Hi - a general comment is that we really don't recommend using
Windows for larger analyses - for one thing, Windows just doesn't
handle large RAM jobs well - I don't know if this is relevant to your
problem or not. Another general thing to check is that you have the
exact version of Cygwin described on the FSL installation page (as
the latest version of Cygwin is broken wrt TC/TK/TIX).
So - to answer your command-line queries:
1. If you are doing command-line processing then all stages of the
pre-stats need doing, does the FEAT GUI work for you? In which case I
would use that maybe. You can do intensity normalisation using "ip" -
though we generally recommend NOT doing intensity normalisation.
2. Same as above - and again this is an option to "ip".
3. Ditto!
Cheers, Steve.
On 26 Sep 2006, at 10:56, David Cousins wrote:
> Hi there
> I am running Melodic on resting state fMRI, in effect trying to
> replicate
> the DeLuca 2006 analysis
>
> Windows XP PC with Cygwin
> Melodic runs well from the command line but not from the GUI - it
> fails to
> make new folders etc (lots of disc space and numerous file
> locations tried)
>
> I was wondering how to set preferences in the command line so that
> i can
> run melodic from there. In particular
>
> 1. How do i request mean-based intensity normalisation in the prestats
> 2. How do i change the spatial smoothing of FWHM to 5mm
> 3. How do i set a high-pass filter cutoff of 250s
>
> Many thanks
> DC
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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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