Hello FreeSurfer Developers,

Greetings of the day.

I am attempting to replicate a previously published work and have applied the recon-all pipeline on our structural MRI data (T1w.nii) using FreeSurfer.

After segmentation and normalization, the output we are obtaining appears unusual to us. I would like to confirm whether these results are expected or if additional preprocessing steps are required prior to running recon-all.

I have also attempted reorientation of the input image; however, I was only able to find GUI-based orientation options. I would appreciate your guidance on the following points:

1. Whether the observed segmentation and normalization outputs are expected, or if further preprocessing steps (such as reorientation, intensity correction, or format conversion) should be performed before running recon-all.

2. If manual reorientation is recommended, how should the orientation be determined (e.g., reference axes, alignment criteria, or specific angles)?

3. Any best practices for preparing T1w.nii files to ensure optimal processing with FreeSurfer.

I am attaching screenshots of the normalization and segmentation results (aseg output) for your reference. Kindly guide me on how to proceed further.

Thank you very much for your time and support.