Hi Joana - You can try our in-house tool for within-subject registration, bbregister, with the --dti option.
a.y On Thu, 13 Oct 2011, Joana Braga Pereira wrote: > 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 Freesurfer@nmr.mgh.harvard.edu 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.
