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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
