Dear HCP experts, I attempted the structural connectome tutorial using the individual HCP dataset (100307) with MRtrix. I am looking to repeat a similar 'whole-brain' tractography analysis using FSL probtrackx. Specifically, I would like to utilize the freesurfer aparc+aseg file as nodes for tracking and including the GM-WM boundary file as a termination mask. However there seems to be less information on how to do this with probtrackx.
Based on what I have read in the tutorial and forum, I would like to check if the following command and options sound about right: probtrackx2 --samples=/Diffusion.bedpostX/merged \ --mask=/Diffusion.bedpostX/nodif_brain_mask \ --seed=listofareas.txt \ --xfm=xfms/standard2acpc_dc \ --invxfm=xfms/acpc_dc2standard \ --stop=stopsurfaces.txt \ --seedref=T1w_restore.2.nii.gz \ --loopcheck \ --forcedir \ -c 0.2 \ --sampvox=2 \ --randfib=1 \ where: To generate seed file: label2surf -s 100307.L.aparc.32k_fs_LR.label.gii -o 100307.L.aparc.32k_fs_LR.label.gii -l listofareas_L.txt label2surf -s 100307.R.aparc.32k_fs_LR.label.gii -o 100307.R.aparc.32k_fs_LR.label.gii -l listofareas_R.txt Combine the text files produced by label2surf. Is there a way of doing this more efficiently rather than copying and pasting? To generate stop file (as per tutorial): surf2surf -i fsaverage_LR32k/100307.L.white.32k_fs_LR.surf.gii \ -o L.white.asc --outputtype=ASCII \ --values=fsaverage_LR32k/100307.L.atlasroi.32k_fs_LR.shape.gii surf2surf -i fsaverage_LR32k/100307.R.white.32k_fs_LR.surf.gii \ -o R.white.asc --outputtype=ASCII \ --values=fsaverage_LR32k/100307.R.atlasroi.32k_fs_LR.shape.gii echo "L.white.asc" >stopsurfaces.txt echo "R.white.asc" >>stopsurfaces.txt I am unsure if it is necessary to include the waypoint masks and if so, which should be used? Also, does it make more sense to do matrix1 or matrix3 in this instance? Thank you very much and I really appreciate any assistance if possible and am sure this will be of great benefit to others whom are attempting to perform such analyses. Best, Michiko _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
