Hi guys,
if you are taking whole-head images with, for example, lots of neck, then
probably the easiest solution is to use the -c option to by default place
the centre of the initial mesh higher than it would be otherwise.
If neck (etc) is not the cause, but weird intensities in the histogram,
then using avwstats and avwmaths (to eg crop more high-end intensities)
can also be a good solution.
Thanks, Steve.
On Mon, 11 Aug 2003, Dr Krish Singh wrote:
> Hi there,
>
> I often have a similar problem using an earlier version of bet. I found that
> it could be simply fixed by applying a 3D bounding box mask which removes
> everything outside a rectangular box which encloses the brain.
>
> This of course requires some user-intervention, but for my particular
> application (visualisation in mri3dX) that isn't a big hassle.
>
> Of course, if you need to automatically skull-strip lots of volumes, without
> user-intervention, the bounding-box approach isn't helpful.
>
> All the best,
>
> Krish
>
>
> On 11/8/03 10:48 am, "Christopher Joseph Bailey" <[log in to unmask]> wrote:
>
> > Dear All,
> >
> > I and others using a 1.5T Siemens Vision scanner have found that with
> > our (common) MPR parameters the automatic brain extraction most often
> > fails. The symptom is without exception left over non-brain tissue just
> > anterior to the pons and inferior to the temporal cortices (will send
> > .gif if needed).
> >
> > I have found a work-around using a modified version of betpremask, after
> > which bet (-f 0.4) works fine.
> >
> > However, after reading the BET section in a MEDx manual, it strikes me
> > that the "cure" for my misbehaving bet could be the adjustement of the
> > initial brain/non-brain thresholding ("10% of the way between the 2% and
> > 98% histogram values").
> >
> > Is it possible that the centre of gravity of the tesselated sphere is
> > consistently misplaced because of gray level properties of our MPRs? If
> > so, would it be possible to add a parameter to the BET command line
> > specifying a different threshold/histogram parcellation?
> >
> > Best regards,
> >
> > Christopher Bailey
>
> --
> Dr K.D. Singh
> Senior Lecturer and Convenor of the Neuroimaging Research Group
> Neurosciences Research Institute
> Aston University, Birmingham B4 7ET, U.K.
> Tel/Fax: +44 (0)121 [359 3611 ext 5176/5190]/[333 4220]
> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
>
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
|