Dear Mark,
Thanks for responding!
> > However, registration-step (1) (EPI -> high res) fails. I am using a
> > Siemens Vision scanner, with an MPRAGE sequence, and use this to
> > register: flirt -in EPI -ref MPRAGE -omat epi2mprage.mat
> > It does produce a matrix without an error message, but the registration
> > is wrong. The two images are already in the same axial orientation.
> >
> > Can anyone give a hint why this would fail? Step (2) does work.
>
> Without seeing the images there is very little I can do to diagnose
> the problem.
I will make the images available to you:
http://www.vlieger.nl/fmrib/ (a slow download, I'm sorry).
mpr=3d image.
> Note that non-brain matter can and should be removed with BET prior to
> registration. Do you do this? If not, then see if this fixes the problem.
No, I did not remove the skull, as BET fails to do this correctly. What
happened is that a part of the eye-muscles was retained. If I asked bet to
remove more, gray matter got wiped out.. I thought I could "correct" this by
registering the 3d to the template with skull, but now I understand that the
epi-3d registration might fail as result of this.
I tried registering the epi with the 3d after "betting" them both, and that
works!
So one question remains: is is possible to improve the "bet-results"?
Thanks a lot,
Erik-Jan Vlieger
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