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-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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