Hi James,
Did mri_annotation2label commands create lh.lobes.annot and rh.lobes.annot in fsaverage/labels directory?
They are annot files. You can use mri_annotation2label to break them into label files.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of James Brown Sent: Thursday, January 19, 2023 7:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit
External Email - Use Caution Dear FS experts, I am working on a surface based analysis using FS 7.1.1 and I would like to run mri_glmfit between two groups using the flag "--label" to restrict analysis within lobes.
I ran these commands on fsaverage
mri_annotation2label --subject fsaverage --hemi lh --lobesStrict lobes mri_annotation2label --subject fsaverage --hemi rh --lobesStrict lobes
This created annotation files within the "labels" folder of fsaverage, then I ran mri_glmfit using the flag --label lh.lobes from fsaverage
I got this error message mri_glmfit: could not scan # of lines from label file
I am ot sure what I am doing wrong. Thanks for guidance
James