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
_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
