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
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