James, what do you mean by restrict the analysis within lobes? An ROI analysis? Adding --label will not give you an ROI analysis.

On 1/20/2023 9:32 AM, Huang, Yujing wrote:

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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