Map subcortical dlabel into right/left

[amirhussein.a]

Hi,

I'm using a subcortical dlabel file, that has not divided the structures into right/left (i.e., only one Putamen label comprising the bilateral structures). Is there a way to generate a new dlabel file based on the existing one, with new label keys for the structures in each hemisphere (e.g., L_putamen and R_putamen)?

Best,

Amir

[Tim Coalson]

You need to give the voxels in the left versus right structures different values (and also values that aren't used by any other structure).  If you have a "dividing line" between left and right, you could represent that as a volumetric ROI, use it to modify the voxel values, and re-import the modified values as a label volume or dlabel file.

The freesurfer structure parcellation already separates left and right structures, is there a reason you don't want to use that as a starting point?

Tim

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[amirhussein.a]

Hi Tim,

Thanks for your reply. I'm using CIT168 CIFTI parcellation dlabels provided here: https://osf.io/am6vz

Our goal is to apply those dlabels on HCP's young adult rsfMRI dtseries data, and check connectivity profiles of the subthalamic nucleus. However, to test our hypothesis we have to have a division between right and left which that dlabel file has not applied.

Are there any right vs. left masks in the atlas space in HCP? I couldn't find any in MNINonLinear folder that I can use as a mask. Or possibly a dscalar file indicating which CIFTI-indices indicate a hemisphere for the subcortical structure.

Best,

Amir

[Tim Coalson]

Based on the provenance, they used our Atlas_ROIs.2.nii.gz file to designate the subcortical voxels, so you can reuse that to separate right from left.  Take that file from here:

https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/91282_Greyordinates

Use wb_command -volume-label-export-table on it, manually delete the pairs of lines that aren't part of one hemisphere (note, brain stem is a structure that we don't split into hemispheric parts), and use -volume-label-import with the -discard-others option to get a single-hemisphere version of it, then use -volume-math 'x > 0' to turn that into a binary ROI.

Tim