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Re: avwmaths precision problem

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

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 ```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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