Hello Dave,
Well, that was such a simple thing to do, I'm sorry I did not think of it myself! The problem was that my "template" design file was not specifying the number of copes the lower-level feat directories would contain, and whether or not to use those copes in the analysis... It's detected automatically when you load the input feat directories in the GUI, but obviously not when you only specify the input directory within the fsf file...
Sorry for the trivial question... Hopefully it will benefit someone in the future!
All the best,
Stephane
--
Stephane Jacobs
Human Neuroimaging and Transcranial Stimulation Lab
36 Straub Hall, 1227 University of Oregon
Eugene, OR 97403 - USA
Email: [log in to unmask]
Tel: (1) 541-346-4184
On Wed, 3 Dec 2008 07:42:51 +0000, Dave Flitney <[log in to unmask]> wrote:
> Curious. Perhaps running through the gui is correcting some problem in your sed'd fsfs? Make copies of your fsf files and diff them against those the gui writes into your feat directories.. Hopefully there'll be a difference that will explain all.
>
> ------Original Message------
> From: Stephane Jacobs
> Sender: FSL - FMRIB's Software Library
> To: [log in to unmask]
> ReplyTo: FSL - FMRIB's Software Library
> Sent: 2 Dec 2008 18:59
> Subject: [FSL] batch scripting higher level analyses
>
> Dear FSL users,
>
> I've been trying to find previous reference to this problem in the archives
> but could not find anything relevant. I'm trying to run higher level
> analyses (across subjects) using batch scripts (either bash or perl), as
> I've successfully done for first-level analyses. Basically, the script edits
> a template design file using sed to generate an appropriate design file, and
> then calls the feat command ("feat design.fsf").
> The analysis starts as it should, but fails to launch the higher level
> stats. It completes without generating any error message, but no copeX.feat
> subdirectory is created, and no result is actually computed.
>
> When I call the same command from a terminal window, the same thing happens.
> When I actually open the FEAT GUI and load the same design file that the
> script uses, the analysis runs fine until the end and generates the expected
> copeX.feat subdirectories.
>
> Is there any reason why higher level analyses across subjects require more
> than calling "feat design.fsf" fom the command line or from a script? I'm
> probably missing something here...
>
> Any help will be very much appreciated!
>
> Thanks,
>
> Stephane
>
>
>
> Sent using BlackBerry® from Orange
>
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