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
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
freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Juan E. -
Nithin Thanissery