Thanks, will see if I can do any better by varying -c and if not I guess
it's back to drawing masks on images... (at least it will be less tedious
than creating the hippocampal masks was)
Fortunately BET worked well for the majority so it's only 20 or so scans I
will need to manually process...
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Matt Glasser
Sent: 23 March 2010 05:01
To: [log in to unmask]
Subject: Re: [FSL] BET in infants
Perhaps its estimation is not optimal for your brains and you can do better.
You might attempt some sort of registration with the skull on to get all the
brains oriented the same way and in about the same coordinate space prior to
BET. You could pick a random subject, register all of your others to that
one, average all the images to make a rough template and then reregister all
of your images to that template. You could then figure out what setting of
-c gives you optimal results and then run the same setting on all your
subjects (the point of all this is to avoid having to manually set -c
independently for every subject, something that I have found to be very
annoying ;)). If you aren't scripting all this, then making this rough
template might be more trouble than it is worth and you might as well set -c
manually.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Xue, Feng
Sent: Monday, March 22, 2010 11:53 PM
To: [log in to unmask]
Subject: Re: [FSL] BET in infants
Hi Matt,
Should -R do that automatically?
On Tue, Mar 23, 2010 at 11:39 AM, Matt Glasser <[log in to unmask]> wrote:
> Moving the center of the initial sphere ( -c X Y Z ) closer to the front
of
> the brain might help.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Xue, Feng
> Sent: Monday, March 22, 2010 10:32 PM
> To: [log in to unmask]
> Subject: Re: [FSL] BET in infants
>
> Hi,
>
> Many be you could try draw a mask on the T1 image in fslview then mask
> out those regions. But this may means a lot of labor as I did before:(
> I wonder if anyone have other good idea?
>
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