I don't know what you are asking. Can you elaborate? It is helpful to indclude commanb lines to show how files were created

On 10/9/2021 1:30 AM, Dongyue Zhou 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'.

Now,I have known that cortical thickness in this file is in standard space.But I don't understand why it is an average of 40 subjects.

Is it not CT measures an individual in standard space?

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 individual ROI in standard space if I want to compute mean CT measures of each ROI?

or Can I use file '$SUBJECTS_DIR/fsaverage/label/?.annot' as atlas directly?
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