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3_extractcortical_volumes.sh
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3_extractcortical_volumes.sh
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#!/bin/bash
#####
# 11/30/15
# Wrapper written by Julia Anglin ([email protected])
#
#
# Script assumes the following structure
# Project_parent_directory/
# -> inputs/ (nii files 1_enigma_runfreesurfer.sh script,
# not used here)
# -> outputs/
# -> subj01(freesurfer outputs)
# -> subj02
# ...
# -> enigma_wrapscripts/ (copied from elsewhere)
#
######
###############
# Setup directory where volumes are
enigmadir=$1
if [ -z ${enigmadir} ] || [ $# -gt 1 ] ; then
echo "One input directory must be specified"
echo "Usage is: ./2_extractcortical_volumes.sh <parent directory of project>"
exit
fi
if [ ! -e ${enigmadir} ]; then
echo "Input directory does not exist"
exit
fi
###############
# Extract volumes
mkdir ${enigmadir}/outputs/cortical
cd ${enigmadir}/outputs
echo ${PWD}
echo 'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > cortical/CorticalMeasuresENIGMA_ThickAvg.csv
echo 'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > cortical/CorticalMeasuresENIGMA_SurfAvg.csv
for subj_id in $(ls -d subj*); do #may need to change this so that it selects subjects with FS output
printf "%s," "${subj_id}" >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
printf "%s," "${subj_id}" >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
for side in lh.aparc.stats rh.aparc.stats; do
for x in bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula; do
printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $5}'` >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $3}'` >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
done
done
printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
echo "" >> cortical/CorticalMeasuresENIGMA_ThickAvg.csv
echo "" >> cortical/CorticalMeasuresENIGMA_SurfAvg.csv
done
###############
# Quality Checking Cortical Measures
###
# Perform outlier detection
cd ${enigmadir}/outputs/cortical
R --no-save --slave < ${enigmadir}/enigma_wrapscripts/R/outliers.R > outliers.log
####### Need to put more here about log file
###
# Internal Surface Method
# Create PNGs for QC
mkdir ${enigmadir}/outputs/cortical/QC
export mdir=${enigmadir}/enigma_wrapscripts/Matlab
export fsdir=${enigmadir}/outputs
export qcdir=${enigmadir}/outputs/cortical/QC
for x in `ls -d ${fsdir}/*subj*`
do
export sub=`basename ${x}`
echo ${sub}
matlab -nosplash < ${enigmadir}/enigma_wrapscripts/Matlab/create_pngs_cortical.m
done
# Create QC webpage
cd ${enigmadir}/outputs/cortical/QC
chmod 777 ${enigmadir}/enigma_wrapscripts/bash/make_cortical_ENIGMA_QC_webpage.sh
${enigmadir}/enigma_wrapscripts/bash/make_cortical_ENIGMA_QC_webpage.sh ${enigmadir}/outputs/cortical/QC
###
# External Surface Method
export SUBJECTS_DIR=${enigmadir}/outputs
mkdir ${enigmadir}/outputs/cortical/fsqc
cd ${enigmadir}/outputs/cortical/fsqc
source ${enigmadir}/enigma_wrapscripts/bash/fsqc.sh
###############
# Generate histogram plots
mkdir ${enigmadir}/outputs/cortical/figures
cp ${enigmadir}/outputs/cortical/CorticalMeasuresENIGMA_ThickAvg.csv ${enigmadir}/outputs/cortical/figures
cp ${enigmadir}/outputs/cortical/CorticalMeasuresENIGMA_SurfAvg.csv ${enigmadir}/outputs/cortical/figures
cd ${enigmadir}/outputs/cortical/figures
R --no-save --slave < ${enigmadir}/enigma_wrapscripts/R/ENIGMA_CortexROI_plots.R