Thanks for your guidance. I already tried recon-all-clinical.sh; however, I was wondering why did this happen? Could it be related to resampling process or the orientation? 

Thanks, 
Nima
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, January 28, 2025 12:41 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation
 
Try using recon-all-clinical.sh; it works a lot better on these thick slice data


On 1/28/2025 12:24 PM, Taghizadeh Mortezaei, Nima wrote:
Hello FreeSurfer Developers and Community,

I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1󪻕.5 mm. I resampled this MRI in 3D Slicer using B-Spline interpolation and then saved it as a mgz file. After running recon-all on this resampled file, I noticed that the right hemisphere抯 segmentation and parcellation are flawed. Also, considering the age and health situation of this patient, i believe the WM hypointensities are overestimated in the left hemisphere. 

I am using the following version of FreeSurfer: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460.
The command line was: 
recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12

I抳e attached the recon-all log file, a screenshot from Freeview to illustrate the issue, and mri_info file. I would greatly appreciate any guidance, troubleshooting advice, or suggestions on what might have gone wrong and how to correct this issue.

Thank you in advance for your help!

Best regards,
Nima

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