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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.
Thanks, Mojdeh Zamyadi, MSc (she/her)
Research Coordinator (Imaging) Centre for Youth Bipolar Disorder Centre for Addiction and Mental Health 80 Workman Way, Toronto 416-535-8501 ext. 33278
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