Difference between revisions of "Documentation/3.4/ReleaseNotes"
(New page: == New Features in Slicer 3.4 == Slicer 3.4 has many new features! The list here highlights most major some new features in Slicer 3.4. Please also note that many of these new features ar...) |
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+ | <noinclude>{{documentation/versioncheck}}</noinclude> | ||
+ | {{documentation/versionlist}} | ||
== New Features in Slicer 3.4 == | == New Features in Slicer 3.4 == | ||
Line 5: | Line 7: | ||
New Features: | New Features: | ||
− | * | + | * Welcome Module at Startup |
+ | * Improved Save Module | ||
+ | * Improved Editor | ||
+ | * New Registration module | ||
+ | * New Slices module | ||
+ | * Fiducial based tractography | ||
+ | * Improved SceneSnapshot Screen Capture functionality | ||
+ | * Compare View and Cross Hairs | ||
+ | * Support for Extension Server for installing plug-ins | ||
+ | * Improved Dicom Support | ||
+ | * MRML scenes and all data load from and save into XNAT desktop | ||
− | + | A summary of new features is also available here: [[Slicer3:Status]] | |
− | |||
− | |||
− | |||
− | |||
== Downloading == | == Downloading == | ||
Line 19: | Line 27: | ||
Release candidate builds are available for: | Release candidate builds are available for: | ||
− | *[http://www.na-mic.org/Slicer/Download/Release Windows] | + | *[http://www.na-mic.org/Slicer/Download/Release Windows] |
*[http://www.na-mic.org/Slicer/Download/Release 32-bit Linux] | *[http://www.na-mic.org/Slicer/Download/Release 32-bit Linux] | ||
*[http://www.na-mic.org/Slicer/Download/Release 64-bit Linux] | *[http://www.na-mic.org/Slicer/Download/Release 64-bit Linux] | ||
Line 50: | Line 58: | ||
* All Platforms: | * All Platforms: | ||
− | ** | + | ** Undo/Redo functionality is available for the Editor Module only at this time. |
+ | ** There is currently a 10 stage Undo history in the Editor Module. | ||
+ | ** Procedural color nodes don't display in the Colors Module. | ||
+ | ** Volume rendering transfer functions are not stored in the MRML scene. | ||
+ | ** Grayed-out tool icons reflect functionality not yet available. | ||
+ | ** To load DWI volumes in DICOM format, use the Converters->Dicom DWI loader, with only one volume in the ''Dicom Directory'' | ||
+ | ** In Color By Orientation mode, you can't adjust window/level | ||
+ | *** Color By Orientation does not work on tracts | ||
+ | ** If you wish to use the Editor module on DWI or DTI volumes, must create a scalar volume first. | ||
* Linux: | * Linux: | ||
− | ** | + | ** You need to have X11 configured to run 3D graphics (opengl/mesa). Confirm that you can run the command <pre>glxgears</pre>. |
− | ** | + | ** For debian/ubuntu you may need to install the libxss1 library in order to run the slicer binary download <pre>sudo apt-get install libxss1</pre> |
+ | ** Some versions of linux have an incompatible libssl that generates an error message related to md5 when trying to launch the python console. | ||
+ | ** If you have trouble with font sizes (all options yield fonts that are ''too large'') then try going to the software install tool and installing as many font packages as you can find. Some default installations will not include the required font packages. | ||
* Windows: | * Windows: | ||
+ | ** Vista: | ||
+ | <pre> | ||
+ | > I get the following error: | ||
+ | > | ||
+ | > | ||
+ | > | ||
+ | > Can't read "::Slicer3_REAL": no such variable while executing....... | ||
+ | > | ||
+ | |||
+ | I seem to have found an alternate fix. Originally I | ||
+ | had 3.2 installed, uninstalled it then installed 3.4 which resulted in | ||
+ | error below. | ||
+ | |||
+ | I uninstalled all Slicers, then installed 3.2 then left 3.2 on system | ||
+ | and installed 3.4. I ran 3.4 & it worked fine, I then un-installed 3.2 | ||
+ | and ran 3.4 again still working OK. | ||
+ | |||
+ | Hope this helps other users. | ||
+ | </pre> | ||
* Mac: | * Mac: | ||
+ | ** On platforms other than Mac, you can edit an entry in a multi-entry list box (for example, a list of fiducials) by double-clicking on the entry. In order to edit the field on the Mac, you need to click the field and then hit Enter. | ||
+ | ** X11: If slicer fails to start, try quitting the X11 application so it will reset. | ||
For users of Mac OS X 10.5 (Leopard) we suggest replacing the standard X11 application with the latest XQuartz version available here: | For users of Mac OS X 10.5 (Leopard) we suggest replacing the standard X11 application with the latest XQuartz version available here: | ||
Line 66: | Line 105: | ||
As a research platform, Slicer includes several modules that are not yet fully implemented, but which the developers still felt were far enough along in functionality to provide utility for the community. As such, you may find that some operations do not behave as expected, particularly where they interact with other slicer functions. Please let us know about these issues by filing appropriate bug reports. | As a research platform, Slicer includes several modules that are not yet fully implemented, but which the developers still felt were far enough along in functionality to provide utility for the community. As such, you may find that some operations do not behave as expected, particularly where they interact with other slicer functions. Please let us know about these issues by filing appropriate bug reports. | ||
+ | |||
+ | * Replaced Linear Registration Module with Rigid Registration (the functionality remains the same) | ||
+ | * Replaced DICOM to NRRD with DICOM DWI to NRRD | ||
+ | * Simple Region Growing has been changed to Statistical Region Growing | ||
+ | * DICOM DWI Loader removed, use DWI to NRRD Loader instead | ||
+ | * Renamed RealignVolume to ACPC Transform, removing the application of the transform, use the Resample Scalar/Vector/DWI Volume module to apply the calculated transform | ||
== Building == | == Building == | ||
Line 84: | Line 129: | ||
== Reporting Bugs == | == Reporting Bugs == | ||
− | + | Please go to the [http://www.na-mic.org/Bug/ Mantis Bug Tracker] and report bugs for Slicer version 3. | |
− | Please go to http://www.na-mic.org/Bug/ and report bugs for Slicer version 3. | ||
== Where to go for Help == | == Where to go for Help == | ||
Line 97: | Line 141: | ||
http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users | http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users | ||
− | == Acknowledgements == | + | ==Acknowledgements== |
− | + | [http://www.slicer.org/wiki/Announcments-3.2-Team The Slicer Development Team] | |
− | [http://www.slicer.org/ | ||
− | This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics. This work was also supported by NIH grant P41 RR13218 | + | This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics. This work was also supported by NIH grant P41 RR13218 [http://nac.spl.harvard.edu NAC] and the [http://www.nbirn.net Biomedical Informatics Research Network]. |
Latest revision as of 21:13, 19 January 2022
Home < Documentation < 3.4 < ReleaseNotes
For the latest Slicer documentation, visit the read-the-docs. |
Nightly 4.10 4.8 4.6 4.5 4.4 4.3 4.2 4.1 4.0 3.6 3.5 3.4 3.2 ALL VERSIONS
Contents
New Features in Slicer 3.4
Slicer 3.4 has many new features! The list here highlights most major some new features in Slicer 3.4. Please also note that many of these new features are still being developed and will be improved in future releases, so you may encounter some unexpected behavior. If you do encounter unexpected behavior, you can join the Slicer users's mailing by sending email to slicer-users-request@massmail.spl.harvard.edu with the subject "subscribe", and report the behavior there to see if there is a work around (or check the archives), and to the bug tracker if it needs to be solved by the developers.
New Features:
- Welcome Module at Startup
- Improved Save Module
- Improved Editor
- New Registration module
- New Slices module
- Fiducial based tractography
- Improved SceneSnapshot Screen Capture functionality
- Compare View and Cross Hairs
- Support for Extension Server for installing plug-ins
- Improved Dicom Support
- MRML scenes and all data load from and save into XNAT desktop
A summary of new features is also available here: Slicer3:Status
Downloading
Download the release candidates here
Release candidate builds are available for:
Installing
Linux
tar -xzvf Slicer3-3.4.2009-xx-xx-linux-x86.tar.gz
or, for 64 bit systems
tar -xzvf Slicer3-3.4.2008-xx-xx-linux-x86_64.tar.gz
Mac
Be sure you have X Windows installed.
From a terminal:
tar -xzvf Slicer3-3.4.2009-xx-xx-darwin-x86.tar.gz
or, for older PPC Macs:
tar -xzvf Slicer3-3.2.2009-xx-xx-darwin-ppc.tar.gz
Windows
Double click on:
Slicer3-3.2.2009-xx-xx-win32.exe
Known Issues: Base Operations
- All Platforms:
- Undo/Redo functionality is available for the Editor Module only at this time.
- There is currently a 10 stage Undo history in the Editor Module.
- Procedural color nodes don't display in the Colors Module.
- Volume rendering transfer functions are not stored in the MRML scene.
- Grayed-out tool icons reflect functionality not yet available.
- To load DWI volumes in DICOM format, use the Converters->Dicom DWI loader, with only one volume in the Dicom Directory
- In Color By Orientation mode, you can't adjust window/level
- Color By Orientation does not work on tracts
- If you wish to use the Editor module on DWI or DTI volumes, must create a scalar volume first.
- Linux:
- You need to have X11 configured to run 3D graphics (opengl/mesa). Confirm that you can run the command
glxgears
. - For debian/ubuntu you may need to install the libxss1 library in order to run the slicer binary download
sudo apt-get install libxss1
- Some versions of linux have an incompatible libssl that generates an error message related to md5 when trying to launch the python console.
- If you have trouble with font sizes (all options yield fonts that are too large) then try going to the software install tool and installing as many font packages as you can find. Some default installations will not include the required font packages.
- You need to have X11 configured to run 3D graphics (opengl/mesa). Confirm that you can run the command
- Windows:
- Vista:
> I get the following error: > > > > Can't read "::Slicer3_REAL": no such variable while executing....... > I seem to have found an alternate fix. Originally I had 3.2 installed, uninstalled it then installed 3.4 which resulted in error below. I uninstalled all Slicers, then installed 3.2 then left 3.2 on system and installed 3.4. I ran 3.4 & it worked fine, I then un-installed 3.2 and ran 3.4 again still working OK. Hope this helps other users.
- Mac:
- On platforms other than Mac, you can edit an entry in a multi-entry list box (for example, a list of fiducials) by double-clicking on the entry. In order to edit the field on the Mac, you need to click the field and then hit Enter.
- X11: If slicer fails to start, try quitting the X11 application so it will reset.
For users of Mac OS X 10.5 (Leopard) we suggest replacing the standard X11 application with the latest XQuartz version available here: http://xquartz.macosforge.org/trac/wiki
Known Issues: Modules
As a research platform, Slicer includes several modules that are not yet fully implemented, but which the developers still felt were far enough along in functionality to provide utility for the community. As such, you may find that some operations do not behave as expected, particularly where they interact with other slicer functions. Please let us know about these issues by filing appropriate bug reports.
- Replaced Linear Registration Module with Rigid Registration (the functionality remains the same)
- Replaced DICOM to NRRD with DICOM DWI to NRRD
- Simple Region Growing has been changed to Statistical Region Growing
- DICOM DWI Loader removed, use DWI to NRRD Loader instead
- Renamed RealignVolume to ACPC Transform, removing the application of the transform, use the Resample Scalar/Vector/DWI Volume module to apply the calculated transform
Building
You don't have to build Slicer yourself to use it. If you want a precompiled version, go here.
To build slicer from source, see Slicer3:Build_Instructions
- Windows
- distributed versions are built with Microsoft Visual Studio .NET in release mode (note that there may be some problems compiling with .NET 2003)
- Linux
- We are building using g++ version 3.4.3 on RedHat Enterprise Linux 4.
- Mac OSX
- We are building using gcc version 4.0.1
Reporting Bugs
Please go to the Mantis Bug Tracker and report bugs for Slicer version 3.
Where to go for Help
Compilation/development questions can be sent to the Slicer Developers Mailing List. Questions about running Slicer can be sent to the Slicer Users Mailing List.
Subscription management tools and archives are available at:
http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel
http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users
Acknowledgements
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics. This work was also supported by NIH grant P41 RR13218 NAC and the Biomedical Informatics Research Network.