Hi Erik-Jan
you're right, FEAT is an interface to many different command-line programs
that carry out the calculations. You can check in detail what (and how)
the feat interface calls by looking at the report.log file that is
generated within the filename.feat directory. These mainly are mcflirt,
betfunc and ip (for data pre-processing), film_gls (parameter estimation),
smoothest, contrast_mgr and cluster (for stats) and overlay, slicer &
tsplot (generating the plots).
When calling (most) of these command-line tools without any options you
will get more details on how to use them (some require --help to print the
usage information), e.g.
>/usr/fs3/beckmann % overlay
Usage: overlay <colour_type> <output_type> [-c] <bg> <bgmin> <bgmax> <s1>
<s1min> <s1max> [s2 s2min s2max] <output>
colour_type: 0=solid 1=transparent colours
output_type: 0=floating point (32 bit real) 1=integer (16 bit signed
integer)
-c : use checkerboard mask for overlay
<bgmin> <bgmax> can be replaced by -a for automatic estimation of bg
display range
hope this helps
Christian
Christian F. Beckmann
Address: 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 Mob: +44(0)7980 691852
On Fri, 21 Jun 2002, E.J.P. Vlieger wrote:
> Hi,
>
> Feat performs a lot of steps, not all of them are clear to me. It looks
> as if the steps are all carried out by separate commandline tools, and I
> would love to know exactely what these tools do and what the options for
> them are. For example, I would like the rendered image of the activated
> clusters to be placed onto another image.
>
> I was unable to find detailled documentation on the web-site, but of
> course I might have overlooked the proper location.
>
> Is anyone able to feed me some details?
>
> Thanks a lot,
> Erik-Jan Vlieger
>
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