they look reasonable. I strongly suggest that  you use freeview to visualize them. It will automatically give each segmentation a color which makes it much easier to evaluate

On 2/20/2026 2:36 AM, Akanksha Upadhyay wrote:

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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.

Normalisation_results.jpg Segmentation_output_aseg.jpeg

-- /*Regards*/ /*Akanksha Upadhyay*/ /*Department of Computer Science*/ /*University of Delhi*/

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