And you can use read_annotation.m in $FREESURFER_HOME/matlab to load it

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Tim Schäfer Sent: Monday, October 11, 2021 4:32 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question about fsaverage

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That file is in standard space, so if you want the Desikan parcellation, the files you are looking for are:

* $FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot

Best,

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

On 10/11/2021 3:00 AM Dongyue Zhou zhoudongyue@mail.dlut.edu.cn wrote:

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Dear FreeSurfer experts:

I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'.

I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices.

Is there any way I can get annot for this file in one sub?

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