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,