Hi Joana, You should use the lowb volume as the moving volume for the registration and then apply the output registration matrix to your FA volume. You can also add the --o flag to your below command so that the resampled and registered volume gets written out at the end. You would want that and your template to be in alignment.
--Lilla On Fri, 14 Oct 2011, Joana Braga Pereira wrote: > Dear Bruce and Anastasia, > > Thanks for the quick reply! > > I tried the bbregister as you suggested but when i visualize the target and > dti image they don't look registered at all. > > This is the comand i used: > > bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg > /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out > /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx > > I tried to use the bbregister tools to align them but I didn't get very far... > > Did i miss something? > > I read in another mail something about using the register.dat created in > bbregister and do mri_label2vol but i'm not sure how to do it. > > Thanks, > > Joana > > > 2011/10/13 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Hi Joana, > > try bbregister. > > cheers > Bruce > 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 > > > > > 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
