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Hi, Andreas! Thank you very much for your prompt response! I tried doing as you suggested (to coregister the B0 image to the T2), but the output is still problematic. The link below give access to three files: 1) The B0 image; 2) The T2 image; 3) The output of the following: flirt -in B0.nii.gz -ref T2.nii -out B0coreg.nii -omat invol2refvol.mat -dof 6 (Coregistration of B0 image to the T2). https://drive.google.com/open?id=0B-D-mq6qMD2Afk14MHh5alRfYXh3YzIyVEJFSDZvLVBJUUxDUWhHVUVVSFQxeVNWSEx5WFE&authuser=0 Is there is anything I am doing wrong? 2015-06-29 2:40 GMT-03:00 Andreas Bartsch <[log in to unmask]>: > 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 > -- Raphael F. Casseb Medical Physicist, Ph.D. Student Medical Physics Lab - State University of Campinas Contact: +55 19 3521-8246