Hello,
I have been having a lot of trouble running my preprocessing script for my resting state data. Everything I try to run my script I get the error message:
ach-dipc-4b290a-15:PS14 alinabenischek$ ./ROI_scriptingPreprocessing_newrevised.sh
/Users/alinabenischek/.fslconf/fsl.sh: line 3: setenv: command not found
The path of where I have saved my fsl.sh file : /usr/local/fsl/etc/fslconf/fsl.sh
I have tried adding-- FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
, reinstalling FSL, and setting other environmental variables to the fsl.sh script that would not work because I do not have access.
Thank you for your help! I really appreciate it!
My script for reference:
#!/bin/bash
#loads the fsl program
export FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
FILE_NAME=/Users/alinabenischek/Documents/PS14/fMRI_test.txt
SUB="`sed 'n' fMRI_test.txt`"
SUB=$1
RESTDATAA=/Users/alinabenischek/Documents/PS14/OriginalData/${SUB}/rest
HIGHRESDATAA=/Users/alinabenischek/Documents/PS14/OriginalData/${SUB}/3DT1_brain
LOWRESDATAA=/Users/alinabenischek/Documents/PS14/OriginalData/${SUB}/T2_brain
OUTPUTDIRR=/Users/alinabenischek/Documents/PS14/AnalyzedData/${SUB}
TEMPLATEDIRR=/Users/alinabenischek/Documents/PS14/
cd $TEMPLATEDIRR
for i in 'First_Level_FEAT_Preprocessing_Template.fsf'; do
sed -e 's@OUTPUTDIR@'$OUTPUTDIRR'@g' \
echo hello
-e 's@HIGHRESDATA@'$HIGHRESDATAA'@g' \
-e 's@LOWRESDATA@'$LOWRESDATAA'@g' \
-e 's@FSLDIR@'$FSLDIRR'@g' \
-e 's@RESTDATA@'$RESTDATAA'@g' <$i> ${OUTPUTDIRR}/${SUB}FEAT_Preprocessing.fsf
done
# Run feat analysis:
feat ${OUTPUTDIR}/${SUBJ}FEAT_Preprocessing.fsf
# -- END USER SCRIPT -- #
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