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