ah - if you've got those coordinates out of fslview then you must have a
non-corner co-ordinate origin set in the image header; sorry, bet doesn't
use the origin, so none of the -c options should be close to zero (ie the
mm values should count from the corner of the image). Does that improve
things?
Cheers.
On Mon, 24 Jan 2005, Cornelius Werner wrote:
> Hi Steve,
>
> I tried that already - somehow "> bet input3d.nii.gz output_bet3d.nii.gz
> -c 0 -25 30" creates empty images (original structural *.nii.gz = 27MB,
> "betted" image = 70kB) ??
> Fiddling with the -f and -g parameters didn't work out so far. Spooky...
>
> Cheers,
> Cornelius
>
>
>
> Am Montag, den 24.01.2005, 10:29 +0000 schrieb Stephen Smith:
> > Hi Cornelius.
> >
> > The first thing to sort is the BETting of the structurals. If you have
> > lots of neck then you should be able to get a good BET output by using the
> > -c option - you can use fslview to get (in mm) a rough guess of the centre
> > of the brain for this option - and if you have a similar field of view for
> > all subjects may be able to use the same values for all subjects.
> >
> > Then you may find that the FLIRT registration works ok between the EPI and
> > the structurals - though if the orientation is basically the same you may
> > improve robustness by setting the search option in the FEAT GUI to "no
> > search" and mabe reducing the DoF.
> >
> > Cheers, Steve.
> >
> >
> > On Mon, 24 Jan 2005, Cornelius Werner wrote:
> >
> > > In a similar vein:
> > >
> > > I have structural T1 scans obtained in a sagittal orientation. After
> > > some work, I figured out how to reslice them (w/ medcon) so that they
> > > matched the image orientation of the EPI functional scans (axial) as
> > > shown by Fslview. I hope I did this one right!
> > >
> > > Still, I have huge difficulties in getting a proper registration! This
> > > partyl seems derive from the fact that we image quite a bit of skull and
> > > throat together with the brain, so BETting that off is difficult, to put
> > > it mildly. And then, MCFLIRT produces really weird results
> > > The anatomical scans don't land anywhere close to the EPIs... and
> > > they're wildly rotated, too!....Could that be because of the
> > > resclicing?!
> > >
> > > As I haven't figured out (yet) how to manually register data and apply
> > > those transforms to my Feat runs, I'm somewhat stuck. So far, I'm left
> > > with registering onto standard brains only, which is a pity, as I'd be
> > > interested in seeing some individual activity on individual anatomy.
> > >
> > > Any help??
> > >
> > > Thanks a million in advance!
> > >
> > > Cornelius
> > >
> > >
> > > Am Montag, den 24.01.2005, 11:02 +0100 schrieb Andreas Bartsch:
> > > > Hi,
> > > > in fact you can even acquire the data in other than the orthogonal angles. Note that axial, sagittal & coronar refer to the brain and the scanner uses his coordinates to define directions. FSL doesn't mind as long as you convert the data right. The choice will depend on the target you are after (i.e. acquiring axial data at a high in-plane resolution but with a huge interslice gap would be rather inappropriate for imaging the temporal lobe).
> > > > Cheers-
> > > > Andreas
> > > >
> > > > ________________________________
> > > >
> > > > Von: FSL - FMRIB's Software Library im Auftrag von R Huang
> > > > Gesendet: Mo 24.01.2005 10:43
> > > > An: [log in to unmask]
> > > > Betreff: [FSL] About T1-weighted anatomical scan
> > > >
> > > >
> > > >
> > > > Hello,
> > > >
> > > > For human brain, T1-weighted anatomical scan can be acquired in three
> > > > ways: Axial (Transversal), sagital and Coronal directions. Does anyone
> > > > know which direction is better choice for acquiring data from MR-scanner
> > > > and using FSL? And why?
> > > >
> > > > Thanks in advance
> > > >
> > > > rhuang
> > > >
> > >
> >
> > --
> > Stephen M. Smith DPhil
> > 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
> >
>
--
Stephen M. Smith DPhil
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
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