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MCA_Subj_Level_MemPrePro+Stats_FSL_oacI.sh
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MCA_Subj_Level_MemPrePro+Stats_FSL_oacI.sh
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#!/bin/bash
#ref: https://wiki.biac.duke.edu/biac:fsl:guide
######### run this preprocessing script from MCA_FMRI/Public/Data directory;
# Based on confounds data available, edits template MCA_Mem_firstleveldesign_template_mpCON_oacKV.fsf or MCA_Mem_firstleveldesign_template_NOmpCON_oacV.fsf from Data folder to do subject specific GLM design
#loads the fsl program
#export FSLDIR=/usr/local/packages/fsl
#.${FSLDIR}/etc/fslconf/fsl.sh
#DATADIR=/Volumes/cerebro/Studies/MCA_FMRI/Public/Data
DATADIR=$PWD
label=$(date +"%m%d%Y_%H%M%S") #suffixes the output directory with timestamp
########################################################################################################################################################################################################################
#makes the compounded GLM design first-level FEAT file
SUBJ=12 # (Next: 43-1-2, 34)
SES=1 # for trial runs or individual runs
# TASK=1 # for trial runs or individual runs
# for SUBJ in {107..111}
# do
# for SES in 1 2
# do
for TASK in 1 2 # Pain code separately written from Memory Preprocessing--see MCA_Subj_Level_PainPrePro+Stats_FSL_oacV.sh
do
if [ -f "${DATADIR}/MCA${SUBJ}_Ses${SES}/Mem${TASK}_func/MCA${SUBJ}_Ses${SES}_Mem${TASK}_corrected.nii.gz" ]; then
INPUT=${DATADIR}/MCA${SUBJ}_Ses${SES}/Mem${TASK}_func/MCA${SUBJ}_Ses${SES}_Mem${TASK}_corrected.nii.gz
NVOLS=$(fslnvols ${INPUT}) # updates fsf file with number of vols/timepoints for the fmri run in this session-task from FSLNVOLS fslutil command
ANAT=${DATADIR}/MCA${SUBJ}_Ses${SES}/T1/MCA${SUBJ}_T1_anat_brain.nii.gz
REGSTD=$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz
CON_MTX=${DATADIR}/MCA${SUBJ}_Ses${SES}/Mem${TASK}_func/MCA${SUBJ}_Ses${SES}_Mem${TASK}_mp-confoundsMtx.txt #confounds matrix from motion outliers
RK_EV=${DATADIR}/FSL_Mem/MCA${SUBJ}_Ses${SES}_Mem${TASK}_RorK_words_FSL.txt # "Remember/Know" words timing file
FGT_EV=${DATADIR}/FSL_Mem/MCA${SUBJ}_Ses${SES}_Mem${TASK}_SF_words.txt # "Forgot" words timing file
SHK_EV=${DATADIR}/FSL_Mem/MCA${SUBJ}_Ses${SES}_Mem${TASK}_shock_timings.txt # "Shock" words timing file
OUTPUTDIR=${DATADIR}/FSL_Mem/First_Level_Subj_Analyses/${SUBJ}-${SES}-m${TASK}_Pre_${label}
if [ -d "${DATADIR}/FSL_Mem/First_Level_Subj_Analyses/${SUBJ}-${SES}-m${TASK}_Pre_"*.feat ]; then #checks if the output directory already exists
echo "Memory Data MCA${SUBJ}_Ses${SES}_Mem${TASK} already processed. Skipping to next run..."
continue;
else
# moving txt files to the FSL_Mem directory for EV input to the fsf file
mv ${DATADIR}/Timing_Calculations/MCA${SUBJ}_Ses${SES}_Mem${TASK}_RorK_words_FSL.txt ${RK_EV}
mv ${DATADIR}/Timing_Calculations/MCA${SUBJ}_Ses${SES}_Mem${TASK}_SF_words.txt ${FGT_EV}
mv ${DATADIR}/Timing_Calculations/MCA${SUBJ}_Ses${SES}_Mem${TASK}_shock_timings.txt ${SHK_EV}
#replacing subject-specific task timing and motion parameters as EVs to the fsf file IF OUTLIERS WERE DETECTED
if [ -f "$CON_MTX" ]; then
echo "Found Motion Confounds Matrix for MCA${SUBJ}_Ses${SES}_Mem${TASK}"
for i in 'MCA_Mem_firstleveldesign_template_mpCON_oacV.fsf'; do # finds marker/flags in the template fsf
sed -e 's@OUTPUTDIR@'${OUTPUTDIR}'@g' \
-e 's@INPUT@'${INPUT}'@g' \
-e 's@NVOLS@'${NVOLS}'@g' \
-e 's@CON_MTX@'${CON_MTX}'@g' \
-e 's@ANAT@'${ANAT}'@g' \
-e 's@REGSTD@'${REGSTD}'@g' \
-e 's@RK_EV@'${RK_EV}'@g' \
-e 's@FGT_EV@'${FGT_EV}'@g' \
-e 's@SHK_EV@'${SHK_EV}'@g' <$i> ${DATADIR}/MCA${SUBJ}_Ses${SES}/Mem${TASK}_func/MCA${SUBJ}_${SES}_${TASK}_Mem_firstleveldesign.fsf
#runs the FSL analysis using the newly created fsf file
if [ -f "$RK_EV" ]; then #check interchangeably w FGT_EV and SHK_EV
echo "Running First Level Stats for MCA${SUBJ}_Ses${SES}_Mem${TASK} ..."
feat ${DATADIR}/MCA${SUBJ}_Ses${SES}/Mem${TASK}_func/MCA${SUBJ}_${SES}_${TASK}_Mem_firstleveldesign.fsf
else
echo "Timing file not avaliable for MCA${SUBJ}_Ses${SES}_Mem${TASK}"
fi
done
else
echo "No Outliers in MCA${SUBJ}_Ses${SES}_Mem${TASK}" # if needed, can change motion outlier threshold in fsl_motion_outliers script for desired metric values
for j in 'MCA_Mem_firstleveldesign_template_NOmpCON_oacV.fsf'; do # finds marker/flags in the template fsf
sed -e 's@OUTPUTDIR@'${OUTPUTDIR}'@g' \
-e 's@INPUT@'${INPUT}'@g' \
-e 's@NVOLS@'${NVOLS}'@g' \
-e 's@ANAT@'${ANAT}'@g' \
-e 's@REGSTD@'${REGSTD}'@g' \
-e 's@RK_EV@'${RK_EV}'@g' \
-e 's@FGT_EV@'${FGT_EV}'@g' \
-e 's@SHK_EV@'${SHK_EV}'@g' <$j> ${DATADIR}/MCA${SUBJ}_Ses${SES}/Mem${TASK}_func/MCA${SUBJ}_${SES}_${TASK}_Mem_firstleveldesign.fsf
#runs the FSL analysis using the updated fsf file
if [ -f "$RK_EV" ]; then #check interchangeably w FGT_EV and SHK_EV && [-f "$FGT_EV"] && [-f "$SHK_EV"]
echo "Running First Level Stats for MCA${SUBJ}_Ses${SES}_Mem${TASK} with NO MOTION CONFOUNDS"
feat ${DATADIR}/MCA${SUBJ}_Ses${SES}/Mem${TASK}_func/MCA${SUBJ}_${SES}_${TASK}_Mem_firstleveldesign.fsf
else
echo "Timing file not avaliable for MCA${SUBJ}_Ses${SES}_Mem${TASK}"
fi
done
fi
fi
else
echo "No Memory Data"
fi
done
# done
# done
echo All Runs Done