Dear FreeSurfers,
I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out.
These are the steps that i carried out:
mri_convert subj_01/mri/brain.mgz brain.nii.gz
fslswapdim brain.nii.gz x z -y brain_swap.nii.gz
flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear
flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat
Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration.
Does anyone know a better way to do this?
Many thanks,
Joana