I wanted to see if anyone knows what part of the file NIFIT header mri_vol2vol or mri_convert uses to write transform information from register.dat acquired from bbregister?  I used the following commands to register the anatiomcal brain.mgz to the last time point of my EPI scan:

bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat --init-header --bold --frame $NP_last --nearest --template-out ${sub}.RS.template.nii

mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/

When i view the images in Afni they look misaligned, but display perfectly in freesurfer (tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat --surf) so I am assuming each program looks at a different field in the nifti file header.  I used mri_vol2vol to apply the inverse transform of register.dat to brain.mgz so that it aligns with the EPI but for some reason it is not showing up correctly in afni so I wanted to get a better understanding of how freesurfer files write transformation information in nifti format (sform, qform, another part of the header) and if there is an easy way to get this into a format that afni reads correctly?

Thanks,

Ajay