runall_OS_X_motioncorrection_DICOM2ASCII_boundingbox.sh

#!/bin/sh

#  Script.sh
#
#
#  Created by Harri Merisaari on 3/10/14.
#
set +e
binaryname="python motioncorrection_1st_boundingbox.py"
binaryname2="python motioncorrection_3rd_DICOM2ASCII.py"
no_folders=$(ls -l -d ../PET_MR_dwis/* | grep '^d' | grep -v 'Carimas27' | grep -v 'ProjectTemplate' | awk '{print $9}' | wc -l)
folders=$(ls -l -d ../PET_MR_dwis/* | grep '^d' | grep -v 'Carimas27' | grep -v 'ProjectTemplate' | awk '{print $9}')
# start
echo $no_folders " folders to be processed"
let "round = 1"
for f in $folders
do
subject_id=$(echo $f | awk -F '/' '{print $3}')

#    subject_id=$(echo "10_moring_hB_1a")
#    f=$(echo "../PET_MR_dwis/10_moring_hB_1a")

xtermcmd=$(echo "$binaryname --dicomdir $f/DICOMconverted --subject $subject_id")
echo $xtermcmd
ret=$(eval $xtermcmd)
if [ "$?" -eq "0" ]
then
echo "SUCCESS"
else
echo "FAILURE"
fi
xtermcmd=$(echo "$binaryname2 --dicomdir $f/DICOMconverted --subject $subject_id")
echo $xtermcmd
ret=$(eval $xtermcmd)
if [ "$?" -eq "0" ]
then
echo "SUCCESS"
else
echo "FAILURE"
fi

let "round = $round + 1"

#    if [ "$round" -gt "3" ]
#    then
#        break
#    fi
done