Dear FSL gurus,
I have a few quick questions about scripting with FSL, especially FEAT.
I (obviously) run the same first level analysis on multiple subjects.
The only difference across runs and subjects typically is functional
files input (and their name, of course) and EV files (each sub/run has a
different random order of the tasks).
It's simple enough to create one "master" .fsf file --typically from the
GUI, open it in some text editor and run a "replace" to change the
folder names, functional and anatomical data-in files and the regressor
file names. Functional files, though, have different number of TRs both
across runs of a single sub and across subjects.
Of course I can set the number in each .fsf file manually, for each
subject/run, what I'd like to know is if it is necessary to do this or
whether FEAT (NOT the GUI though, the command line) will verify the
number of TRs in each input-file as it starts-up runs or whether it will
"believe" the number of TRs specified in the .fsf file.
Following up on that, say that I do all of the above:
- create on e "master" .fsf file using the GUI with one of my subjects
- replace, in some text editor, filenames and # of TRs and create .fsf
files for all of the remaining subjects
is there any necessity of opening the file in the GUI and saving it from
there prior to submitting it via the command line (i.e. feat
Sub1_run1.fsf ), except for the fact that it will nicely help me detect
missing/incorrect files should there be any? (for example, do I need all
the additional files to be created beforehand?)
all the best
martin
"I've often seen a Cat without a Grin, but a Grin without a Cat! It's
the most curious thing I ever saw in all my Life!", thought Alice.
--------------------------------------------
Martin M. Monti, PhD
Princeton University
Department of Psychology
Green Hall 3-S-8
(609) 258-5679
www.webmartin.net
--------------------------------------------
|