Hello,
If you remove the following lines from $FSLDIR/bin/fs_sub your script should be able to run:
if [ "X$FSLSUBALREADYRUN" = "Xtrue" ] ; then
METHOD=NONE
echo "Warning: job on queue attempted to submit parallel jobs - running jobs serially instead" >&2
fi
Kind Regards
Matthew
> We are having problems running a Feat analysis script since switching from a Linux based FSL network pipeline to a Mac computer based pipeline.
>
> We have 2 runs of an fmri task: fmr1 and fmri2 which we run separately in Feat as 1stlevel.fsf, and then combine in a fixed effects analysis using FFX.fsf.
>
> Below is the script that we previously used to ensure that the FFX analysis did not run until the two 1st level analyses had finished.
>
> We now get an error as follows, which then in the log results in a fatal error just after the feat analysis has deleted the first 4 volumes. The 1stlevel.fsf and FFX.fsf work fine when running them individually from the command line.
>
>>>>>>>>>>>
> Warning: job on queue attempted to submit parallel jobs - running jobs serially instead
> while executing
> "fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -init" -b 10 -N feat0_init -l logs "
> (procedure "fullFirstLevelAnalysis" line 146)
> invoked from within
> "fullFirstLevelAnalysis $session"
> invoked from within
> "if { $done_something == 0 } {
>
> if { ! $fmri(inmelodic) } {
> if { $fmri(level) == 1 } {
> for { set session 1 } { $session <= $fmri(multiple..."
> (file "/Users/student/fsl/bin/feat" line 389)
>>>>>>>>>>>>>>>
>
>
>
> In the script, $main_dir is the main directory path, $i refers to the subject number, and $j the scan number.
>
> How do we alternatively script this to ensure that the FFX analysis only runs once the 1st level analyses have finished?
> Thanks
> Tony
>
> --------
> Dr Tony Goldstone
> Computational, Cognitive and Clinical Neuroimaging laboratory
> Imperial College London, UK
>
> [log in to unmask]
>
> ---------------------------------------------
>
> for i in $main_dir; do
>
> for j in $main_dir/$i/????; do
> cd $j/func/fmri/fmri1;
>
> k1=`fsl_sub -q long.q feat 1stlevel.fsf`
>
> cd $main_dir/$i
>
> cd $j/func/fmri/fmri2;
>
> k2=`fsl_sub -q long.q feat 1stlevel.fsf`
>
> cd $main_dir/$i/$j/func/fmri
>
> fsl_sub -q long.q -j ${k1},${k2} feat FFX.fsf
>
> done
>
> cd $main_dir
>
> done
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