Hi Caspar

Usually that means the lh.smoothwm and the lh.sphere.reg don’t have the same topology (number of vertices,edges and triangles), frequently caused by one of them having been recreated and the other not. Run mris_info on them and see if they match

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Caspar Schwiedrzik
Sent: Tuesday, September 27, 2022 4:11 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] issue with mris_ca_label and mrisReadTriangleFile

        External Email - Use Caution        

Hi!

I am having issue with mris_ca_label while trying to apply the Yeo 2011 atlas to single subject surfaces.

Specifically, I am getting "surface doesn't match" from mrisReadTriangleFile  and "could not read spherical coordinate system" from mris_ca_label.

lh.smoothwm and lh.sphere.reg both exist in the specified places.

It does not matter from where I run the below command. I also tried adding -sdir, which did not change anything.

It happens with v5.3 and v7.

I have seen a couple of bug reports on this specific error, but no solution other than re-running recon all, which is not an option in my case.

Any advice would be appreciated.

Thank you! Caspar

mris_ca_label -l /home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/label/lh.cortex.label \

9152127433 lh /home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/surf/lh.sphere.reg \

/home/local/GWDG/cschwie3/ukme11/common/Software/YeoParcellation/lh.Yeo2011_17Networks.gcs \

/home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/label/lh.Yeo2011_17Networks_N1000.annot

$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $

$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $

reading atlas from /home/local/GWDG/cschwie3/ukme11/common/Software/YeoParcellation/lh.Yeo2011_17Networks.gcs...

reading color table from GCSA file....

average std = 8.4   using min determinant for regularization = 0.705

0 singular and 246 ill-conditioned covariance matrices regularized

mrisReadTriangleFile(/home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/surf/lh.sphere.reg): surface doesn't match /neuro_tools/freesurfer/subjects/9152127433/surf/lh.smoothwm

No such file or directory

mrisReadTriangleFile failed.

No such file or directory

mris_ca_label: could not read spherical coordinate system from /home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/surf/lh.sphere.reg for 9152127433

No such file or directory