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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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