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:
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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.zamy...@camh.ca> wrote:
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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
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