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

External Email - Use Caution 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-allhttps://secure-web.cisco.com/1nqW39ubw2AyrvIfDDZNWB66KB47XSeO6tS5QZO8RBYGIE_HEX0L_9ky5BplO2g3f5Yype5vdBj4W0De7S1NBLNdvHFPI1k0DayuUt2hc8j52YzXFhR7ng6pxJ4WM9WsiFPnfTnLRWLH7RHeMEPW8DMqOq4bEtJHfRx81pXgSbL9KqbThH3rR-G7j34pXg15cg8R__sP3dfS4Te9UczFajxl3ED3vYroskCPgsbZZfvIqegttwogROzyTE40I9jKEPHbTC0ad0azXoFQhZh0312sG9dthj8QouCdrRS3UGD3lb7Z6ZEAyu8iwXtIgnOzh1aGKos3EBeMGRghRHiFnXQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-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/ReleaseNoteshttps://secure-web.cisco.com/1vUPpLJpZFWtBAPAZsBnTOCfqihx6dgklkyFygBvPMdyx7egogmPbZrtHwz8GVBBctGuDY99I9NnZfKG1jKUmWJ5aqaEOn1QU0WGVi-mGQOpV_8hc-GGg1nVkplvhR_AH0QLrM9rYmeJJ6WOfAhGJftjmZSK4fsKHwYrZ8Bro6e82ktqUL4ijtCobfRW5TMxI7SXZpDjHhN6rEdoBdi6VWw5qx1fbGGZtLa8NHhcwjbuVf0h0E97zMwPFyXEVb3ZhTCkNu5-wVG3pexTcTvG1AxBkIiCsEyxQk236UYmFDDNazzSD6x3TTLqWsj4PH4KVbLl6uVvzEMJ9lVLZqLbtcA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes) 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

[Description: Universitair Medisch Centrum Utrecht]

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

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.