First off, this part: -row-surface fdt_paths_surface.func.nii -col-surface fdt_paths_surface.func.nii
Those files should be named .func.gii, they are GIFTI metric files, not NIfTI volumes. Second, you appear to be doing tractography to subcortex and left hemisphere (only?) at once. In order to convert these, you will need to make a CIFTI subcortical and left cortex file with the same ordering of structures (and vertices/voxels within a structure), and use this with the -row-cifti and -col-cifti options instead of -row-surface and -col-surface. Tim On Wed, May 27, 2015 at 7:26 PM, Kristian M. Eschenburg <[email protected]> wrote: > Hi FSL > > I'm trying to generate connectivity matrices from the HCP data. Here is > my probtrackx2 call: > > SAMPLES=${HOME}Diffusion.bedpostX/merged > MASK=${HOME}Diffusion/nodif_brain_mask.nii.gz > SEED=${SurfDir}${SUBJ_NAME}.L.white.32k_fs_LR.surf.gii > WAYPOINTS=${HOME}ROIS/Left_WM_Bin.nii.gz > STOP=${SurfDir}${SUBJ_NAME}.L.pial.32k_fs_LR.surf.gii > AVOID=${HOME}ROIS/Total_Exclusion_Mask.nii.gz > TARG = list pointing to subcortical ROIs and > ${SurfDir}${SUBJ_NAME}.L.white.32k_fs_LR.surf.gii > SEEDREF = mask in seed space > XFM / INVXFM = linear transforms between T1 and DWI > TARGET2=${MASK} > > /usr/share/fsl/5.0/bin/probtrackx2 --samples=${SAMPLES} --mask=${MASK} > --seed=${SEED} --waypoints=${WAYPOINTS} --stop=${STOP} --avoid=${AVOID} > --targetmasks=${TARG} --distthresh=2 --nsamples=1000 --xfm=${XFM} > --invxfm=${INVXFM} --seedref=${SEEDREF} --dir=${DIR} --omatrix2 > --target2=${TARGET2} --opd --forcedir --pd --verbose=2 > > I am successfully able to run this call for both --omatrix2 and --omatrix > 4 (and by switching target2 and target4 masks). > > I convert the fdt_paths.nii volume using wb_command > -volume-to-surface-mapping <fdt_paths.nii> > <${SurfDir}${SUBJ_NAME}.L.white.32k_fs_LR.surf.gii> > <fdt_paths_surface.func.nii> -cubic. I can visualize this successfully > using Connectome Workbench on the L.white.32k_fs_LR.surf.gii. > > However, when I try to run wb_command -probtrackx-dot-convert using: > > wb_command -probtrackx-dot-convert fdt_matrix2.dot fdt_matrix2.dconn.nii > -row-surface fdt_paths_surface.func.nii -col-surface > fdt_paths_surface.func.nii, with out without the -transpose call, I am > getting this error: > > ERROR: found invalid index pair in dot file: 32472, 24335, perhaps you > need to use -transpose. > When adding the -transpose call, I receive: > > ERROR: found invalid index pair in dot file: 24335, 32472, perhaps you > need to remove -transpose. > > Do you have any suggestions as to what I'm doing wrong with this specific > call of -probtrackx-dot-convert? > > Likewise, when I try to convert the output from --omatrix4, from looking > at a previous thread by Dr. Glasser ( > https://www.mail-archive.com/[email protected]/msg00415.html), > I see that the -convert-matrix4-to-workbench-sparse call requires an > "orientation-file", which he calls > > > ${BedpostXFolder}/Whole_Brain_Trajectory_${DiffusionResolution}.fiberTEMP.nii > > > Where is this file? Looking through my bedpostX outputs, I don't see any > orientation files. > > Any help would be much appreciated! Thanks! > > > > Kristian > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
