Hello FreeSurfer Developers and Community,

I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1×1×5.5 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’s 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. 

The command line was: 

recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12

I’ve 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.

Nima