that's right - that is often the fix for relatively bad results that can
sometimes occur when lots of neck is included (or you can use the new -c
option to tell BET where to centre the initial surface).
note, just in case: you should not be running anything (even BET) before
SIENA, because SIENA does that for you, but I guess you knew that already!
if you use SIENAX or the -m option with SIENA, then registration to
Talairach space gets carried out. if you don't have standard axial
orientation then it is probably worth increasing the registration search
space to the whole space to make this a little more robust; edit
fsl/bin/siena and find the two flirt lines after "Talairach space masking"
and for BOTH add the options at the end:
-searchrx -180 180 -searchry -180 180 -searchrz -180 180
feel free to email me directly a compressed example image and we can have
a quick play with BET.
Thanks, Steve.
On Thu, 23 Jan 2003, Hauke Heekeren wrote:
> Hey Isa,
> bet sometimes has trouble with images that include the neck and all
> sorts of other stuff,
> using avwroi might help:
>
> avwroi 3danat 3d_roi 0 170 0 256 75 160
> bet 3d_roi 3d_roi_brain
>
>
> cheers,
>
> h.
>
>
>
> On Thu, 2003-01-23 at 07:17, Isabell Wartenburger wrote:
>
> > dear fsl-experts,
> > using T1-weighted images i have severe problems in brain extraction
> > using SIENA (i.e. BET): the *brain*.imgs still contain the eye muscles
> > and also some muscles below the temporal poles. (changing the -f, -m
> > and -2 settings didn't help.)
> >
> > (1) what is the best way to "preprocess" the images in order to remove
> > the eye muscles etc. before starting BET/SIENA?
> >
> > (2) the images were recorded using a 1.5 t siemens vision scanner in
> > sagittal orientation (MPRage sequence, 1x1x1mm resolution). the aim
> > is to do a long term study on healthy subjects, would you suggest to
> > acquire the images in a different orientation?
> >
> > thank you very much in advance, isabell.
> >
> >
> > Isabell Wartenburger
> > Dept. of Neurology
> > Clinical Research Group
> > Charité, Humboldt-University
> > Schumannstr. 20/21
> > 10117 Berlin, Germany
> >
> > Phone: ++49-30-450 560 194
> > Fax: ++49-30-450 560 952
> > http://www.charite.de/ch/neuro/forschung/teams/klinisch/index.html
>
> --
> Hauke Heekeren <[log in to unmask]>
> Lab of Brain and Cognition
>
Stephen M. Smith MA DPhil CEng MIEE
Associate Director, FMRIB and Analysis Research Coordinator
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
|