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:
```bash
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.
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