Hi - sure, this is quite straightforward. You're right to say that it's
quite inconvenient to attempt to work from the report.com to reproduce a
FEAT run. The easy thing to do, if there's things you want to change that
aren't available in the design.fsf, is to edit $FSLDIR/tcl/feat.tcl
instead. So just edit that, find the line that creates the mcflirt command
(easiest way: do a bottom-up search for "mcflirt"), and change any options
you want to in there.
Cheers, Steve.
On Sun, 14 Nov 2004, BettyAnn Chodkowski wrote:
> hello all,
>
> i am running FSL/FEAT v3.1 in an automated fashion. i created a
> "master" design.fsf file and change (via sed) the line defining
> feat_files(1) to point to the dataset d'jour. i now wish to set some
> options that are not available via the FEAT GUI. specifically, i'd like
> to enable the -mats option in MCFLIRT. i do not see a recognizable
> option in the design.fsf file to set. how can i set options that are
> not available from within the FEAT GUI (and not defined in design.fsf)?
>
> one idea is to work from the report.com file in the same manner i now
> use the design.fsf file. a significant drawback to using the report.com
> file is that i would have to duplicate the logic that FEAT does (such as
> create a .feat directory that is unique, etc). another idea is to alias
> the mcflirt command to include the -mats option. i prefer this idea to
> the previous idea. but is there a better way?
>
> any suggestions are appreciated.
> thanks,
> - bettyann
> _____________________________________
> BettyAnn Chodkowski F.M. Kirby Center
> e: [log in to unmask] Kennedy Krieger Institute
> v: 443.923.9524 707 N. Broadway
> f: 443.923.9279 Baltimore, MD, USA 21205
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
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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