Hi Matt, Here is my probtrack call. I ran it for the left hemisphere.
probtrackx2 --samples=merged --mask=/T1w/L_Cerebral_Trajectory_1.25.nii.gz --seed=100307.L.white.32k_fs_LR.surf.gii --waypoints=100307.L.white.32k_fs_LR.surf.gii --stop=100307.L.pial.32k_fs_LR.surf.gii --target4=L_Cerebral_Trajectory_1.25.nii.gz --seedref=L_Cerebral_Trajectory_1.25.nii.gz --dir=/data/probtrack100307/left --nsamples=5000 --cthr=0.2 --steplength=0.3 --forcedir --meshspace=caret --nsteps=2000 --fibthresh=0.05 --loopcheck --randfib=2 --forcefirststep --opd --omatrix1 --omatrix4 --sampvox=1.25 --verbose=1 Thanks, Sarah On 14/04/14 19:05, Glasser, Matthew wrote: > Can you send us your probtrackx call? > > Peace, > > Matt. > > On 4/14/14, 1:01 PM, "Sarah Parisot" <[email protected]> wrote: > >> Dear all, >> >> I am working on brain parcellation based on structural connectivity >> matrices. I ran FSL's probtrackx on an HCP subject, seeding from the >> WM/GM 32k surface to get the seedxseed connectivity matrix (matrix1) and >> I am struggling a little with the outputs of probtrackx and the use of >> the workbench for visualization. It would be great if I could have some >> answers to a few questions: >> >> -I obtained a matrix1.dot file that I would like to be able to visualize >> using the connectome workbench. I tried running the >> probtrackx-dot-convert command (I used a metric file with all ones for >> all nodes as -row/col-surface.) but the converted file appears to be all >> zeros when I load it in the workbench. Maybe I'm using the wrong metric >> file? >> >> -Is there a way to keep knowledge of the different tracts evaluated from >> one seed point to another? >> I am getting an image that counts all the tracts that go through a >> voxel, but I would like to know how seed A is connected to seed B. I was >> told this information is kept in the 'matrix4' output, which apparently >> cannot be read at the moment. >> >> Thanks. >> Best Regards, >> Sarah >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
