Hi! I am trying to use a bash script to run FEAT on some already preprocessed data. I am not sure if it is due to the script or due to the design template I made, I cannot get it up and running, and hope someone may help/guide my troubleshoot. Below is my script and the error message. If you believe it would be helpful to also check my design please let me know and I can find a way to send you.
Thanks!
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1. Here's my bash script:
TASK=MID
sub=$1
run=$2
ppi=$3 # 0 for activation, otherwise name of the roi
sm=$4
MAINOUTPUT=${maindir}/derivatives/fsl_task-${TASK}/sub-${sub}
mkdir -p $MAINOUTPUT
DATA=${maindir}/derivatives/preprocessed/sub-${sub}/functional/mid_run${run}/smoothed_spm8/swarf_4D.nii
EVDIR=${maindir}/derivatives/fsl_task-MID/EVfiles/sub-${sub}_task-${TASK}_run-${run}
if [ "$ppi" == "0" ]; then
TYPE=act
OUTPUT=${MAINOUTPUT}/L1_task-${TASK}_model-01_type-${TYPE}_run-0${run}_sm-${sm}
else
TYPE=ppi
OUTPUT=${MAINOUTPUT}/L1_task-${TASK}_model-01_type-${TYPE}_seed-${ppi}_run-0${run}_sm-${sm}
fi
# check for output and skip existing
if [ -e ${OUTPUT}.feat/cluster_mask_zstat1.nii.gz ]; then
exit
else
echo "missing: $OUTPUT " >> ${maindir}/re-runL1.log
rm -rf ${OUTPUT}.feat
fi
ITEMPLATE=${maindir}/derivatives/fsl_task-MID/templates/L1_task-MID_model-01_type-act.fsf
OTEMPLATE=${MAINOUTPUT}/L1_task-${TASK}_model-01_seed-${ppi}_run-0${run}_variant-${dtype}.fsf
if [ "$ppi" == "0" ]; then
sed -e 's@OUTPUT@'$OUTPUT'@g' \
-e 's@DATA@'$DATA'@g' \
-e 's@EVDIR@'$EVDIR'@g' \
-e 's@SMOOTH@'$sm'@g' \
<$ITEMPLATE> $OTEMPLATE
else
PHYS=${MAINOUTPUT}/ts_task-${TASK}_mask-${ppi}_run-0${run}.txt
MASK=${maindir}/derivatives/masks/${ppi}.nii
fslmeants -i $DATAPPI -o $PHYS -m $MASK
sed -e 's@OUTPUT@'$OUTPUT'@g' \
-e 's@DATA@'$DATA'@g' \
-e 's@EVDIR@'$EVDIR'@g' \
-e 's@PHYS@'$PHYS'@g' \
-e 's@SMOOTH@'$sm'@g' \
<$ITEMPLATE> $OTEMPLATE
fi
# runs feat on output template
feat $OTEMPLATE
# fix registration as per NeuroStars post:
# https://neurostars.org/t/performing-full-glm-analysis-with-fsl-on-the-bold-images-preprocessed-by-fmriprep-without-re-registering-the-data-to-the-mni-space/784/3
mkdir -p ${OUTPUT}.feat/reg
ln -s $FSLDIR/etc/flirtsch/ident.mat ${OUTPUT}.feat/reg/example_func2standard.mat
ln -s $FSLDIR/etc/flirtsch/ident.mat ${OUTPUT}.feat/reg/standard2example_func.mat
ln -s ${OUTPUT}.feat/mean_func.nii.gz ${OUTPUT}.feat/reg/standard.nii.gz
# delete unused files
rm -rf ${OUTPUT}.feat/stats/res4d.nii.gz
rm -rf ${OUTPUT}.feat/stats/corrections.nii.gz
rm -rf ${OUTPUT}.feat/stats/threshac1.nii.gz
if [ ! "$ppi" == "0" ]; then
rm -rf ${OUTPUT}.feat/filtered_func_data.nii.gz
fi
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2. Here's the error message:
child process exited abnormally
while executing
"fsl:exec "${FSLDIR}/bin/feat_model design" $fmri(featModelOpts) -N feat0_model -l logs "
(procedure "firstLevelMaster" line 43)
invoked from within
"firstLevelMaster $session"
invoked from within
"if { $done_something == 0 } {
if { ! $fmri(inmelodic) } {
if { $fmri(level) == 1 } {
for { set session 1 } { $session <= $fmri(mult..."
(file "/usr/lib/fsl/5.0/feat" line 387)
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