Re: [HCP-Users] Extracting Thalamus Brainordinates

[Ely, Benjamin]

Hi Claude,

Are you using workbench viewer? If so, you should be able to identify
particular thalamus or other subcortical MNI coordinates in the Volume tab
(brainordinate subcortical coordinates = MNI coordinates). You can also
split the thalamus structure out from subject¹s CIFTI file, if you want to
view/manipulate the data with other tools. The command would look
something like:

wb_command -cifti­separate ${input_file}.dscalar.nii COLUMN -volume
THALAMUS ${extracted_thalamus_file}.nii

Best,
-Ely


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