Dear Freesurfer users,
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/
brain.mgz --o $out_dir/brain_aligned.nii --inv --no-save-reg --reg
$out_dir/${sub}_RS_register.dat
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
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