No CSV file in DiffusionMessurements folder in WMA

Community SlicerDMRI
1

Hi there, I am doing whitematteranalysis along with WMA tutorial: whitematteranalysis/subject-specific-tractography-parcellation.md at master · SlicerDMRI/whitematteranalysis · GitHub. In the last step of tutorial, " 8. Fiber tract diffusion measurements", I could not get any CSV file in the created new DiffusionMeasurements folder with error message of below:

brain@l4n:~/Desktop/WMA_tutorial_data$ wm_diffusion_measurements.py ./FiberClustering/SeparatedClusters/tracts_commissural/ ./DiffusionMeasurements/commissural_clusters.csv /home/brain/Downloads/Slicer-5.2.2-linux-amd64/NA-MIC/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/FiberTractMeasurements
Importing whitematteranalysis package.
<wm_diffusion_measurements>. Starting scalar measurement extraction.

=====input directory======
./FiberClustering/SeparatedClusters/tracts_commissural/
=====output directory=====
./DiffusionMeasurements
=====3D Slicer====
/home/brain/Downloads/Slicer-5.2.2-linux-amd64/NA-MIC/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/FiberTractMeasurements

/home/brain/Downloads/Slicer-5.2.2-linux-amd64/NA-MIC/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/FiberTractMeasurements: error while loading shared libraries: libSlicerBaseLogic.so: cannot open shared object file: No such file or directory
<wm_diffusion_measurements> Measurements done at: ./DiffusionMeasurements/commissural_clusters.csv

This is happened to both tutorial data and my own DTI data, and either input is SeparatedClusters or AnatomicalTracts. I think the folder structure for SlicerDMRI in my PC is correct.
Anyone who has advice on this issue?

Thank you,
Fumi

2

Hi,

Please try Slicer launcher to call the fiber measurement module:

wm_diffusion_measurements.py ./FiberClustering/SeparatedClusters/tracts_commissural/ ./DiffusionMeasurements/commissural_clusters.csv “/home/brain/Downloads/Slicer-5.2.2-linux-amd64/Slicer --launch FiberTractMeasurements”

Regards,
Fan

3

Hi Fan, thank you for a very quick reply. I tried your command, but it was error again:

wm_diffusion_measurements.py ./FiberClustering/SeparatedClusters/tracts_commissural/ ./DiffusionMeasurements/commissural_clusters.csv “/home/brain/Downloads/Slicer-5.2.2-linux-amd64/Slicer --launch FiberTractMeasurements”
Importing whitematteranalysis package.
usage: wm_diffusion_measurements.py [-h] [-v] inputDirectory outputCSV Slicer
wm_diffusion_measurements.py: error: unrecognized arguments: --launch FiberTractMeasurements”

Do you know why this is happen?

Thanks a lot!

Fumi