Dear Nithin,

Please try the –-crop option. Otherwise, you’ll need to either…

1. Manually crop the image around the brain, as tight as possible.
2. Use a machine with more RAM

Sorry for the inconvenience!

/E

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: Nithin Thanissery <nithin.cogsci@gmail.com>
Date: Tuesday, June 10, 2025 at 9:33 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] WMH-SynthSeg: program "killed" while Pushing data through the CNN

        External Email - Use Caution        

Dear FreeSurfer experts,

I am trying to use WMH-SynthSeg on FLAIR images to segment and quantify WMH. However, this error keeps popping up:
The code I ran: 

mri_WMHsynthseg   --i flair.nii   --o output_dir/output.nii.gz   --csv_vols volumes.csv --save_lesion_probabilities

Message I got:
Arguments seem correct; loading Python packages...
Using cpu
Using 1 thread(s)
Preparing model and loading weights
Working on image 1 of 1: flair.nii
     Loading input volume and normalizing to [0,1]
     Upscaling to target resolution
     Pushing data through the CNN
Killed

I am using Ubuntu 18.04 and using the FreeSurfer 8.0.0 installed using the .deb file. I have 32GB RAM. The nifti file is 100.7 MB (I am hoping that's not the problem).  I checked my RAM utilization during the process. I could see it going upto 28GB before the process was killed. Read similar problems on the freesurfer mail list that were dated at least a year ago. But, I was not able to find any solution. Would you have any suggestions/solutions or recommendations to make this work? 

Thanks and regards