Hi Pete,
I do not know what math is used to calculate the spatial smoothing
sigma for ip, but you can see what FSL calculates by trying a couple
of smoothing widths and then looking at the report.log...I have found
this identifies a constant relationship.
For example, in my analyses I see that 4mm smoothing involves -s
1.69851380042 , and 8mm smoothing involves 3.39702760085. This shows
that dividing the desired mm smoothiing by 2.355 gives you the sigma
FSL uses ...I am not sure whether any of the other variable
preprocessing parameters alters this number.
Dan
On 7/20/07, Steve Smith <[log in to unmask]> wrote:
> Hi - please see the usage description that you get when you type
> "ip". The -s flag is followed by the spatial sigma width - i.e.
> approx half of the FWHM. Hence you would want to specify 3 here to
> get 6mm FWHM.
>
> Cheers.
>
>
>
> On 19 Jul 2007, at 22:44, Peter Fried wrote:
>
> > Hi All,
> >
> > To perform gaussian spatial smoothing of 6mm FWHM in the command-
> > line, do
> > I simply run the command:
> >
> > ip <input> <output> -s 6
> >
> > Or do I need to calculate a different value for -s?
> >
> > Also is the threshold value arbitrary?
> >
> > Thanks.
> >
> > -Pete Fried
>
>
> ------------------------------------------------------------------------
> ---
> 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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