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 1×1×5.5 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
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