You can use fslmaths -bin on the edited image.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Jeremy Young
Sent: Wednesday, July 01, 2009 4:49 PM
To: [log in to unmask]
Subject: Re: [FSL] fiducial marker showing up after bet with dti
Hello all,
Also after manually removing the remaining part of the fiducial
marker, is there a way of regenerating the brain mask from the
current edit?
I've tried to regenerate it by using bet on the edited volume with
low thresholds, but I can't seem to find a threshold value that
perfectly regenerates the brain mask minus the edits.
Thanks!
Jeremy
On Jul 1, 2009, at 11:05 AM, Jeremy Young wrote:
> Hi all,
>
> We use a fiducial marker, a beekley spot (vitamin e capsule), to
> mark the right side of our subjects. In our re-oriented and eddy
> corrected 1st b0 volume of our diffusion acquisition, after using
> bet, the capsule is still present.
>
> It may be because for bet to not extract the whole brain, I use a
> threshold of .14 with a -g of .29. Has anyone else encountered
> this? Is it ok for the fiducial marker to show up? I'm assuming
> that it's not. If that is the case, is there an elegant way to
> remove this fiducial marker or should I manually edit it out of all
> of my slices?
>
> Thanks!
> Jeremy
>
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