SPIE 2013 Course Preparation

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  • Copy datasets and software on memory sticks
  • Update slides

  • Please find in this table the status concerning all the extensions:
Tool Platform Visible in Extension Manager Visible in Module List GUI displaid from Slicer Usable*
DTIAtlasBuilder Windows Y Y N N
DTIAtlasBuilder Mac Y Y Y N
DTIAtlasBuilder Linux Y Y Y Y
DTIAtlasFiberAnalyzer Windows Y Y N Y
DTIAtlasFiberAnalyzer Mac Y Y Y Y
DTIAtlasFiberAnalyzer Linux Y Y Y Y
DTIPrep Windows Y N N/A Y
DTIPrep Mac Y  ?  ? Y
DTIPrep Linux Y N N/A Y
DTIProcess Windows Y Y N/A Y
DTIProcess Mac Y Y N/A Y
DTIProcess Linux Y Y N/A Y
FiberViewerLight Windows Y Y N Y
FiberViewerLight Mac Y Y Y Y
FiberViewerLight Linux Y Y Y Y
* From within Slicer or in command line, depending on the software.

Please see below for special instructions:

  • On Windows, some of the tools that appear in the module list fail to load their user interfaces.

It possible to launch them by running these commands in the windows "cmd.exe" terminal:

"C:\Program Files\Slicer 4.2.2-1\Slicer.exe" --launch C:\Users\<username>\AppData\Roaming\NA-MIC\Extensions-21513\DTIPrep\lib\Slicer-4.2\cli-modules\DTIPrep.exe
"C:\Program Files\Slicer 4.2.2-1\Slicer.exe" --launch C:\Users\<username>\AppData\Roaming\NA-MIC\Extensions-21513\DTIAtlasFiberAnalyzer\lib\Slicer-4.2\cli-modules\DTIAtlasFiberAnalyzer.exe
"C:\Program Files\Slicer 4.2.2-1\Slicer.exe" --launch C:\Users\<username>\AppData\Roaming\NA-MIC\Extensions-21513\FiberViewerLight\lib\Slicer-4.2\cli-modules\FiberViewerLight.exe
"C:\Program Files\Slicer 4.2.2-1\Slicer.exe" --launch C:\Users\<username>\AppData\Roaming\NA-MIC\Extensions-21513\DTIAtlasBuilder\lib\Slicer-4.2\cli-modules\DTIAtlasBuilder.exe (pipeline does not work because GreedyAtlas fails to compile)

Do no forget to update <username> with the actual username.

It is still possible to run the tools that do not need a user interface through Slicer.

  • On Mac, the DTIAtlasBuilder pipeline fails because of GreedyAtlas, but you can still display the user interface

  • On Linux, DTIPrep is not loaded as a module in Slicer. To start it, open a terminal and run:
/path/to/Slicer/Slicer --launch ~/.config/NA-MIC/Extensions-21513/DTIPrep/lib/Slicer-4.2/cli-modules/DTIPrep

  • If you downloaded the latest nightly build version, adapt the revision number in the extension path to the adequate Slicer revision number.