your command line looks right. Try using the .lta file created by bbregister instead of the .dat file
On 11/15/2024 10:34 AM, Pandey, Shraddha wrote:
External Email - Use Caution
We are experiencing issues with `mri_vol2surf` generating an incorrect surface for the `Paramagnetic.nii` volume. Although the registration file (`volume_transform.dat`), created using `bbregister`, appears accurate, the output surface file (`Paramagneticsurface.mgh`) does not look correct. Specifically, some voxel values in the cortical areas are incorrectly predicted as zero.
Command:
input_volume=Paramagnetic.nii output_surface=Paramagneticsurface.mgh output_reg_file=volume_transform.dat mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface"Any guidance on resolving this issue with the surface generation would be greatly appreciated.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer