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Subject:

Re: avwmaths precision problem

From:

Johannes Klein <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 14 Apr 2004 15:57:58 +0200

Content-Type:

text/plain

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text/plain (91 lines)

Hi Christian, hi Steven,
thanks for your replies. The 32R trick did it, but now I need to figure
out how to get it back to 16SI format (to make it compatible with some
software ;) ).
When I use avwmaths_16SI to convert my resulting data back, I get the
same loss of scaling. Is there a way to stretch the intensity range of
my 32 bit real image to the full 16 bit signed range? I don't care about
the absolute values in that case, so I'm not concerned about the scaling
factor.
Thanks again
Johannes


----- Original Message -----
From: Stephen Smith <[log in to unmask]>
Date: Wednesday, April 14, 2004 2:23 pm
Subject: Re: [FSL] avwmaths precision problem

> Yep - can I add to that that FSL doesn't use funused1 (which some
> softwareuses 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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