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L2_Gam_PPI.sh
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L2_Gam_PPI.sh
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#!/bin/bash
basedir=`pwd`
MAINDATADIR=${basedir}/data
MAINOUTPUTDIR=${basedir}/fsl
subj=$1
INPUT1=${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/tfMRI_GAMBLING_LR/L1_Gam_PPI.feat
INPUT2=${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/tfMRI_GAMBLING_RL/L1_Gam_PPI.feat
OUTPUT=${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/L2_Gam_PPI
# checking L2 output
NCOPES=7 #check last cope since they are done sequentially
if [ -e ${OUTPUT}.gfeat/cope${NCOPES}.feat/cluster_mask_zstat1.nii.gz ]; then
exit
else
rm -rf ${OUTPUT}.gfeat
fi
for run in LR RL; do
rm -rf ${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/tfMRI_GAMBLING_${run}/L1_Gam_PPI.feat/reg
mkdir -p ${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/tfMRI_GAMBLING_${run}/L1_Gam_PPI.feat/reg
ln -s $FSLDIR/etc/flirtsch/ident.mat ${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/tfMRI_GAMBLING_${run}/L1_Gam_PPI.feat/reg/example_func2standard.mat
ln -s $FSLDIR/etc/flirtsch/ident.mat ${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/tfMRI_GAMBLING_${run}/L1_Gam_PPI.feat/reg/standard2example_func.mat
ln -s $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz ${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/tfMRI_GAMBLING_${run}/L1_Gam_PPI.feat/reg/standard.nii.gz
done
#find and replace
ITEMPLATE=${basedir}/templates/L2_all_PPI.fsf
OTEMPLATE=${MAINOUTPUTDIR}/${subj}/MNINonLinear/Results/L2_Gam_PPI.fsf
sed -e 's@OUTPUT@'$OUTPUT'@g' \
-e 's@INPUT1@'$INPUT1'@g' \
-e 's@INPUT2@'$INPUT2'@g' \
<$ITEMPLATE> $OTEMPLATE
#runs feat on output template
feat $OTEMPLATE
for C in `seq $NCOPES`; do
rm -rf ${OUTPUT}.gfeat/cope${C}.feat/filtered_func_data.nii.gz
rm -rf ${OUTPUT}.gfeat/cope${C}.feat/var_filtered_func_data.nii.gz
done