Yep - can I add to that that FSL doesn't use funused1 (which some software
uses as a scaling factor) - it doesn't use a scaling factor in the header
at all. Indeed, to be safe you should make sure that these operations are
being carried out in floating point.
Thanks.
On Wed, 14 Apr 2004, Christian F. Beckmann wrote:
> Johannes,
>
> if the original data is stored as integers you might want to use
> avwmaths_32R instead. All the avw tools write the output in the same
> format as the input, e.g. if the input is int the output will be, too.
> I suspect that this is what's causing the problems. Using the blah_32R
> version of the binary will enforce writing the output as 32 bit reals.
>
> hope this helps
> cheers
> christian
>
>
>
> On 14 Apr 2004, at 12:52, Johannes Klein wrote:
>
> > Hello everyone,
> > I'm having trouble with scaling some PET images. What I'm trying to do
> > is scale them to their respective overall mean so I can calculate a
> > template image for FLIRT registration.
> > I masked out all values <=0 with avwmaths -thr 0 and then calculated
> > the
> > mean of the remaining voxels with avwstats -M. Now, I'd like to divide
> > my data by that factor to achieve scaling to the mean. When I do the
> > avwmaths -div, the scaling factor (funused1?) is not adjusted, and the
> > effect is quite deleterious. I've made a picture and put it to
> > http://www.mpifnf.de/~johannes/snap_norm.gif
> > Is there a way to get around this issue? And what happens when I sum
> > the
> > mean-scaled images up, are the individual scaling factors respected?
> > I'd appreciate any comments.
> > Thanks
> > Johannes
> >
> --
> Christian F. Beckmann
> Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
>
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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