Hi,
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 as follows:
3dAllineate -1Dmatrix_apply anat_fs_brain_al_mat.aff12.1D -prefix anat_fs_al anat_fs.nii
3dcalc -a anat_fs.nii -expr a -prefix anat_fs
3dAllineate -1Dmatrix_apply anat_fs_brain_al_mat.aff12.1D -prefix anat_fs_al anat_fs+orig
The 'anat_fs_al+orig' output from 'anat_fs+orig' always aligns properly with the target dataset, while the output from 'anat_fs.nii' does not.
Any suggestion?
Thanks,
Phoebe
