Hi Jakob,

I believe we fixed the bug in FS 7.4 release. Can you give it a try?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Litsch, Jakob Benjamin
Sent: Wednesday, December 6, 2023 10:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segmentation error with T2w

        External Email - Use Caution        

Dear Freesurfer Team,

I am a master student from Berlin and pretty new to preprocessing MRI data, so please bear with me. 

I am attempting to use Freesurfer as Part of my fMRIprep pipeline to preprocess patient data. When running fmriprep with only the T1w and the BOLD image it works fine. As soon as I put in my T2w image as well recon-all crashes at some point. 

My patient data has lesions like brain tumors, just in case this could make freesurfer struggle. 

Starting loop over 250145 vertices
   vno = 0, t = 5.16114
error: Numerical argument out of domain
error: MRIhistogramLabelRegion: constant image
error: Numerical argument out of domain
error: MRIhistogramLabelRegion: constant image
Segmentation fault

1) Freesurfer version:  freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275

2) platform: Windows 11, Ubuntu 22.04.2 LTS (GNU/Linux 5.15.133.1-microsoft-standard-WSL2 x86_64)

3) recon-all log: see attached

Looking forward to hear from you,

Jakob Litsch