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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer