As a guess, did you use "-crop" when you used -cifti-separate to get the amygdala ROI? If so, that changes the volume space (specifically the FOV), so indices don't correspond with the normal 2mm volume space. This would mean that you now need to make a label volume in this new FOV space. Alternatively, you could get the ROI without using -crop, rerun probtrackx, and then the standard Atlas_ROIs file will work.
The <label-vol> must have the same dimensions and origin/spacing as the roi file you used in probtrackx, otherwise the indices won't match. I would not call an amygdala-only volume "Atlas_ROIs", that would be misleading, and you should double check your amygdala ROI file for its value, as it probably uses 1 rather than 18, and fix the labels text file based on that, but the -volume-label-import command otherwise looks like it would produce something that should work for your current probtrackx results. Tim On Wed, Nov 2, 2016 at 7:20 AM, Maarten Vaessen <[email protected]> wrote: > Hello, > > I'm trying to convert a .dot from probtrackx2 with -matrix3 option to a > dconn.nii. The -lrtarget was a list containing all volumes and surfaces > conforming to the HCP grayordinate file. The -target3 is the L (or R) > amygdala from Atlas_ROI.2.nii.gz. The output from probtrackx2 looks > sensible. > > I use the following command and get this error: > wb_command -probtrackx-dot-convert fdt_matrix3.dot fdt_matrix3.dconn.nii > -col-cifti 91282_Greyordinates.dscalar.nii COLUMN -row-voxels > coords_for_fdt_matrix3 amyL_label_from_Atlas.nii.gz > > ERROR: voxel index in list file did not match a structure: 0, 1, 56 > > > Now, I am not sure what to use as input for -probtrackx-dot-convert > -row-voxels: > > [-row-voxels] - the output mapping along a row will be voxels > > <voxel-list-file> - a text file containing IJK indices for the voxels > used > --> this should be the coords_for_fdt_matrix3 right? > > <label-vol> - a label volume with the dimensions and sform used, with > structure labels > --> here I am a bit lost. I tried several options, the probably most > sensible being: > wb_command -volume-label-import subj/MNINonLinear/ROIs/Atlas_ROIs.2.nii > amyL_label.txt amyL_label_from_Atlas.nii.gz -discard-others > > amyL_label.txt = > AMYGDALA_LEFT > 18 103 255 255 255 > > What would be the correct input to get this to work? > > Thx, > > -Maarten > > _______________________________________________ > 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
