Hi Paul
mri_vol2label maps the volume into an ascii label structure but has no
knowledge of surfaces. You then need to run mri_label2label with options like
–sample to sample it onto a surface
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Paul Dhami
Sent: Sunday, October 10, 2021 6:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Creating a surface parcellation from a volume atlas
External Email - Use Caution
Dear Freesurfer community,
I have a .nii volume atlas (CAREN), defining 5 networks, in MNI (ICBM152) space.
However, I wish to do my analysis in surface rather than volume space, and for
the software I am using, that means I need to load in a .annot file.
For the first step, I used:
mri_vol2label --c CAREN_5networks.nii --id 1 --l 1.label
and did this for values 1 to 5 (for each of the networks). However, looking at
the resulting label file, the first column is nothing but -1 values. I believe
this should be the vertex number, and trying to combine these labels into an
.annot file is not working.
Apologizes for the naive question, but can anyone share as to how I can
ultimately create a surface atlas when I have the volume.nii atlas file? Was I
wrong with mri_vol2label as my first step?
I am using Freesurfer version 7.2.0.
Thank you,
Paul
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