Hi - sounds odd - can you send the output from:
avwhd <input>
avwstats++ <input> -v -V -r -R -m -M
Cheers.
On 18 May 2007, at 21:36, Pat Vee wrote:
> Hi Steve,
>
> Thanks for the quick reply. One follow up question though... For
> avwstats, I'm still confused b/c my voxels are 2x2x2mm (confirmed
> by avwhd). Therefore, if I multiply that by the number of voxels,
> I shouldn't get a decimal. And, the number ( e.g., 13560.75) is
> much larger than my number of voxels (826) times the volume
> (8mm^3). Am I doing something wrong?
>
> Thanks,
> Pat
>
> On 5/18/07, Steve Smith <[log in to unmask]> wrote:Hi,
>
> On 18 May 2007, at 02:23, Pat Vee wrote:
>
> > Hi all,
> >
> > I'm trying to use avwstats to count the number of voxels and find
> > the mean
> > within a masked image. What I've done is created a binary mask,
> then
> > multiplied that by an image to only leave values in the non-masked
> > regions.
> >
> > So, to count voxels I'm typing:
> > avwstats <input> -V
> > It outputs 2 values; I understand that the 1st value is the number
> > of voxels
> > that are non-zero. I've been getting whole numbers for this on the
> > order of
> > hundreds (e.g., 826), which is what I expect. However, I don't
> > understand
> > what the 2nd value is. I've been getting numbers on the order of
> > thousands,
> > with decimals for this (e.g., 13560.75). Can someone explain what
> > this
> > number is?
>
> If you just type "avwstats" you get the usage;
> the second number is the volume, i.e. the first number X voxel volume.
>
> > To find the mean, I'm typing:
> > avwstats <input> -M
> > It outputs a value that I believe is the mean for all the non-zero
> > voxels.
> > However, I realized that it's possible that some of the volumes
> > will have
> > zero values within the non-masked regions. So, is there some way
> > to mask
> > regions so that the masked area is converted to NaNs - or some
> > other method
> > that would allow me to include zeros when calculating the mean?
>
> We don't use NaNs, This is easy in avwstats++ with the -k (masking)
> option.
>
> Cheers.
>
>
> ----------------------------------------------------------------------
> --
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR 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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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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