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.
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’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.
Thank you in advance for your help!
Best regards, Nima
