External Email - Use Caution
If you have not already tried making sure no other applications, e.g., browsers, etc. are running on your machine before running that command, then I would do so. The process was likely killed because the machine does not have the memory (and/or memory management) resources to run that python code. It could be that newer versions of Ubuntu Linux will provide more efficient memory management and allow it to run, but that is not for certain. However, Ubuntu 18 is end of life’d and future freesurfer releases will not be available for Ubuntu18. At some point you should consider upgrading, e.g., to Ubuntu 22, which is more current.. - R. On Jun 10, 2025, at 09:32, Nithin Thanissery <nithin.cogsci@gmail.com> wrote: External Email - Use Caution Dear FreeSurfer experts,å 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_probabilitiesMessage 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 mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1iA1vIZjaXS6o9hokJaSMWEbIHxI1na9HQJehQQsC0WXZO2...