Hi Monami,

It looks like you two ran the program on different machines with different kernel versions. I think that could cause the differences in output.

Linux cubic-login5 3.10.0-1160.21.1.el7.x86_64 #1 SMP Tue Mar 16 18:28:22 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Linux 211affn003 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Monami Nishio Sent: Thursday, October 19, 2023 10:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Problem with mri_glmfit

External Email - Use Caution Dear whom may concern

Hello Freesurfer Developers, I recently ran the mri_glmfit-sim command to replicate a previous PhD student's result, and found out that his output and mine are different, although the code and input is exactly the same. The previous PhD student ran the code in 2022 April, and I ran it in 2023 October. This is the exact command I run mri_glmfit-sim --glmdir data/ses-0${timepoint}/${hem}_MM_${variable}_n31_ fwhm_src5trg5.glmdir/ --perm 1000 $sig abs --perm-resid --cwp 0.05 --2spaces; According to the log, the difference is in the simulation section, this is his log (2022.04.log) Starting simulation sim over 1000 trials mri_glmfit simulation done 42.124 this is mine (2023.10.log) Starting simulation sim over 1000 trials INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry().... mri_glmfit simulation done 27.9102 I attached log files for each to this email.

I searched for what "INFO: MRImask() using MRImaskDifferentGeometry()" means in FreeSurferWiki, but I can't find any answer. Could you let me know if there are any updates about this command recently?

1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Platform: Linux version 3.10.0-1160.21.1.el7.x86_64 (mockbuild@kbuilder.bsys.centos.orgmailto:mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) )

Sincerely, Monami