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 feat via GUI vs. command line		  New Topic  Reply to Topic
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smoski
New Member

16 Posts
Posted - Sep 11 2013 :  4:02:54 PM  Show Profile  Reply with Quote
I am running into a problem on a 2nd level FSL script. Subject-specific .fsf files are getting generated just fine based on a template.fsf. But when feat is run on the template, either in the script or from a command line, it is not completing correctly. No errors are shown in the log, but the copeX.gfeat directories are not generating. However, if I open the subject-specific .fsf file in the FEAT GUI and run it from there, it runs just fine. Any ideas of why it works from the GUI but not from the command line?

Thanks!

Basics of the script:

Output=${FSLDATADIR}/2ndLevel
TEMPLATE=${EXPERIMENT}/Scripts/MID/template_2nd.fsf
echo $Output

for i in $TEMPLATE; do
sed -e 's@OUTPUT@'$Output'@g'\
-e 's@RunFile_01@'$RunFile_01'@g'\
-e 's@RunFile_02@'$RunFile_02'@g'\
<$i> ${FSLDATADIR}/2nd_$1_$2.fsf
done

feat ${FSLDATADIR}/2nd_$1_$2.fsf
Edited by - smoski on Sep 11 2013 4:05:06 PM

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Sep 11 2013 :  4:25:41 PM  Show Profile  Reply with Quote
It's hard to tell without exactly seeing the .fsf file that failed. If you send the path to me separately, I can try to figure out what may have happened.
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petty
BIAC Staff

USA
453 Posts
Posted - Sep 11 2013 :  4:38:55 PM  Show Profile  Reply with Quote
In your particular case .. there's something missing from the template, but opening the fsf file and clicking "go" is adding it for you:

# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 4

# Use lower-level cope 1 for higher-level analysis
set fmri(copeinput.1) 1

# Use lower-level cope 2 for higher-level analysis
set fmri(copeinput.2) 1

# Use lower-level cope 3 for higher-level analysis
set fmri(copeinput.3) 1

# Use lower-level cope 4 for higher-level analysis
set fmri(copeinput.4) 1



In the template, you have:
set fmri(ncopeinputs) 0

Meaning run the stats on none of the copes.
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petty
BIAC Staff

USA
453 Posts
Posted - Sep 11 2013 :  4:44:00 PM  Show Profile  Reply with Quote
fyi: if you take the design.fsf from the one that worked through the gui and make that your template, you'll be good to go
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smoski
New Member

16 Posts
Posted - Sep 11 2013 :  4:44:18 PM  Show Profile  Reply with Quote
Thanks for the help!
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