Ah - I see. I am assuming that the registration has worked fine; check the
registration report linked to from the main FEAT web page report to check
that. What is going on is that the Renderhighres script only shows every
second slice in the gif, because normally you have so many slices in the
structural that the image gets annoyingly big otherwise! You can easily
change this:
edit fsl/bin/renderhighres
change the line that calls "slicer":
change the
-S 2
option to just
-A
I'm sure this will fix it for you.
Thanks, Steve.
On Fri, 6 Dec 2002, David Krauss wrote:
> Thanks for the quick response...
>
> 1) Both my functionals and structurals contain 12 slices in the same
> location and orientation. So, I am thinking it should be a pretty basic
> overlay of the functionals onto the structurals. The first-level FEAT
> report works out just fine. The output contains all 12 of my functional
> slices. However, when I try to use the renderhighres function, only 6
> slices are contained in the outputted Rendered_hr_thresh_zstat1.gif.
> Hopefully, this is enough info. Any suggestions?
>
> 2) Thanks...I'll give it a try.
>
>
> On Friday, December 6, 2002, at 10:22 AM, Stephen Smith wrote:
>
> > Hi.
> >
> > 1) is it the original functional or the structural that contains 12
> > slices
> > originally? I'm not quite clear what you are asking - a little more
> > details would probably be useful: the FEAT report shows activaiton
> > overlaid in lowres (original FMRI resolution) for a first-level
> > analysis;
> > the registration page shows various views of the registration results;
> > if
> > you use the Renderhighres function (a separate GUI from FEAT) then the
> > resulting images will either be in the space of the highres images or
> > standard space.
> >
> > 2) sure - you can change the orientation using avwswapdim. For example,
> > you could do
> >
> > avwswapdim inputimage x y -z outputimage
> > to get the slices in the reverse order, OR
> >
> > avwswapdim inputimage -x y -z outputimage
> > to achieve a rotation about the line from nose to the back of the
> > head...
> >
> > Thanks, Steve.
> >
> >
> > On Fri, 6 Dec 2002, David Krauss wrote:
> >
> >> 1) In FEAT, when rendering the activation maps onto the high res
> >> images, the output only contains 6 slices even though my slice
> >> prescriptions contained 12 slices. Are these slices just a random
> >> sampling of my slices, are they chosen somehow systematically, or am I
> >> just doing something wrong?
> >>
> >> 2) I have one subject whose brain I need to invert. Are there any good
> >> FSL tools to do this, and can I apply the same tool to my functional
> >> and hi-res images?
> >>
> >>
> >> David Krauss
> >> Graduate Student
> >> UCLA Department of Psychology
> >> [log in to unmask]
> >>
> >
> > Stephen M. Smith
> > Head of Image Analysis, FMRIB
> >
> > 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
Head of Image Analysis, FMRIB
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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