6 Jul
2025
6 Jul
'25
6:28 p.m.
It is not clear from the log what is happening. Is it possible that you ran out of memory?
On 7/5/2025 10:30 AM, Nader Razmara wrote:
External Email - Use Caution
Dear Freesurfer is very sensitive to: 1-memory of system 2- coordinate system of FLAIR image 3- contrast equalization Check them I hope be usefull Nader
On Thu, 3 Jul 2025, 22:54 Mojdeh Zamyadi, Mojdeh.Zamyadi@camh.ca wrote:
External Email - Use Caution Hi FreeSurfer developers, I’m attempting to use FLAIR images to improve the segmentation quality of some of my subjects after successfully running recon-all –all with the T1 images. After QCing the initial results some segmentation needed improvement which is why I am trying to use the FLAIR images on the recon-all –all results with T1. This is the command I am using: recon-all -s ${subject_id}_T1 -FLAIRpial -autorecon2 -autorecon3 but I am getting errors at the “mris_place_surface” stage. I have also tried manually running mri_normalize first and then running recon-all with the –FLAIRpial flag (command below), but I still get the same errors. mri_normalize $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.mgz $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.norm.mgz I have attached my recon-all.log file here in case it’s of any use. Additional info: 1- recon-all --version freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a 2-Mac info: ProductName: macOS ProductVersion: 15.5 BuildVersion: 24F74 3- uname -a Darwin iMac.local 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:26 PDT 2025; root:xnu-11417.121.6~2/RELEASE_X86_64 x86_64 Also, a note that we have been able to run recon-all v6 with –FLAIR flag on the same subject on an older Mac system. I would appreciate any insights you might have to how to improve my results using Flair images using v8 of FreeSurfer. 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