Hi all, for the question below, is it correct this command?
probtrackx2 --network -x /dir/subj001/mask/masks.txt -V 1 --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 50 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /dir/subj001/bedpostX/merged -m /dir/subj001/bedpostX/nodif_brain_mask --dir=/dir/subj001/track_network
Do I have to adjust matrix for the number of voxel in each mask? or only to divide each row for the corresponding waytotal (is it available in the output?)?
thank you!
Angela
Hi all, I have a series of volumetric GM masks that I used to calculate a functional connectivity matrix. Now I want to use the same masks to calculate a structural connectivity matrix (number of streamlines). I registered all masks in diffusion space for all subjects. My idea was to use probtrackx2 with a matrix option (and list of waypoints), but I am really unsure about which options I have to use: --omatrix1 and then sum all voxels of the mask or --omatrix3?
Could you help me in writing my script? Thank you for any help
Angela
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