The main problem with AVMs ist that the lesion itself is usually hypointense on T2*-BOLD-EPIs. Thus, it may eveade intensity-based maskings (such as in SPM, at least the old versions) but even BET when it is large and peripheral enough. Then it may look like that there is "no limit for the AVM" but if I get you right then you will already have excluded the malformation from the analysis. Which you certainly don't want to (even when considering the fact that the shunting inherent to an AVM calls the adequate oxygen supply by the AVM vessels themself massively into question, but that is another issue).
So if you don't want to switch off BET then I'd suggest to run it very liberal first, make the adjustments you need to the mask (using specific BET calls and fslmaths, for example) and then restart FEAT for the rest of the processing (i.e. split up FEAT into preproc, "manual "adjustments, rest of FEAT).
GHope that helps,
Andreas
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Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Matt Glasser [[log in to unmask]]
Gesendet: Freitag, 23. Oktober 2009 22:51
An: [log in to unmask]
Betreff: Re: [FSL] BET
You preserve the skull by not using BET, what specifically are you needing BET for if you want to keep the skull? Alternatively, if some parts of your processing stream require BETed images, you can BET the images and then apply whatever is generated (transform, bias field, etc) to the non-betted images to process them the same way.
Peace,
Matt.
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From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Ignacio Letelier
Sent: Friday, October 23, 2009 12:54 PM
To: [log in to unmask]
Subject: [FSL] BET
Hi
I am doing arterioveous malformation (AVM) studies, and I would like to know if there is some way to preserve the skull when doing BET, beacuase the options I have seen so far, erases the skull and makes seems like there was no limit for the (AVM) especially in axial views.
Thanks, best regards.
--
Ignacio Letelier Aguirre.
Estudiante Ingeniería Civil Biomédica
Universidad de Valparaíso, Viña del Mar.
Teléfono: 97139955
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