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
any suggestions are appreciated.
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