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
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