Hi Antonín

You can specify what surfaces to use in mris_thickness:

mris_thickness -pial <path to pial surface> -white <path to white surface> …

cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Antonín Škoch
Sent: Wednesday, December 9, 2020 6:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Computing thickness from woT2.pial surfaces

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Dear experts,

I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0.

Thank you in advance,

Antonin Skoch