br /> :Testing framework to test Slicer application. It complements unit tests.<br /> <br /> |}<br /> <br /> &lt;hr /&gt;<br /> <br /> <br /> [[{{collaborator|logo|slicer4}}|x300px|center]]</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Plots&diff=64052 2022-04-17T22:12:28Z

<p>Lasso: moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/plots.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly&diff=64032 2022-04-04T15:47:29Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> __NOTOC__<br /> <br /> {{documentation/versionlist}}<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> |-<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> |- <br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Where to start ?&lt;/span&gt;<br /> ----<br /> <br /> * [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]<br /> <br /> :Quick overview about Slicer<br /> <br /> *[[Documentation/{{documentation/version}}/Training|Training pages]]<br /> <br /> :Information on how to use Slicer {{documentation/version}}<br /> <br /> *[[Documentation/{{documentation/version}}/FAQ|FAQ]]<br /> <br /> :Set of common questions/answers<br /> <br /> *[https://discourse.slicer.org Discussion Forum]<br /> <br /> :The most effective way to get help from the community<br /> <br /> &lt;!--<br /> * [http://slicer-users.65878.n3.nabble.com/ Search users mailing list]<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How to&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}<br /> <br /> ----<br /> {{:{{FULLPAGENAME}}/SlicerApplication}}<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Modules&lt;/span&gt;<br /> ----<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> | width=&quot;5%&quot; |<br /> &amp;nbsp;<br /> <br /> | width=&quot;45%&quot; |<br /> <br /> [[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]<br /> &lt;br /&gt;<br /> <br /> [[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]<br /> &lt;br /&gt;<br /> <br /> [[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]<br /> &lt;br /&gt;<br /> <br /> [[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerModels-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/models.html Models]<br /> &lt;br /&gt;<br /> <br /> [[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]<br /> &lt;br /&gt;<br /> <br /> [[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]<br /> &lt;br /&gt;<br /> <br /> [[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]<br /> &lt;br /&gt;<br /> <br /> [[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]<br /> &lt;br /&gt;<br /> <br /> [[Image:ViewControllersIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/viewcontrollers.html View Controllers]<br /> &lt;br /&gt;<br /> <br /> [[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]<br /> &lt;br /&gt;<br /> <br /> [[Image:Welcome.png|32px]] [[{{FULLPAGENAME}}/Modules/Welcome|Welcome to Slicer]]<br /> &lt;br /&gt;<br /> <br /> | width=&quot;50%&quot; |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}<br /> <br /> |}<br /> <br /> <br /> &lt;!--<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Extension Categories&lt;/span&gt; {{new}}<br /> ----<br /> {{note}} What are these categories ? See [[Documentation/{{documentation/version}}/Extensions/CatalogPolicies|here]]<br /> --&gt;<br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Developers Corner&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}<br /> <br /> :Source code, contribute patch, develop modules<br /> <br /> &lt;!--<br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Developers mailing list] / [http://slicer-devel.65872.n3.nabble.com/ Browse archives]<br /> : Intended for discussion of programming related questions<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Miscellaneous&lt;/span&gt;<br /> ----<br /> &lt;!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --&gt;<br /> <br /> *[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]<br /> <br /> :Slicer user documentation principle and guidelines<br /> <br /> *[[Slicer4:VisualBlog|Visual blog]]<br /> <br /> :Set of screenshots showing Slicer in action.<br /> <br /> *[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br /> <br /> :Platform specific issues and considerations<br /> <br /> *[[Documentation/{{documentation/version}}/Announcements|Announcements]] &amp; [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]<br /> <br /> *[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]<br /> <br /> :Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Documentation in other languages&lt;/span&gt;<br /> ----<br /> {{:{{FULLPAGENAME}}/Lang/ES}}<br /> <br /> <br /> <br /> |}<br /> <br /> &lt;!--<br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing}}<br /> --&gt;<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}<br /> <br /> |<br /> &lt;br /&gt;<br /> &lt;br /&gt;<br /> =Modules by category=<br /> <br /> ==Converters==<br /> <br /> *[[Documentation/Nightly/Modules/CropVolume|Crop Volume]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VectorToScalarVolume|Vector To Scalar Volume]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOM Series]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==Diffusion==<br /> <br /> *[[Documentation/Nightly/Modules/DMRIInstall|DMRI Install]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Data_Conversion&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Data Conversion===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Tensor_Images&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Weighted Images===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Import_and_Export&quot;&gt;&lt;/span&gt;<br /> ===Import and Export===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Process&quot;&gt;&lt;/span&gt;<br /> ===Utilities===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Endoscopy&quot;&gt;&lt;/span&gt;<br /> ==Endoscopy==<br /> <br /> *[[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filter&quot;&gt;&lt;/span&gt;<br /> ==Filter==<br /> <br /> *IslandRemoval &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering&quot;&gt;&lt;/span&gt;<br /> ==Filtering==<br /> <br /> *[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4 ITK Bias Field Correction]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Arithmetic&quot;&gt;&lt;/span&gt;<br /> ===Arithmetic===<br /> <br /> *[[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Denoising&quot;&gt;&lt;/span&gt;<br /> ===Denoising===<br /> <br /> *[[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Morphology&quot;&gt;&lt;/span&gt;<br /> ===Morphology===<br /> <br /> *[[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_IGT&quot;&gt;&lt;/span&gt;<br /> ==IGT==<br /> <br /> *[[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLink IF]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics&quot;&gt;&lt;/span&gt;<br /> ==Informatics==<br /> <br /> *[[Documentation/Nightly/Modules/SEG2NRRD|SEG 2 NRRD]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Tables|Tables]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Data|Data]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *DumpSEGFrame &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Terminologies|Terminologies]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Units|Units]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SampleData|Sample Data]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Colors|Colors]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Annotations|Annotations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Markups|Markups]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/EncodeSEG|Encode SEG]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy&quot;&gt;&lt;/span&gt;<br /> ==Legacy==<br /> &lt;span id=&quot;Modules_by_category_Legacy_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Filtering&quot;&gt;&lt;/span&gt;<br /> ===Filtering===<br /> <br /> *[[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Registration&quot;&gt;&lt;/span&gt;<br /> ===Registration===<br /> <br /> *Test Grid Transform Registration &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==MultiVolume Support==<br /> <br /> *[[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolume Importer]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolume Explorer]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Quantification&quot;&gt;&lt;/span&gt;<br /> ==Quantification==<br /> <br /> *[[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *SegmentStatistics &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINSLabelStats &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataProbe|Data Probe]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration&quot;&gt;&lt;/span&gt;<br /> ==Registration==<br /> <br /> *[[Documentation/Nightly/Modules/Transforms|Transforms]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *BRAINSResize &lt;small&gt;(cli)&lt;/small&gt;<br /> *PerformMetricTest &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSResample|BRAINS Resample]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSFit|General registration (BRAINS)]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *[[Documentation/Nightly/Modules/ACPCTransform|AC-PC Transform]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINS Demon Warp]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Reformat|Reformat]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *VBRAINSDemonWarp &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation&quot;&gt;&lt;/span&gt;<br /> ==Segmentation==<br /> <br /> *[[Documentation/Nightly/Modules/Segmentations|Segmentations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Editor|Editor]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EMSegment|EMSegment]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> *EMSegmentQuick &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *BRAINS ROI Auto &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment CommandLine &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Surface_Models&quot;&gt;&lt;/span&gt;<br /> <br /> ==Surface Models==<br /> <br /> *[[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelMaker|Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelToLabelMap|Model To LabelMap]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MergeModels|Merge Models]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMap Smoothing]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities&quot;&gt;&lt;/span&gt;<br /> ==Utilities==<br /> <br /> *[[Documentation/Nightly/Modules/ScreenCapture|Screen Capture]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataStore|Data Store]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicompatcher.html DICOM Patcher] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINS Strip Rotation &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment Transform To New Format &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities_BRAINS&quot;&gt;&lt;/span&gt;<br /> ===BRAINS===<br /> <br /> *BRAINS Transform Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Wizards&quot;&gt;&lt;/span&gt;<br /> ==Wizards==<br /> <br /> *[[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools&quot;&gt;&lt;/span&gt;<br /> ==Developer Tools==<br /> <br /> *[[Documentation/Nightly/Modules/Cameras|Cameras]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtensionWizard|Extension Wizard]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EventBroker|Event Broker]]<br /> *Double Arrays &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools_DICOM_Plugins&quot;&gt;&lt;/span&gt;<br /> ===DICOM Plugins===<br /> <br /> *DICOMParametricMapPlugin<br /> *DicomUltrasoundPlugin<br /> *DICOMSegmentationPlugin<br /> *DICOMSlicerDataBundlePlugin<br /> *DICOMTID1500Plugin<br /> *[[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]<br /> *DICOMScalarVolumePlugin<br /> *DICOMDiffusionVolumePlugin<br /> *DICOMLongitudinalPETCTPlugin<br /> *DicomSroImportPlugin<br /> *[[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]<br /> *DicomRtImportExportPlugin<br /> *MultiVolumeImporterPlugin<br /> <br /> |}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ViewControllers&diff=64031 2022-04-04T15:46:27Z

<p>Lasso: Moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/viewcontrollers.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly&diff=64030 2022-04-04T15:43:35Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> __NOTOC__<br /> <br /> {{documentation/versionlist}}<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> |-<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> |- <br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Where to start ?&lt;/span&gt;<br /> ----<br /> <br /> * [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]<br /> <br /> :Quick overview about Slicer<br /> <br /> *[[Documentation/{{documentation/version}}/Training|Training pages]]<br /> <br /> :Information on how to use Slicer {{documentation/version}}<br /> <br /> *[[Documentation/{{documentation/version}}/FAQ|FAQ]]<br /> <br /> :Set of common questions/answers<br /> <br /> *[https://discourse.slicer.org Discussion Forum]<br /> <br /> :The most effective way to get help from the community<br /> <br /> &lt;!--<br /> * [http://slicer-users.65878.n3.nabble.com/ Search users mailing list]<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How to&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}<br /> <br /> ----<br /> {{:{{FULLPAGENAME}}/SlicerApplication}}<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Modules&lt;/span&gt;<br /> ----<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> | width=&quot;5%&quot; |<br /> &amp;nbsp;<br /> <br /> | width=&quot;45%&quot; |<br /> <br /> [[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]<br /> &lt;br /&gt;<br /> <br /> [[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]<br /> &lt;br /&gt;<br /> <br /> [[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]<br /> &lt;br /&gt;<br /> <br /> [[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerModels-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/models.html Models]<br /> &lt;br /&gt;<br /> <br /> [[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]<br /> &lt;br /&gt;<br /> <br /> [[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]<br /> &lt;br /&gt;<br /> <br /> [[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]<br /> &lt;br /&gt;<br /> <br /> [[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]<br /> &lt;br /&gt;<br /> <br /> [[Image:ViewControllersIcon.png|32px]] [[{{FULLPAGENAME}}/Modules/ViewControllers|View Controllers]]<br /> &lt;br /&gt;<br /> <br /> [[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]<br /> &lt;br /&gt;<br /> <br /> [[Image:Welcome.png|32px]] [[{{FULLPAGENAME}}/Modules/Welcome|Welcome to Slicer]]<br /> &lt;br /&gt;<br /> <br /> | width=&quot;50%&quot; |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}<br /> <br /> |}<br /> <br /> <br /> &lt;!--<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Extension Categories&lt;/span&gt; {{new}}<br /> ----<br /> {{note}} What are these categories ? See [[Documentation/{{documentation/version}}/Extensions/CatalogPolicies|here]]<br /> --&gt;<br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Developers Corner&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}<br /> <br /> :Source code, contribute patch, develop modules<br /> <br /> &lt;!--<br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Developers mailing list] / [http://slicer-devel.65872.n3.nabble.com/ Browse archives]<br /> : Intended for discussion of programming related questions<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Miscellaneous&lt;/span&gt;<br /> ----<br /> &lt;!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --&gt;<br /> <br /> *[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]<br /> <br /> :Slicer user documentation principle and guidelines<br /> <br /> *[[Slicer4:VisualBlog|Visual blog]]<br /> <br /> :Set of screenshots showing Slicer in action.<br /> <br /> *[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br /> <br /> :Platform specific issues and considerations<br /> <br /> *[[Documentation/{{documentation/version}}/Announcements|Announcements]] &amp; [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]<br /> <br /> *[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]<br /> <br /> :Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Documentation in other languages&lt;/span&gt;<br /> ----<br /> {{:{{FULLPAGENAME}}/Lang/ES}}<br /> <br /> <br /> <br /> |}<br /> <br /> &lt;!--<br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing}}<br /> --&gt;<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}<br /> <br /> |<br /> &lt;br /&gt;<br /> &lt;br /&gt;<br /> =Modules by category=<br /> <br /> ==Converters==<br /> <br /> *[[Documentation/Nightly/Modules/CropVolume|Crop Volume]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VectorToScalarVolume|Vector To Scalar Volume]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOM Series]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==Diffusion==<br /> <br /> *[[Documentation/Nightly/Modules/DMRIInstall|DMRI Install]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Data_Conversion&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Data Conversion===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Tensor_Images&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Weighted Images===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Import_and_Export&quot;&gt;&lt;/span&gt;<br /> ===Import and Export===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Process&quot;&gt;&lt;/span&gt;<br /> ===Utilities===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Endoscopy&quot;&gt;&lt;/span&gt;<br /> ==Endoscopy==<br /> <br /> *[[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filter&quot;&gt;&lt;/span&gt;<br /> ==Filter==<br /> <br /> *IslandRemoval &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering&quot;&gt;&lt;/span&gt;<br /> ==Filtering==<br /> <br /> *[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4 ITK Bias Field Correction]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Arithmetic&quot;&gt;&lt;/span&gt;<br /> ===Arithmetic===<br /> <br /> *[[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Denoising&quot;&gt;&lt;/span&gt;<br /> ===Denoising===<br /> <br /> *[[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Morphology&quot;&gt;&lt;/span&gt;<br /> ===Morphology===<br /> <br /> *[[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_IGT&quot;&gt;&lt;/span&gt;<br /> ==IGT==<br /> <br /> *[[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLink IF]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics&quot;&gt;&lt;/span&gt;<br /> ==Informatics==<br /> <br /> *[[Documentation/Nightly/Modules/SEG2NRRD|SEG 2 NRRD]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Tables|Tables]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Data|Data]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *DumpSEGFrame &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Terminologies|Terminologies]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Units|Units]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SampleData|Sample Data]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Colors|Colors]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Annotations|Annotations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Markups|Markups]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/EncodeSEG|Encode SEG]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy&quot;&gt;&lt;/span&gt;<br /> ==Legacy==<br /> &lt;span id=&quot;Modules_by_category_Legacy_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Filtering&quot;&gt;&lt;/span&gt;<br /> ===Filtering===<br /> <br /> *[[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Registration&quot;&gt;&lt;/span&gt;<br /> ===Registration===<br /> <br /> *Test Grid Transform Registration &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==MultiVolume Support==<br /> <br /> *[[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolume Importer]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolume Explorer]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Quantification&quot;&gt;&lt;/span&gt;<br /> ==Quantification==<br /> <br /> *[[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *SegmentStatistics &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINSLabelStats &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataProbe|Data Probe]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration&quot;&gt;&lt;/span&gt;<br /> ==Registration==<br /> <br /> *[[Documentation/Nightly/Modules/Transforms|Transforms]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *BRAINSResize &lt;small&gt;(cli)&lt;/small&gt;<br /> *PerformMetricTest &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSResample|BRAINS Resample]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSFit|General registration (BRAINS)]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *[[Documentation/Nightly/Modules/ACPCTransform|AC-PC Transform]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINS Demon Warp]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Reformat|Reformat]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *VBRAINSDemonWarp &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation&quot;&gt;&lt;/span&gt;<br /> ==Segmentation==<br /> <br /> *[[Documentation/Nightly/Modules/Segmentations|Segmentations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Editor|Editor]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EMSegment|EMSegment]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> *EMSegmentQuick &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *BRAINS ROI Auto &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment CommandLine &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Surface_Models&quot;&gt;&lt;/span&gt;<br /> <br /> ==Surface Models==<br /> <br /> *[[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelMaker|Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelToLabelMap|Model To LabelMap]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MergeModels|Merge Models]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMap Smoothing]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities&quot;&gt;&lt;/span&gt;<br /> ==Utilities==<br /> <br /> *[[Documentation/Nightly/Modules/ScreenCapture|Screen Capture]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataStore|Data Store]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicompatcher.html DICOM Patcher] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINS Strip Rotation &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment Transform To New Format &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities_BRAINS&quot;&gt;&lt;/span&gt;<br /> ===BRAINS===<br /> <br /> *BRAINS Transform Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Wizards&quot;&gt;&lt;/span&gt;<br /> ==Wizards==<br /> <br /> *[[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools&quot;&gt;&lt;/span&gt;<br /> ==Developer Tools==<br /> <br /> *[[Documentation/Nightly/Modules/Cameras|Cameras]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtensionWizard|Extension Wizard]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EventBroker|Event Broker]]<br /> *Double Arrays &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools_DICOM_Plugins&quot;&gt;&lt;/span&gt;<br /> ===DICOM Plugins===<br /> <br /> *DICOMParametricMapPlugin<br /> *DicomUltrasoundPlugin<br /> *DICOMSegmentationPlugin<br /> *DICOMSlicerDataBundlePlugin<br /> *DICOMTID1500Plugin<br /> *[[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]<br /> *DICOMScalarVolumePlugin<br /> *DICOMDiffusionVolumePlugin<br /> *DICOMLongitudinalPETCTPlugin<br /> *DicomSroImportPlugin<br /> *[[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]<br /> *DicomRtImportExportPlugin<br /> *MultiVolumeImporterPlugin<br /> <br /> |}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly&diff=64029 2022-04-03T18:26:28Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> __NOTOC__<br /> <br /> {{documentation/versionlist}}<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> |-<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> ! |<br /> ! width=&quot;33%&quot; |<br /> |- <br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Where to start ?&lt;/span&gt;<br /> ----<br /> <br /> * [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/getting_started.html Getting started]<br /> <br /> :Quick overview about Slicer<br /> <br /> *[[Documentation/{{documentation/version}}/Training|Training pages]]<br /> <br /> :Information on how to use Slicer {{documentation/version}}<br /> <br /> *[[Documentation/{{documentation/version}}/FAQ|FAQ]]<br /> <br /> :Set of common questions/answers<br /> <br /> *[https://discourse.slicer.org Discussion Forum]<br /> <br /> :The most effective way to get help from the community<br /> <br /> &lt;!--<br /> * [http://slicer-users.65878.n3.nabble.com/ Search users mailing list]<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How to&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}<br /> <br /> ----<br /> {{:{{FULLPAGENAME}}/SlicerApplication}}<br /> <br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Modules&lt;/span&gt;<br /> ----<br /> <br /> {| width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> | width=&quot;5%&quot; |<br /> &amp;nbsp;<br /> <br /> | width=&quot;45%&quot; |<br /> [[Image:SlicerAnnotationsV2-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Annotations|Annotations]]<br /> &lt;br /&gt;<br /> <br /> [[Image:DataIcon.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/data.html Data]<br /> &lt;br /&gt;<br /> <br /> [[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]<br /> &lt;br /&gt;<br /> <br /> [[Image:DICOM.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM]<br /> &lt;br /&gt;<br /> <br /> [[Image:Editor.png|32px]] [[{{FULLPAGENAME}}/Modules/Editor|Editor]]<br /> &lt;br /&gt;<br /> <br /> [[Image:Markups.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/markups.html Markups]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerModels-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/models.html Models]<br /> &lt;br /&gt;<br /> <br /> [[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]<br /> &lt;br /&gt;<br /> <br /> [[Image:Segmentations.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmentations.html Segmentations]<br /> &lt;br /&gt;<br /> <br /> [[Image:SegmentEditor.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor]<br /> &lt;br /&gt;<br /> <br /> [[Image:Transforms.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/transforms.html Transforms]<br /> &lt;br /&gt;<br /> <br /> [[Image:ViewControllersIcon.png|32px]] [[{{FULLPAGENAME}}/Modules/ViewControllers|View Controllers]]<br /> &lt;br /&gt;<br /> <br /> [[Image:VolumeRendering.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumerendering.html Volume Rendering]<br /> &lt;br /&gt;<br /> <br /> [[Image:SlicerVolume-Small.png|32px]] [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/volumes.html Volumes]<br /> &lt;br /&gt;<br /> <br /> [[Image:Welcome.png|32px]] [[{{FULLPAGENAME}}/Modules/Welcome|Welcome to Slicer]]<br /> &lt;br /&gt;<br /> <br /> | width=&quot;50%&quot; |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}<br /> <br /> |}<br /> <br /> <br /> &lt;!--<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Extension Categories&lt;/span&gt; {{new}}<br /> ----<br /> {{note}} What are these categories ? See [[Documentation/{{documentation/version}}/Extensions/CatalogPolicies|here]]<br /> --&gt;<br /> | bgcolor=&quot;#CCCCCC&quot; |<br /> | valign=&quot;top&quot; |<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Developers Corner&lt;/span&gt;<br /> ----<br /> <br /> *[[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}<br /> <br /> :Source code, contribute patch, develop modules<br /> <br /> &lt;!--<br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Developers mailing list] / [http://slicer-devel.65872.n3.nabble.com/ Browse archives]<br /> : Intended for discussion of programming related questions<br /> --&gt;<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Miscellaneous&lt;/span&gt;<br /> ----<br /> &lt;!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --&gt;<br /> <br /> *[[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]<br /> <br /> :Slicer user documentation principle and guidelines<br /> <br /> *[[Slicer4:VisualBlog|Visual blog]]<br /> <br /> :Set of screenshots showing Slicer in action.<br /> <br /> *[[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br /> <br /> :Platform specific issues and considerations<br /> <br /> *[[Documentation/{{documentation/version}}/Announcements|Announcements]] &amp; [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]<br /> <br /> *[[Documentation/Nightly/Registration/RegistrationLibrary|Registration Library]]<br /> <br /> :Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.<br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Documentation in other languages&lt;/span&gt;<br /> ----<br /> {{:{{FULLPAGENAME}}/Lang/ES}}<br /> <br /> <br /> <br /> |}<br /> <br /> &lt;!--<br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing}}<br /> --&gt;<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;100%&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot; valign=&quot;top&quot;<br /> <br /> |- style=&quot;vertical-align:top; border-style:hidden;&quot;<br /> <br /> |<br /> <br /> {{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}<br /> <br /> |<br /> &lt;br /&gt;<br /> &lt;br /&gt;<br /> =Modules by category=<br /> <br /> ==Converters==<br /> <br /> *[[Documentation/Nightly/Modules/CropVolume|Crop Volume]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VectorToScalarVolume|Vector To Scalar Volume]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOM Series]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==Diffusion==<br /> <br /> *[[Documentation/Nightly/Modules/DMRIInstall|DMRI Install]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Data_Conversion&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Data Conversion===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Diffusion_Tensor_Images&quot;&gt;&lt;/span&gt;<br /> ===Diffusion Weighted Images===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Import_and_Export&quot;&gt;&lt;/span&gt;<br /> ===Import and Export===<br /> <br /> *DWI Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Diffusion_Process&quot;&gt;&lt;/span&gt;<br /> ===Utilities===<br /> <br /> *BRAINS DWI Cleanup &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWI Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Endoscopy&quot;&gt;&lt;/span&gt;<br /> ==Endoscopy==<br /> <br /> *[[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filter&quot;&gt;&lt;/span&gt;<br /> ==Filter==<br /> <br /> *IslandRemoval &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering&quot;&gt;&lt;/span&gt;<br /> ==Filtering==<br /> <br /> *[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4 ITK Bias Field Correction]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Arithmetic&quot;&gt;&lt;/span&gt;<br /> ===Arithmetic===<br /> <br /> *[[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Denoising&quot;&gt;&lt;/span&gt;<br /> ===Denoising===<br /> <br /> *[[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Filtering_Morphology&quot;&gt;&lt;/span&gt;<br /> ===Morphology===<br /> <br /> *[[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_IGT&quot;&gt;&lt;/span&gt;<br /> ==IGT==<br /> <br /> *[[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLink IF]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics&quot;&gt;&lt;/span&gt;<br /> ==Informatics==<br /> <br /> *[[Documentation/Nightly/Modules/SEG2NRRD|SEG 2 NRRD]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Tables|Tables]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Data|Data]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *DumpSEGFrame &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Terminologies|Terminologies]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Units|Units]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html DICOM] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SampleData|Sample Data]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Colors|Colors]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Annotations|Annotations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Markups|Markups]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Informatics_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/EncodeSEG|Encode SEG]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy&quot;&gt;&lt;/span&gt;<br /> ==Legacy==<br /> &lt;span id=&quot;Modules_by_category_Legacy_Converters&quot;&gt;&lt;/span&gt;<br /> ===Converters===<br /> <br /> *[[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Filtering&quot;&gt;&lt;/span&gt;<br /> ===Filtering===<br /> <br /> *[[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Legacy_Registration&quot;&gt;&lt;/span&gt;<br /> ===Registration===<br /> <br /> *Test Grid Transform Registration &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> ==MultiVolume Support==<br /> <br /> *[[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolume Importer]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolume Explorer]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Quantification&quot;&gt;&lt;/span&gt;<br /> ==Quantification==<br /> <br /> *[[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *SegmentStatistics &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINSLabelStats &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataProbe|Data Probe]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration&quot;&gt;&lt;/span&gt;<br /> ==Registration==<br /> <br /> *[[Documentation/Nightly/Modules/Transforms|Transforms]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *BRAINSResize &lt;small&gt;(cli)&lt;/small&gt;<br /> *PerformMetricTest &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSResample|BRAINS Resample]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSFit|General registration (BRAINS)]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Registration_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *[[Documentation/Nightly/Modules/ACPCTransform|AC-PC Transform]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINS Demon Warp]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Reformat|Reformat]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *VBRAINSDemonWarp &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation&quot;&gt;&lt;/span&gt;<br /> ==Segmentation==<br /> <br /> *[[Documentation/Nightly/Modules/Segmentations|Segmentations]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/segmenteditor.html Segment Editor] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/Editor|Editor]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EMSegment|EMSegment]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> *EMSegmentQuick &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Segmentation_Specialized&quot;&gt;&lt;/span&gt;<br /> ===Specialized===<br /> <br /> *BRAINS ROI Auto &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment CommandLine &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Surface_Models&quot;&gt;&lt;/span&gt;<br /> <br /> ==Surface Models==<br /> <br /> *[[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelMaker|Model Maker]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ModelToLabelMap|Model To LabelMap]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/MergeModels|Merge Models]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMap Smoothing]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities&quot;&gt;&lt;/span&gt;<br /> ==Utilities==<br /> <br /> *[[Documentation/Nightly/Modules/ScreenCapture|Screen Capture]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/DataStore|Data Store]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicompatcher.html DICOM Patcher] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *BRAINS Strip Rotation &lt;small&gt;(cli)&lt;/small&gt;<br /> *EMSegment Transform To New Format &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Utilities_BRAINS&quot;&gt;&lt;/span&gt;<br /> ===BRAINS===<br /> <br /> *BRAINS Transform Convert &lt;small&gt;(cli)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Wizards&quot;&gt;&lt;/span&gt;<br /> ==Wizards==<br /> <br /> *[[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools&quot;&gt;&lt;/span&gt;<br /> ==Developer Tools==<br /> <br /> *[[Documentation/Nightly/Modules/Cameras|Cameras]] &lt;small&gt;(loadable)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] &lt;small&gt;(cli)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/ExtensionWizard|Extension Wizard]] &lt;small&gt;(scripted)&lt;/small&gt;<br /> *[[Documentation/Nightly/Modules/EventBroker|Event Broker]]<br /> *Double Arrays &lt;small&gt;(loadable)&lt;/small&gt;<br /> <br /> &lt;span id=&quot;Modules_by_category_Developer_Tools_DICOM_Plugins&quot;&gt;&lt;/span&gt;<br /> ===DICOM Plugins===<br /> <br /> *DICOMParametricMapPlugin<br /> *DicomUltrasoundPlugin<br /> *DICOMSegmentationPlugin<br /> *DICOMSlicerDataBundlePlugin<br /> *DICOMTID1500Plugin<br /> *[[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]<br /> *DICOMScalarVolumePlugin<br /> *DICOMDiffusionVolumePlugin<br /> *DICOMLongitudinalPETCTPlugin<br /> *DicomSroImportPlugin<br /> *[[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]<br /> *DicomRtImportExportPlugin<br /> *MultiVolumeImporterPlugin<br /> <br /> |}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/Models&diff=64028 2022-04-03T18:25:17Z

<p>Lasso: moved to readthedocs</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/models.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AirwaySegmentation&diff=64021 2022-03-21T20:53:45Z

<p>Lasso: Moved to github</p> <hr /> <div>{{documentation/banner<br /> | text = [https://github.com/Slicer/SlicerAirwaySegmentation This page has been moved to github.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Style_Guide/CMake&diff=64004 2022-03-15T20:35:49Z

<p>Lasso: Moved readthedocs</p> <hr /> <div>{{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/developer_guide/style_guide.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Style_Guide/Python&diff=64003 2022-03-15T20:33:18Z

<p>Lasso: Moved to readthedocs</p> <hr /> <div>{{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/developer_guide/style_guide.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Style_Guide/Cpp&diff=64002 2022-03-15T20:32:57Z

<p>Lasso: Moved to readthedocs</p> <hr /> <div>{{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/developer_guide/style_guide.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Style_Guide&diff=64001 2022-03-15T20:32:37Z

<p>Lasso: Moved to readthedocs</p> <hr /> <div>{{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/developer_guide/style_guide.html This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/FAQ/General&diff=63979 2022-02-12T21:03:10Z

<p>Lasso: /* Any other issues */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;__TOC__<br /> ={{#titleparts: {{PAGENAME}} | | -1 }}=&lt;/noinclude&gt;&lt;includeonly&gt;<br /> {{#ifeq: {{#titleparts: {{PAGENAME}} | 3 }} | Documentation/{{documentation/version}}/Developers | | ='''User FAQ: {{{1}}}'''=}}<br /> &lt;/includeonly&gt;<br /> == What is Slicer ? ==<br /> {{:Documentation/{{documentation/version}}/Slicer}}<br /> <br /> <br /> == Where can I download Slicer? ==<br /> 3DSlicer is available for download by visiting the following link: '''http://download.slicer.org'''<br /> <br /> You can also get older releases by using the offset parameter in the download page. For example, download page from 7 days ago: http://download.slicer.org/?offset=-7<br /> <br /> To get a direct download link of previous revision on a selected operating system: http://download.slicer.org/download?os=macosx&amp;stability=any&amp;offset=-1<br /> <br /> Always include these parameters:<br /> * ''stability'', which can be ''release'', ''nightly'', or ''any''<br /> * ''os'', which can be ''win'', ''macosx'', or ''linux''<br /> <br /> Additional options:<br /> * revision built before or on the date: ''date=2015-01-01''<br /> * same but checkout date: ''checkout-date=2015-02-01''<br /> * exact revision: ''revision=27000''<br /> * revision less than of equal: ''closest-revision=26000''<br /> * latest revision of 4.3 branch, can include patch as well: ''version=4.3''<br /> <br /> Any of these queries can be combined with the offset param, which will step forward or backward a given number of revisions. So,<br /> ''stability=release&amp;version=4.5.0&amp;offset=-1'' should give you the revision just before the first 4.5 release.<br /> <br /> == Where can I download older release of Slicer ? ==<br /> <br /> Older releases of 3DSlicer are available here: https://slicer-packages.kitware.com/#collection/5f4474d0e1d8c75dfc70547e/folder/5f4474d0e1d8c75dfc705482<br /> <br /> == Does Slicer work for non-English computing? ==<br /> <br /> At this point no, Slicer uses US English conventions. Specifically this means that directory paths should use ASCII characters only.<br /> <br /> There has been some discussion and planning about internationalization but it is not yet available:<br /> * https://www.slicer.org/wiki/Documentation/Labs/I18N<br /> * https://discourse.slicer.org/t/slicer-internationalization/579<br /> <br /> == How to install Slicer ? ==<br /> <br /> {{:Documentation/{{documentation/version}}/Slicer/Install}}<br /> <br /> <br /> ==Is Slicer really free?==<br /> <br /> Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).<br /> <br /> See [http://www.slicer.org/pages/LicenseText the Slicer License page] for the legal version of this.<br /> <br /> ==Where can I find someone to help me use Slicer?==<br /> <br /> We rely on the community of users and developers to share their expertise. Slicer Community support and development discussions are hosted on Discourse, which provides a modern web forum as well as email-only interaction:<br /> <br /> https://discourse.slicer.org<br /> <br /> If you post to any public forum, be sure not to include any [http://en.wikipedia.org/wiki/Protected_health_information Protected Health Information (PHI)] or any other data that would get you or anyone else in trouble. However, posting example data can be very important to people who are interested in helping you solve your problems. If you can replicate your question using data from the [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] or [[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] modules that's the first choice.<br /> <br /> The [[Documentation/Nightly | Users Manual]] gives descriptions for using each module, and you can check out the [[Documentation/Nightly/Training | Training pages]] for in depth tutorials about workflows.<br /> <br /> Mailing list discussions before 2017 April are [https://www.slicer.org/wiki/Help#Mailing_List_.28discontinued.29_Archives archived]<br /> <br /> ==Can I use slicer for patient care?==<br /> <br /> Slicer is intended for research work and ''has no FDA clearances or approvals of any kind''. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.<br /> <br /> <br /> ==How to cite Slicer?==<br /> {{:CitingSlicer}}<br /> <br /> == How do I create an account for the Slicer wiki? ==<br /> <br /> Current content of this wiki will be moved to https://slicer.readthedocs.io, https://www.slicer.org, and https://github.com/Slicer/Slicer/wiki websites and legacy content will be archived. New user accounts are no longer offered for this wiki.<br /> <br /> ==Can I install Slicer without administrator rights?==<br /> <br /> The most convenient way to install Slicer is to run the installer package (Slicer-{{documentation/currentversion}}....exe) as administrator. However, installation is not necessary, you just need to unpack the files in the installer package and copy them to your user directory or a USB drive and start it by running ''Slicer.exe''.<br /> <br /> You can unpack the installation package by one of the following methods:<br /> * Install Slicer on any computer where you have administrator access. All the files that you need to run Slicer are in the C:\Program Files\Slicer... directory.<br /> * Unpack the installation package by using 7zip or using the InstallExplorer plugin in Total commander or FAR manager (http://nsis.sourceforge.net/Can_I_decompile_an_existing_installer). All the Slicer files will be in the $_OUTDIR directory, except Slicer.exe, so you have to copy Slicer.exe into $_OUTDIR and run it from there. You can rename the $_OUTDIR directory and discard all the other directories ($COMMONFILES, $PLUGINSDIR, etc).<br /> <br /> <br /> ==What if I have problems with Slicer installation?==<br /> You can read our guide explaining [https://slicer.readthedocs.io/en/latest/user_guide/get_help.html#i-want-to-report-a-problem how to report a problem].<br /> <br /> ==Slicer does not start==<br /> <br /> === &quot;Insufficient graphics capability&quot; popup is displayed ===<br /> <br /> In Slicer-4.9, minimum graphics requirements have been increased compared to earlier versions. Computers running Slicer must support OpenGL 3.2. This OpenGL version was released in 2009 and so all desktop and laptop computers should already support it. However, on virtual machines or when connecting to a computer via remote desktop, this minimum requirements may not be met.<br /> <br /> * If you are trying to connect through Windows remote desktop (RDP):<br /> ** Recent Intel integrated GPUs and some NVidia GPUs (Quadro series) running on Windows 10 now support running current OpenGL versions. You may consider upgrading your hardware and operating system.<br /> ** You can use other remote desktop applications, such as [https://www.realvnc.com/ RealVNC], [https://anydesk.com/ AnyDesk], or [https://remotedesktop.google.com/ Google remote desktop] (all free, or free for personal use)<br /> ** If your computer can normally run Slicer but when started through remote desktop it displays &quot;Insufficient graphics capability&quot; popup: You need to start Slicer in normal desktop mode and then establish remote connection. You can achieve this by following these steps:<br /> *** Connect to the remote computer using remote desktop<br /> *** Start Slicer on the remote computer<br /> *** Click &quot;Retry&quot; when &quot;Insufficient graphics capability&quot; popup appears<br /> *** Grant administrator access in the displayed user account control popup (administrator access is needed for termination of the current remote desktop session), this will close the remote desktop connection<br /> *** Reconnect to the remote computer using remote desktop - you should see Slicer application started up successfully<br /> <br /> === Any other issues ===<br /> <br /> See [https://slicer.readthedocs.io/en/latest/user_guide/get_help.html#slicer-application-does-not-start debugging application startup issues].<br /> <br /> ==How to uninstall Slicer?==<br /> *On Windows, choose &quot;Uninstall&quot; option from the Start menu.<br /> *On the Mac, remove the Slicer.app file. To clean up settings, remove &quot;~/.config/www.na-mic.org/&quot;<br /> *On Linux, remove the directory where the application is located. To clean up settings, remove &quot;~/.config/NA-MIC/&quot;<br /> <br /> See the information about the location of [[Documentation/{{documentation/version}}/SlicerApplication/Settings|Settings]] for all platforms. If the uninstaller is not working on windows you may need to remove the settings manually.<br /> <br /> == Where can I find Slicer tutorials? ==<br /> Slicer tutorials associated with the latest {{documentation/currentversion}} stable release are available by visiting the following link: [[Documentation/Nightly/Training|Click Here]].<br /> <br /> <br /> ==I read errors in the logs complaining about memory==<br /> <br /> Errors such as “Description: Failed to allocate memory for image.” indicate that you don’t have enough memory space.<br /> This can be a common issue if you run a 32-bit version of Slicer. You cannot expect a 32-bit executable to deal with any moderately complex problem. The [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration#32_bit_versus_64_bit|recommended solution]] is to download/build/use Slicer in 64-bit mode.<br /> <br /> Possible workarounds:<br /> * Use a 64-bit version of Slicer <br /> * You have somewhat more memory if you run the module in a separate process. To do that open [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Modules|Edit / Application Settings / Modules]] and check the “Prefer Executable CLIs” option, then restart Slicer.<br /> * Decrease the size and/or resolution of the input and output images<br /> ** Consider [[Documentation/{{documentation/version}}/Modules/Crop_Volume|Crop Volume]] to focus on just your area of interest.<br /> ** Consider [[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] or [[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|ResampleScalarVolume]] increase the sample spacing (decrease the resolution) of your data.<br /> <br /> <br /> == Which Slicer version should I use: 3.X or 4.X ? ==<br /> <br /> In general slicer3 and slicer4 have roughly similar functionality with respect to registration basics. Probably the most important thing to keep in mind is that slicer3 is no longer actively maintained.<br /> <br /> Slicer4, on the other hand, has benefited from literally hundreds of bug fixes over the past several years, and typically has better features and much better performance. Also, the nightly builds of slicer4 are now using ITKv4, which has significantly improved registration code. I am told by active users/developers of ITK that ITKv4 should provide significantly better results in many cases. Also, several new registration techniques are being actively developed for slicer4.<br /> <br /> Source: http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006190.html<br /> <br /> <br /> == What is my HOME folder ? ==<br /> <br /> {|width = &quot;100%&quot;<br /> ! width=&quot;50%&quot; style=&quot;border-bottom: 1px solid darkgrey;font-size: 75%;&quot;| Linux or MacOSX<br /> ! width=&quot;50%&quot; style=&quot;border-bottom: 1px solid darkgrey;font-size: 75%;&quot;| Windows<br /> |-<br /> | valign=&quot;top&quot; |<br /> Start a terminal.<br /> {{pre2|&lt;nowiki&gt;<br /> $ echo ~<br /> /home/jchris<br /> &lt;/nowiki&gt;}}<br /> | valign=&quot;top&quot; |<br /> <br /> Start Command Prompt (Start Menu -&gt; All Programs -&gt; Accessories -&gt; Command Prompt)<br /> {{pre2|&lt;nowiki&gt;<br /> &gt; echo %userprofile%<br /> C:\Users\jcfr<br /> &lt;/nowiki&gt;}}<br /> |}</div>

Lasso https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/Tutorials/Troubleshooting&diff=63978 2022-02-12T21:02:45Z

<p>Lasso: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> <br /> {{documentation/banner<br /> | text = [https://slicer.readthedocs.io/en/latest/user_guide/get_help.html#slicer-application-does-not-start This page has been moved to read-the-docs.]<br /> | background-color = 8FBC8F }}</div>

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