Thanks for the quick reply Tim.
After converting the correct metric files, how can I generate a customized
CIFTI file containing only the left subcortical ROIs and left cortex? To
clarify, I generated the left hemisphere subcortical ROIs from the
aparc+aseg.nii.gz volume in ${Subject}/T1w/. In my target list, I
specified the subcortical ROI volume first, followed by the left white
matter surface file.
>From looking through previous threads, it looks like wb_command
-cifti-create-dense-scalar might be what I need, but I need a volume label
file for the -volume <volume-data> and <label-volume> options. How can I
create a volume label file for only the left hemisphere subcortical ROIs?
Thanks!
kristian
On Wed, May 27, 2015 at 6:13 PM, Timothy Coalson <[email protected]> wrote:
> First off, this part:
>
> -row-surface fdt_paths_surface.func.nii -col-surface
> fdt_paths_surface.func.nii
>
> Those files should be named .func.gii, they are GIFTI metric files, not
> NIfTI volumes.
>
> Second, you appear to be doing tractography to subcortex and left
> hemisphere (only?) at once. In order to convert these, you will need to
> make a CIFTI subcortical and left cortex file with the same ordering of
> structures (and vertices/voxels within a structure), and use this with the
> -row-cifti and -col-cifti options instead of -row-surface and -col-surface.
>
> Tim
>
>
> On Wed, May 27, 2015 at 7:26 PM, Kristian M. Eschenburg <[email protected]>
> wrote:
>
>> Hi FSL
>>
>> I'm trying to generate connectivity matrices from the HCP data. Here is
>> my probtrackx2 call:
>>
>> SAMPLES=${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
>>
>
>
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