Hi,
I'm not sure what these images would look like and so how difficult it
would be to improve BET. Ultimately the last resort is to manually edit
the image, which is relatively easy to do with FSLView.
As for the registration of the Angio to the T1w with an initialization - what
cost function did you use? It might be worth trying Mutual Info or
Normalised Mutual Info if you haven't already. When the images contain
quite different information this can definitely help. And use the -nosearch
option if you haven't done so already.
All the best,
Mark
On 17 Jan 2011, at 10:18, Renate Schweizer wrote:
> Dear Registration experts,
>
> I have a registration / brainstripping problem with a small volume, high-resolution, double-oblique oriented ToF-MRAngiography, which I want to register to a normally oriented T1-weighted whole brain data-set.
>
> Right now I do a flirt registration of the ToF-MRA to an EPI partialvolume (same orientation, same small volume coverage) which is registered to a "whole brain" EPI (same orientation, covering the whole brain) which is then registered to the normally oriented (ACPC) T1 weighted whole brain volume.
>
> I then take the concatenated transformation matrix from Angio -> partVol EPI -> whole brain EPI -> whole brain T1 to reorient the original angio-volume to the right position on the T1 weighted image. Because of the high spatial resolution of both the T1 and the angio, I do see registration errors. I therefore tried a final registration step in which I used the former transformation matrix as the initialization matrix for the registration of the ToF-MRA to T1, but this worsened the error.
>
> From my various attempts to find out the critical parameters, why this last step fails, I suspect that it is the small volume of the ToF-MRA in combination with the incomplete brain-extraction that excludes a precise registration . Applying bet small Z and -f 0.1 to the ToF-MRA removes the skull but not the CFS/meninges above the cortical surface.
>
> I' d appreciate any suggestions on further options in "bet" to possibly increase the efficiency of brainstripping the angio, or any ideas on alternative routes for registration.
>
> Thanks,
>
> Renate
>
> --
> Dr. Renate Schweizer,
> Biomedizinische NMR Forschungs GmbH am
> Max-Planck-Institut fuer biophysikalische Chemie
> Am Fassberg 11
> 37077 Goettingen
>
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