No CSV file in DiffusionMessurements folder in WMA

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

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

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