For the list's benefit. Tim
---------- Forwarded message ---------- From: Maarten Vaessen <[email protected]> Date: Thu, Nov 3, 2016 at 3:45 AM Subject: Re: [HCP-Users] -probtrackx-dot-convert volume label problem To: Timothy Coalson <[email protected]> The problem was that the coords_for_fdt_matrix3 file (from probtrackx2) has 5 colums (x,y,z,something,something), while the -probtrackx-dot-convert expects just the x,y,z in a file. It works now! Thanks, -Maarten On Wed, Nov 2, 2016 at 9:43 PM, Timothy Coalson <[email protected]> wrote: > 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
