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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

 

Twitter: @CYBDatCAMH

Website: camh.ca/CYBD

 

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If you are in crisis or need urgent help:

·                Call the Kids Help Phone: 1-800-668-6868 or text 686868

·                In Toronto, contact the Youthdale Crisis Service Line: 416-363-9990

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·                Call 911

 

 

 

 



 

 

 

 


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