This is from your recon-all.log

“

mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

mri_convert: extra argument ("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")

“

There is a space in your path to nii.gz. Can you remove the space by renaming the directory?

Also, your SUBJECTS_DIR points to your Freesurfer install directory - /usr/local/freesurfer/subjects. You might run into permission or symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Flemister, Abeoseh B.
Sent: Friday, January 5, 2024 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

        External Email - Use Caution        

Hi FreeSurfer Team,

I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our dataset and using .nii files and got the same result. I saw a recent thread where someone's issue was improperly labeled WM lesions but my dataset is composed of healthy brains. 

I attached my recon-all.logs. I am using a Linux virtual machine (FreeSurfer version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if you have any questions!

Thanks,

Abeoseh Flemister