Sorry, I'm not sure what the problem is that you are describing. I see
from the recon-all file that
MNI_freesurfer_T1.nii.gz is your input. What is that? Is that after skull
stripping? Why not just give it the full head?
On 6/20/2024 3:52 PM, Gaurav Ambwani wrote:
External Email - Use Caution
Dear Freesurfer developers,
I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain
extraction tool in 3D slicer, and then I registered it in fsl to a
skull stripped version of a T1 weighted image of a Stroke patient
(which I got from Openneuro).
The purpose of doing this is to, get the aseg.mgz file and overlay
that onto the MRI of the stroke patient.
Previously I have taken the T1 1mm MNI image and received an aseg.mgz
file which I have overlayed onto my MNI registered T1 weighted stroke
MRI and that worked perfectly. However, This time I have taken the T1
1mm MNI image registered that to my stroke T1 MRI, and the registered
image hasn't gone through freesurfer.
I have attached the recon-all.log file in this email.
Freesurfer version:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1
SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Distributor ID: Ubuntu
Description: Ubuntu 22.04.4 LTS
Release: 22.04
Codename: jammy
I am using a WSL in windows 11 (64 bit)
Thank you,
Best Wishes,
Gaurav Ambwani.
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