pstchan Wrote:
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> When I apply '3dAllineate' or 'align_epi_anat.py'
> to align a T1 anatomical dataset, I find a
> difference in the output for the same input
> dataset in NIFTI and BRIK format
AFNI can store additional transformations in the fields
- ALLINEATE_MATVEC_B2S_000000
- ALLINEATE_MATVEC_S2B_000000
- WARPDRIVE_MATVEC_FOR_000000
- WARPDRIVE_MATVEC_INV_000000
which is probably what is happening here (you can view the .HEAD file in a text editor to verify this). When loading AFNI files in the viewer, the transformation in these fields is used to map voxel indices to world coordinates. My guess is that when storing the output as NIFTI these fields are ignored.
