Hi Francisco

My guess is that some of the versions you are using outputted the raw sulc (in mm) and some z-normalized it. So you can either take all your sulc files and z-normalize them, or rerun mris_inflate on all your subjects and give it the flag

-mm

You can also add -sulc <new sulc file name>

So you don’t overwrite the old one if you want.

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Guerreiro Fernandes-3, F.D. (Francisco David)
Sent: Sunday, February 20, 2022 5:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] sulc surface error: unit mismatch between FreeSurfer 5.3.0 and 6.0.1

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Dear FreeSurfer Developers,

I'm attempting to correlate the sulcal depth information present in the ?h.sulc files with activation in particular brain regions during  an overt language task in an fMRI paradigm. For this matter, a dataset was gathered throughout the years with several subjects and the cortical reconstruction process (as described in: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) was performed at the time of data acquisition. However, for subjects where recon-all was run in different FreeSurfer versions (5.3.0 or 6.0.1), I get an order of magnitude difference in the sulc values in the ?h.sulc volumes.

I've searched the list and the official FreeSurfer Release Notes (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) and found no information of a change of magnitude in sulc values. Does anyone have any thoughts on how to trouble-shoot this one?

1) FreeSurfer versions: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 & freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

2) Platform: Linux blue 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt11-1+deb8u3 (2015-08-04) x86_64 GNU/Linux

Kind Regards,

Francisco D. Guerreiro Fernandes

Francisco David Guerreiro Fernandes, PhD Candidate   |   BCI Group   |   UMC Utrecht Brain Center  

Dept. Neurology & Neurosurgery   |   University Medical Center Utrecht

Room STR 4.119   |   Heidelberglaan 100   |   3584CX Utrecht   |   The Netherlands

Email: F.GuerreiroFernandes-3@umcutrecht.nl |  Tel: +31 88 75 50080

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