Hello,

I'm having a very difficult time with registration in FSL--been using AFNI for too long--and I think I need some clarification. I have a functional image, and I want to register it to my anatomical. I do NOT want to standardize anything nor resample. From what I have gathered off of the internet (primarily the NITRC website), I need to extract a subbrick from my functional image, coregister that one subbrick, and then apply that transform to my actual functional image. My code looks like this:

3dcalc -a ${subj}_resting_moco_ss+orig'[7]' -expr 'a' -prefix coreg_func_slice.nii.gz
flirt -ref ${subj}_anat_brain -in coreg_func_slice -out coreg_func_slice_post -omat coregistration_e2a.mat -cost corratio -dof 6 -interp trilinear

When I view the output of this, the alignment looks amazing, but my functional was resampled to my anatomical, which I do not want. Next, I try to apply the matrix from the above step to my functional image using this code:

flirt -in ${subj}_resting_moco_ss_b6_LP -ref ${subj}_resting_moco_ss_b6_LP -out ${subj}_resting_moco_ss_b6_LP_e2a -init coregistration_e2a.mat -applyxfm

When I view the results, it's pretty much all truncated and what's left is completely off in alignment. I don't know what to put in for the -ref argument. I have tried using my input image for it, because I don't want anything resampled, but the registration is still off. Any thoughts? Your help is much appreciated!