| T O P I C R E V I E W |
| smoski |
Posted - Sep 11 2013 : 4:02:54 PM
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 |
| 4 L A T E S T R E P L I E S (Newest First) |
| smoski |
Posted - Sep 11 2013 : 4:44:18 PM
Thanks for the help! |
| petty |
Posted - Sep 11 2013 : 4:44:00 PM
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 |
| petty |
Posted - Sep 11 2013 : 4:38:55 PM
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.
|
| syam.gadde |
Posted - Sep 11 2013 : 4:25:41 PM
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. |
