View source for 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:

{| 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.