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:

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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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