Difference between revisions of "SPIE 2013 Course Preparation"

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* Copy datasets and software on memory sticks  
 
* Copy datasets and software on memory sticks  
 
* Update slides
 
* Update slides
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* Data uploaded on Jan 25: [[File:Spie2013SC1065UNCdata.tar.gz]]
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* Full DTIAtlasBuilder output data on Midas: http://hdl.handle.net/1926/1768
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* Slicer Extensions Tutorial: [[File:Spie2013SC1065UNCSlicerTutorial.pdf‎]]
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* Slicer Extensions Tutorial (Editable pptx version): [[File:Spie2013SC1065UNCSlicerTutorial.pptx]]
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* DTIAtlasBuilder Tutorial: http://www.nitrc.org/docman/view.php/636/1189/DTIAtlasBuilder_Tutorial.pdf
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* DTIAtlasBuilder Tutorial (Editable pptx version): http://www.nitrc.org/docman/view.php/636/1219/DTIAtlasBuilder_Tutorial.pptx
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* Please find in this table the status concerning all the extensions:
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{| class="wikitable sortable" border="1"
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|-
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! scope="col" | Tool
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! scope="col" | Platform
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! scope="col" | Visible in Extension Manager
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! scope="col" | Visible in Module List
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! scope="col" | GUI displaid from Slicer
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! scope="col" | Usable*
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|-
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| DTIAtlasBuilder || Windows || Y || Y || N || N
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|-
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| DTIAtlasBuilder || Mac || Y || Y || Y || N
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|-
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| DTIAtlasBuilder || Linux || Y || Y || Y || Y
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|-
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| DTIAtlasFiberAnalyzer || Windows || Y || Y || N || Y
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|-
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| DTIAtlasFiberAnalyzer || Mac || Y || Y || Y || Y
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|-
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| DTIAtlasFiberAnalyzer || Linux || Y || Y || Y || Y
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|-
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| DTIPrep || Windows || Y || N || N/A || Y
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|-
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| DTIPrep || Mac || Y || ? || ? || Y
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|-
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| DTIPrep || Linux || Y || N || N/A || Y
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|-
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| DTIProcess || Windows || Y || Y || N/A || Y
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|-
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| DTIProcess || Mac || Y || Y || N/A || Y
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|-
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| DTIProcess || Linux || Y || Y || N/A || Y
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|-
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| FiberViewerLight || Windows || Y || Y || N || Y
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|-
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| FiberViewerLight || Mac || Y || Y || Y || Y
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|-
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| FiberViewerLight || Linux || Y || Y || Y || Y
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|}
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* From within Slicer or in command line, depending on the software.
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Please see below for special instructions:
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* On Windows, some of the tools that appear in the module list fail to load their user interfaces.
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It possible to launch them by running these commands in the windows "cmd.exe" terminal:
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"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
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"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
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"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
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"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)
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Do no forget to update <username> with the actual username.
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It is still possible to run the tools that do not need a user interface through Slicer.
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* On Mac, the DTIAtlasBuilder pipeline fails because of GreedyAtlas, but you can still display the user interface
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* On Linux, DTIPrep is not loaded as a module in Slicer. To start it, open a terminal and run:
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/path/to/Slicer/Slicer --launch ~/.config/NA-MIC/Extensions-21513/DTIPrep/lib/Slicer-4.2/cli-modules/DTIPrep
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* If you downloaded the latest nightly build version, adapt the revision number in the extension path to the adequate Slicer revision number.

Latest revision as of 22:29, 8 February 2013

Home < SPIE 2013 Course Preparation
  • 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.
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