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 fischl@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

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