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Modules:BRAINSROIAuto-Documentation-3.6 - Revision history
2024-03-28T16:59:39Z
Revision history for this page on the wiki
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https://www.slicer.org/w/index.php?title=Modules:BRAINSROIAuto-Documentation-3.6&diff=15479&oldid=prev
KentWilliams at 15:37, 7 May 2010
2010-05-07T15:37:03Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:37, 7 May 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l81" >Line 81:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><!<del class="diffchange diffchange-inline">== </del>===Source code & documentation===</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><!<ins class="diffchange diffchange-inline">--</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>===Source code & documentation===</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Links to the module's source code:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Links to the module's source code:</div></td></tr>
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KentWilliams
https://www.slicer.org/w/index.php?title=Modules:BRAINSROIAuto-Documentation-3.6&diff=15478&oldid=prev
KentWilliams at 15:34, 7 May 2010
2010-05-07T15:34:40Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:34, 7 May 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l56" >Line 56:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**Otsu <del class="diffchange diffchange-inline">Threshold </del>Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**Otsu Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Closing Size: The size for the largest void to fill in the mask, in voxels.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Closing Size: The size for the largest void to fill in the mask, in voxels.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Output Image Pixel Type: the scalar type of the masked output volume.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Output Image Pixel Type: the scalar type of the masked output volume.</div></td></tr>
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KentWilliams
https://www.slicer.org/w/index.php?title=Modules:BRAINSROIAuto-Documentation-3.6&diff=15439&oldid=prev
KentWilliams at 20:18, 6 May 2010
2010-05-06T20:18:55Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:18, 6 May 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l59" >Line 59:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Closing Size: The size for the largest void to fill in the mask, in voxels.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Closing Size: The size for the largest void to fill in the mask, in voxels.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Output Image Pixel Type: the scalar type of the masked output volume.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**Output Image Pixel Type: the scalar type of the masked output volume.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|[[Image:<del class="diffchange diffchange-inline">BRAINSFitUI</del>.png|thumb|280px|User Interface]]</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[Image:<ins class="diffchange diffchange-inline">BRAINSROIAutoUI</ins>.png|thumb|280px|User Interface]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td></tr>
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KentWilliams
https://www.slicer.org/w/index.php?title=Modules:BRAINSROIAuto-Documentation-3.6&diff=15438&oldid=prev
KentWilliams at 20:17, 6 May 2010
2010-05-06T20:17:55Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:17, 6 May 2010</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>--></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>--></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Quick Tour of Features and Use===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Quick Tour of Features and Use===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">A list panels in the interface, their features, what they mean, and how to use them. For instance:</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 81:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>===Source code & documentation===</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><!== </ins>===Source code & documentation===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Links to the module's source code:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Links to the module's source code:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Publications related to this module go here. Links to pdfs would be useful.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Publications related to this module go here. Links to pdfs would be useful.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">--></ins></div></td></tr>
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KentWilliams
https://www.slicer.org/w/index.php?title=Modules:BRAINSROIAuto-Documentation-3.6&diff=15437&oldid=prev
KentWilliams: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== BRAINSROIAuto {| |[[Image:B…'
2010-05-06T20:16:52Z
<p>Created page with '<a href="/wiki/Documentation-3.6" class="mw-redirect" title="Documentation-3.6">Return to Slicer 3.6 Documentation</a> <a href="/wiki/Announcements:Slicer3.6#Highlights" title="Announcements:Slicer3.6">Gallery of New Features</a> __NOTOC__ ===Module Name=== BRAINSROIAuto {| |[[Image:B…'</p>
<p><b>New page</b></p><div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
BRAINSROIAuto<br />
<br />
{|<br />
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Registration<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author1: Hans Johnson, University of Iowa<br />
* Contributor1: Kent WIlliams, University of Iowa<br />
* Contact: Hans Johnson, hans-johson at uiowa.edu<br />
<br />
===Module Description===<br />
BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain. <br />
== Usage ==<br />
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.<br />
<!-- ===Use Cases, Examples===<br />
<br />
This module is especially appropriate for these use cases:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
Examples of the module in use:<br />
<br />
* Example 1<br />
* Example 2<br />
<br />
===Tutorials===<br />
<br />
Links to tutorials explaining how to use this module:<br />
<br />
* Tutorial 1<br />
** Data Set 1<br />
--><br />
===Quick Tour of Features and Use===<br />
<br />
A list panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|<br />
|<br />
*IO Parameters<br />
**Input Image Volume: Image for which mask should be generated<br />
**Output Mask: Output binary image volume, defining the mask.<br />
**Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.<br />
*Configuration Parameters<br />
**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.<br />
**Otsu Threshold Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.<br />
**Closing Size: The size for the largest void to fill in the mask, in voxels.<br />
**Output Image Pixel Type: the scalar type of the masked output volume.<br />
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
===Dependencies===<br />
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.<br />
===Tests===<br />
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>
KentWilliams