Hello! 

I am currently having trouble with using FSL's flirt to register EPI to T1. We were originally using epi_reg for functional registration; however, that was warping our scans in strange ways and was not working at all. When we ran epi_reg line by line, we found the error to be in the flirt pre-alignment step. To try to correct this, we ran flirt separately to register EPI to T1. 

We started out with a functional scan (f01.nii) and an anatomical scan (t1.nii). For the functional scan, we ran slice time correction (using FSL's slicetimer) and motion correction (using FSL's mcflirt). We then took the first volume of the slice time corrected and motion corrected functional scan to use in flirt. 

Our files are the following: 
f01.nii (functional scan)
f01_stc.nii (functional scan with slice time correction)
f01_stc_mc.nii (functional scan with slice time correction and motion correction)
firstvol_stc_mc.nii (first volume of functional scan with slice time correction and motion correction)

We then applied fslreorient2std, robustfov, and bet on both firstvol_stc_mc.nii and t1.nii separately, as that was previously suggested on this forum. This created the following files: 

firstvol_stc_mc_reorient_fov_bet.nii
t1_reorient_fov_bet.nii

We then ran flirt, using these outputs. We ran the following in terminal: 

flirt -in firstvol_stc_mc_reorient_fov_bet.nii -ref t1_reorient_fov_bet.nii -dof 6 -omat func2struct.mat -out func2struct.nii


The FLIRT step did not work in most of our subjects. We also tried different degrees of freedom (6, 7, 9, 12) and none of those worked either.

Is there anything else that I can do to fix functional registration at this point? I would really appreciate any help or direction. We've tried pretty much everything recommended to use so far, and we still cannot get the EPI registered to the T1.

I've attached two pictures: one trial using 6 degrees of freedom and another using 12. I was not able to attach all output images, due to a limit on message size.

Additional Info: 
First volume of functional scan (firstvol_stc_mc_reorient_fov_bet.nii) is 64x64x33
Anatomical (t1_reorient_fov_bet.nii) is 224x300x213

Thank you so much for your time!

Best, 
Yasmine Bassil



########################################################################

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1