I'm assuming you want them to match a standard grayordinate space, so that
they can be compared across subjects.

The simple way that doesn't account for residual subject differences in
subcortical locations is to first resample the data to the appropriate
resolution/orientation MNI space (222 for the 91k grayordinates), then use
-cifti-create-dense-from-template with the -volume-all option.

The better but more involved way is to take the subject's subcortical
structure labels from freesurfer, import them to workbench format with the
names that -cifti-create-label specifies, use -cifti-create-label to make a
subject-specific cifti file (you will also need to provide some dummy
surface data for the next step to work), and then use -cifti-resample to
use only the same-structure-overlap information, and dilate to fill in any
holes if desired.

We use this second method for fMRI data in the pipelines, see here:


Though that script actually only outputs a volume file, and therefore it
doesn't bother with having surface data in those temporary cifti files.


On Tue, Aug 8, 2017 at 3:19 PM, Xavier Guell Paradis <xavie...@mit.edu>

> Dear HCP experts,
> I have several subcortical nifti files, each containing one cluster. I
> would like to convert them to dlabel files, so that then I can use wb_view
> to see the functional connectivity from each of these clusters (using your
> group .dconn file).
> How can I convert subcortical nifti files to dlabel files?
> I have been exploring several wb_commands but I cannot figure it out.
> Thank you very much,
> Xavier.
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