On 30 Jun 2023, at 15:16, Huang, Yujing <YHUANG43@MGH.HARVARD.EDU> wrote:

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Hi Akansha,

Can you try mri_segstats with option '--slabel subject hemi full_path_to_label' - https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9ndTV9_ZapgsK_3NzhU8bMJOJY0uIz_LMPNGNff9ofQdi41lbl_z4LOot-PyyIAOkplCuie52WEoC25283K_FLApVE15eUqnyiaVpMRry06hp5_XGPLrNRm50KNv6woZtoPOOJi35Ep6MuRJkBknO4l1bQnjCysJ1851eBgeeHAOcGNtQnlEJSxyMSyXX9hlATC-lcdqDSa3tSwnR3HxF8HRuwC8fhqYKaAFcuhOJ6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats

Best,

Yujing

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Akansha Mahesh Naraindas
Sent: Thursday, June 29, 2023 3:47 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Extracting cortical thickness values for each subject using labels

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Hi
I have made custom labels to use as ROIs,

I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files,

So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ?

Do you know of a way to do this?

Thanks
Akansha

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