Dear Jean-Sebastien,
It is difficult to know might be going wrong without knowing more.
A complete failure, with very wrong orientation, is not uncommon when things
go wrong. However, something with the right "orientation" but poor registration
is really no better and you should not use either.
It is probably best to use the brain extracted version if you have this and the
brain extraction is good. In that case I would try the following options with FLIRT
(in various combinations):
-usesqform
-nosearch (you may already by using this)
-cost mutualinfo
If none of these (or combinations of these) help then let us know.
All the best,
Mark
On 2 Apr 2012, at 17:38, Jean-Sebastien Provost wrote:
> Dear FSL experts,
>
> Like many, I'm trying to register into the standard space scans with extensive lesions. So far, I have followed the instructions that was previous given in another email, and they have been working well. Basically, I have created a mask by manually drawing a ROI over the stroke area, inverted the mask with the following command "fslmaths originalmask -mul -1 -add 1 -thr 0.5 -bin invertedmask", and registered using FLIRT and putting my inverted mask into the weighting option as an input.
>
> Like I said, it has been working well for 2 subjects, but didn't for 2 others. In the latter case, when I look at the data in FSLview, the image is no longer aligned: it has suffered a severe rotation making the axial view now the coronal view with a 90 degree rotation, and so on for the other views.
> Now, I also tried to do the registration with a betted anatomical scan. Here the orientation is fine, but the registration itself doesn't look good.
>
> Any suggestions would be useful.
>
> Thank you in advance,
> Kindest regards,
>
> Jean-Sebastien
>
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