Grrreat!
Thanks,
Hauke
On Tue, 2002-07-23 at 09:40, Stephen Smith wrote:
> Hi Hauke,
>
> To convert a cluster mask (eg cluster_mask_zstat1) into a binary mask for
> just one of the enclosed clusters (eg cluster number 4 as indexed in the
> HTML cluster table), do
>
> avwmaths cluster_mask_zstat1 -mul -1 -thr -4.5 -mul -1 \
> -thr 3.5 -bin cluster_5_mask_zstat1
>
> where the -4.5 and 3.5 are got from the cluster number
> ie -1*(n+0.5) and (n-0.5)
>
>
>
> to apply this to eg a cope image and get standard deviation in that mask
> avwmaths stats/cope1 -mas cluster_5_mask_zstat1 masked_cope1
> avwstats masked_cope1 -S
>
> ( you will need the latest version of avwstats - get the linux binary from
> http://www.fmrib.ox.ac.uk/~steve/ftp/avwstats )
>
>
>
> OR if you want to get the std of say the filtered 4D data you can do
> avwmaths filtered_func_data -mas cluster_5_mask_zstat1 masked_data
> avwmaths masked_data -Tstd masked_data_std
>
> this gives a 3D image of the temporal std; if you want the average over
> the masked area do
> avwstats masked_data_std -M
>
> Thanks, Steve.
>
>
>
> On Sat, 20 Jul 2002, Hauke Heekeren wrote:
>
> > standard deviation of the PE or Cope values within a given cluster per
> > TR.
> >
> > Thanks,
> >
> > Hauke
> >
> >
> > On Sat, 2002-07-20 at 06:34, Stephen Smith wrote:
> > > Hi - do you mean standard deviation of the PE or COPE values over the
> > > cluster, or some 3D/4D standard deviation of the original/filtered data?
> > >
> > > Thanks, Steve.
> > >
> > > On Fri, 19 Jul 2002, Hauke wrote:
> > >
> > > > I'd like to calculate the standard deviation across the voxels in a
> > > > cluster over time. Is there a flag to make avwmeants spit this out?
> > > >
> > > >
> > > > thanks,
> > > > h.
> > > >
> > >
> > > 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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