Hello,
I am looking to extract tractwise information based on probabilistic tractography output from probtrackx2. Is there anything particular I need to specify in my probtrackx2 call aside from verbose=2 to obtain proper output that would allow me to export tract-based statistics including:
-FA for fiber tracts
-Mean diffusitivity (MD) of fiber tracts
-Radial diffusitivity (RD) of fiber tracts
-Curvature of fiber tracts
-Length of fiber tracts
Here is my probtrackx2 call:
probtrackx2 -s merged -m nodif_brain_mask.nii.gz -x GM_vol_in_Diff.nii.gz --s2tastext --os2t --opd -l -c 0.2 -S 2000 --steplength=0.5 -P 1000 --verbose=2 --forcedir –dir= probtrackresults/omatrix1/GM_GM/p1000 --targetmasks= GM_vol_in_Diff.nii.gz --omatrix1
I know that in Deterministic tractography implemented in DSI Studio, it is possible to export tract-based statistics at the command line using:
dsi_studio --action=ana --source=my.fib.gz --tract=my.tract.trk --export=stat
In sum, I am looking to perform an analogous function that extracts tract-based statistics from probtrackx2 output. Is first necessary to threshold the GM x GM adjacency matrix at some connectivity probability to define probabilistic "tracts"?
Thanks for your help!
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