Hi Saad
Thanks for your help! I misunderstood which of orig.mgz and rawavg.mgz were in "struct" and "freesurfer" space.
Another related question. Is there any reason why we can't directly compute the transformation from FreeSurfer to Diffusion space using something like the following:
mri_convert \
$SUBJECTS_DIR/${subj}/mri/brain.mgz \
fs_brain.nii.gz
flirt \
-in ../dtifit/dtifit_FA \
-ref fs_brain.nii.gz \
-omat fa2freesurfer.mat
convert_xfm \
-omat freesurfer2fa.mat \
-inverse fa2freesurfer.mat
Is there a benefit to use the in-session struct.nii.gz to align with the FA map since they, presumably, start very close? Thus calculating the larger transformation between two high-res T1 images?
Cheers,
Ryan
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