Hi,

try the other way around, i.e. registering the lower-resolution B0 to the higher resolution T2 image.

This >may< work if your B0 image is distortion corrected or has low distortions (e.g., by segmented EPI aquisitions / RESOLVE).

If your B0 has lots of distortions you may try FNIRT but your chances are low to get a good registration.

Cheers,

Andreas

Von: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "Raphael F.C." <[log in to unmask]>
Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
Datum: Montag, 29. Juni 2015 05:15
An: <[log in to unmask]>
Betreff: [FSL] Issue with coregistration of spinal cord images

Dear all,

I am trying to corregister the B0 image from a spinal cord DTI with a T2 structural image.

I first tried using the following code:
    flirt -in T2.nii -ref B0.nii.gz -out T2correg.nii -omat invol2refvol.mat -dof 6
But the output image was a weird pyramid in the corner of the volume.

Then I tried including the cost function, because maybe the weight could enhance the result:

    flirt -in T2.nii -ref B0.nii.gz -out T2correg.nii -omat invol2refvol.mat -dof 6
But I got just one peace of the image as the output.

I am sorry for such a basic issue, but are the codelines above ok? Is there any limitation which would forbid to use flirt with non-brain images?

Any lights on how to make it work? I would appreciate very much any help.

Thank you very much,

--

Raphael F. Casseb

Medical Physicist, Ph.D. Student 

Medical Physics Lab - State University of Campinas

Contact: +55 19 3521-8246