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 | ||
| + | |||
* Data uploaded on Jan 25: [[File:Spie2013SC1065UNCdata.tar.gz]] | * Data uploaded on Jan 25: [[File:Spie2013SC1065UNCdata.tar.gz]] | ||
| + | * Full DTIAtlasBuilder output data on Midas: http://hdl.handle.net/1926/1768 | ||
| + | |||
| + | |||
* Slicer Extensions Tutorial: [[File:Spie2013SC1065UNCSlicerTutorial.pdf]] | * Slicer Extensions Tutorial: [[File:Spie2013SC1065UNCSlicerTutorial.pdf]] | ||
| + | * Slicer Extensions Tutorial (Editable pptx version): [[File:Spie2013SC1065UNCSlicerTutorial.pptx]] | ||
| + | |||
| + | |||
| + | * DTIAtlasBuilder Tutorial: http://www.nitrc.org/docman/view.php/636/1189/DTIAtlasBuilder_Tutorial.pdf | ||
| + | * DTIAtlasBuilder Tutorial (Editable pptx version): http://www.nitrc.org/docman/view.php/636/1219/DTIAtlasBuilder_Tutorial.pptx | ||
| + | |||
| + | |||
| + | * Please find in this table the status concerning all the extensions: | ||
| + | |||
| + | {| class="wikitable sortable" border="1" | ||
| + | |- | ||
| + | ! scope="col" | Tool | ||
| + | ! scope="col" | Platform | ||
| + | ! scope="col" | Visible in Extension Manager | ||
| + | ! scope="col" | Visible in Module List | ||
| + | ! scope="col" | GUI displaid from Slicer | ||
| + | ! scope="col" | 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. | ||
Latest revision as of 22:29, 8 February 2013
Home < SPIE 2013 Course Preparation- Copy datasets and software on memory sticks
- Update slides
- Data uploaded on Jan 25: File:Spie2013SC1065UNCdata.tar.gz
- Full DTIAtlasBuilder output data on Midas: http://hdl.handle.net/1926/1768
- Slicer Extensions Tutorial: File:Spie2013SC1065UNCSlicerTutorial.pdf
- Slicer Extensions Tutorial (Editable pptx version): File:Spie2013SC1065UNCSlicerTutorial.pptx
- DTIAtlasBuilder Tutorial: http://www.nitrc.org/docman/view.php/636/1189/DTIAtlasBuilder_Tutorial.pdf
- DTIAtlasBuilder Tutorial (Editable pptx version): http://www.nitrc.org/docman/view.php/636/1219/DTIAtlasBuilder_Tutorial.pptx
- 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.
