Re: [Freesurfer] Extracting cortical thickness values for each subject using labels

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Hi Yujing

Thanks for your response, would this only provide the mean cortical thickness though? Is there a way to output cortical thickness values at each vertex in each participant?

Im also a bit confused about the segstats call, is this what you are proposing?

mri_segstats --i combatlh.thickness.fwhm0.fsaverage.mgh --slabel $SUBJECTS_DIR/fsaverage/label/DLPFC_LH.label --sum lhDLPFClabel.sum

Thanks Akansha

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_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9nd...

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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