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If you want region-based measurements (e.g., for Desikan atlas), you can use the 'aparcstats2table' tool that comes with FreeSurfer to generate a CSV file with aggregated data for several subjects.

For vertex-wise measurements, you most likely want to use the standard space files in the surf directory (e.g., surf/lh.thickness.fswhm10.fsaverage.mgh) for thickness. There are 2 such files per subject (for the 2 hemispheres). They are in binary curv format. I read you use Python, so you should be able to open them with nibabel.

If you want a wrapper around it that can open a whole SUBJECTS_DIR at once, you can try my brainload module:

import brainload as bl subjects_dir = "path/to/recon-all-output" subjects_list = ["subject1", "subject2", "subject3"] group_data, group_data_subjects, group_meta_data, run_meta_data = bl.group('area', fwhm='15', surf='white', hemi='lh', subjects_dir=subjects_dir, subjects_list=subjects_list)

print group_data.shape # will print '(3, 163842)' for the 3 subjects. Note that 163842 is the number of vertices of the left hemisphere of the 'fsaverage' subject.

Tim

On 02/23/2022 2:10 PM REEM ABU BAKR BAHATHIQ rbahathiq0001@stu.kau.edu.sa wrote:

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Hello Freesurfer experts How can I get a text file of the cortical measurements of a group of images after they have been processed with recon -all??

Best,

Reem _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1hwiAF59CyQDsENJM6UsG2FXUzpsAHg5LBr9syGd9Rbe9AA...

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