Hi Nys
.gcs is a different format for storing different information (surface-based
parcellation) than .gca, so mri_convert won't be able to read it. There might
be matlab code for loading .gcs files if you want. Or maybe mris_convert? I'm
not sure, possibly someone else can take a look?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Siegel, Nys Tjade
Sent: Monday, August 5, 2024 9:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question/potential bug regarding mri_convert and .gca
files
External Email - Use Caution
Dear Freesurfer community,
I'm trying to extract labels from a .gca atlas volume using the following
command:
mri_convert atlas.gca -nth 1 labels.mgz (from
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat)
I've found a .gca file in the /average folder for which this works
(RB_all_2020-01-02.gca), but for the cortical parcellations I'm actually
interested in (e.g. lh.DKTatlas40.gcs), I get the following error:
ERROR: cannot determine file type for lh.DKTatlas40.gcs
I'm pretty confused, because the documentations, as well as other support
requests, are pretty clear on that my problem should be solved using the
mentioned command. Notably, mri_convert -u, does not list GCA under the
supported file-types, maybe this is a versioning issue?
I'm using freesurfer 7.2.0 with Ubunutu 22.04.4.
Any help is much appreciated.
Best regards,
Nys Tjade Siegel
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