Many thanks Steve, I will certainly give it a try.
BTW: Is Jackie Chen's algorithm(method) available in any publications
already? Will the method be implemented in FSL or any other independent
programs?
Regards,
Wei Wen
----- Original Message -----
From: "Stephen Smith" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Friday, February 22, 2002 1:54 AM
Subject: Re: [FSL] BET and FAST
> Hi.
>
> On Thu, 21 Feb 2002, Wei Wen wrote:
>
> > Before using FAST to segment g/w matters, we need to use BET. The output
of
> > FAST is 3 segmented parts: gm, wm and csf. If we want to have an
accurate
> > estimation of csf (cortical csf), then output of BET must not introduce
> > loss/gain of csf. However, I have the impression that BET is a
> > pre-processing tool basically designed to remove non-brain tissues
(cortical
> > csf was not one of the major aims to be targeted as to be kept
accurately?).
> > This is fine with g/w segmentation (ventricle csf is fine too), but not
fine
> > if I wish to have an accurate csf estimation. Am I right on this about
BET?
>
> This is all correct, although the limitation is not so much with what the
> software is designed to find, as with the problem of separating CSF from
> other dark "tissues" such as skull, in T1-weighted imaging (which I assume
> you're talking about). If you use T2-weighted images then BET will tend to
> include cortical CSF in the "brain" and this will I guess be more useful
> to you.
>
> > The reason for me to consider getting a reliable csf volume is to have a
> > measure of atrophy: the ratio of total brain tissue against total csf.
>
> In this case, there is a better way of doing this anyway - use SIENAX
> (part of siena in FSL) - this normalises using the external surface of the
> skull and then finds the normalised (G&W) brain volume - so you don't need
> to worry about CSF at all.
>
> > One more thing: is there any way of extracting ventricular csf in order
to
> > get the measure of ventricle size and atrophy ratio please?
>
> This is something we've been doing more recently - Jackie Chen has a
> presenetation at ISMRM, partly on doing exactly that, using ventricular
> masks.
>
> Thanks, Steve.
>
> Stephen M. Smith
> Head of Image Analysis, FMRIB
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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