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

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