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KUL_dcm2bids.sh
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KUL_dcm2bids.sh
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#!/bin/bash
# set -x
# Bash shell script to convert dicoms to bids format
#
# Requires dcm2bids, dcm2niix, Mrtrix3
#
# @ Stefan Sunaert - UZ/KUL - [email protected]
# @ Ahmed Radwan - KUL - [email protected]
#
version="v0.9 - dd 29/11/2021"
# Notes
# - NOW USES https://github.com/UNFmontreal/Dcm2Bids
# - works for GE/Siemens/Philips
# - wrap around for multiple subjects: use KUL_multisubjects_dcm2bids
export LANG=us.UTF-8
# ----------------------------------- MAIN ---------------------------------------------
# this script defines a few functions:
# - Usage (for information to the novice user)
# - kul_e2cl from KUL_main_functions (for logging)
# - kul_dcmtags (for reading specific parameters from dicom header)
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir is made in main_functions
# BEGIN LOCAL FUNCTIONS --------------
# --- function Usage ---
function Usage {
cat <<USAGE
`basename $0` converts dicoms to bids format
Usage:
`basename $0` -d dicom_dir -p subject (participant) -c config_file -o bids_dir <OPT_ARGS>
Depends on a config file that defines parameters with sequence information, e.g.
For Philips dicom we need to manually specify the mb and pe_dir:
# Identifier,search-string,fmritask/inteded_for,mb,pe_dir,acq_label
# Structural scans
T1w,T1_PRE
cT1w,T1_Post
FLAIR,3D_FLAIR
T2w,3D_T2
SWI,SWI
MTI,mtc_2dyn
# functional scans
func,rsfMRI_MB6,rest,6,j,singleTE
sbref,rsfMRI_SBREF,rest,1,j,singleTE
func,MB_mTE,rest,4,j,multiTE
sbref,mTE_SBREF,rest,4,j,multiTE
func,MB2_hand,HAND,2,j
func,MB2_lip,LIP,2,j
func,MB2_nback,nback,2,j
sbref,MB2_SBREF,HAND nback,1,j
# fmap: 'task' is now 'IntendedFor' (the func images/tasks that the B0_map is used for SDC)
fmap,B0_map,[HAND LIP nback]
# dMRI
dwi,p1_b1200,-,3,j-,b1200
dwi,p2_b0,-,3,j-,b0
dwi,p3_b2500,-,3,j-,b2500
dwi,p4_b2500,-,3,j,rev
# ASL support is very limited (not BIDS compliant for now)
# Indentifier, search-string
ASL,pCASL
explains that the T1w scan should be found by the search string "T1_PRE"
func by rsfMRI, and has multiband_factor 6, and pe_dir = j
the sbref will be used for the tb_fMRI for both tasks (hands and nback)
For Siemens and GE dicom it can be as simple as:
# Identifier,search-string,fmritask/inteded_for,mb,pe_dir,acq_label
# Structural scans
T1w,T1_PRE
cT1w,T1_Post
FLAIR,3D_FLAIR
T2w,3D_T2
# functional scans
func,rsfMRI_MB6,rest,-,-,singleTE
sbref,rsfMRI_SBREF,rest,-,-,singleTE
func,MB_mTE,rest,-,-,multiTE
sbref,mTE_SBREF,rest,-,-,multiTE
func,MB2_hand,HAND,-,-
func,MB2_lip,LIP,-,-
func,MB2_nback,nback,-,-
sbref,MB2_SBREF,HAND nback,-,-
# dMRI
dwi,p1_b1200,-,-,-,b1200
dwi,p2_b0,-,-,-,b0
dwi,p3_b2500,-,-,-,b2500
dwi,p4_b2500,-,-,-,rev
# fmap, SWI, MTC and ASL have not been tested on Siemens or GE
Example:
`basename $0` -p pat001 -d pat001.zip -c definitions_of_sequences.txt -o BIDS
Required arguments:
-d: dicom_zip_file (the zip or tar.gz containing all your dicoms, or directory containing dicoms)
-p: participant (anonymised name of the subject in bids convention)
-c: definitions of sequences (T1w=MPRAGE,dwi=seq, etc..., see above)
Optional arguments:
-o: bids directory
-s: session (for longitudinal study with multiple timepoints)
-t: temporary directory (default = /tmp)
-e: copy task-*_events.tsv from config to BIDS dir
-a: further anonymise the subject by using pydeface (takes much longer)
-v: verbose
USAGE
exit 1
}
# check if jsontool is installed and install it if not
if [[ $(which jsontool) ]]; then
echo " jsontool already installed, good" $log
else
echo " jsontool not installed, installing it with pip using pip install jsontool" $log
pip install jsontool
fi
# check if pydeface is installed and install it if not
if [[ $(which pydeface) ]]; then
echo " pydeface already installed, good" $log
else
echo " pydeface not installed, installing it with pip using pip install jsontool" $log
pip install pydeface
fi
# check if the correct dcm2bids is installed and install it if not
if [[ $(which dcm2bids_scaffold) ]]; then
echo " dcm2bids already installed, good" $log
else
echo " dcm2bids not installed, installing it with pip using pip install dcm2bids" $log
pip uninstall Dcm2Bids
pip install dcm2bids
fi
# check if jq is installed and install it if not
if [[ $(which jq) ]]; then
echo " jq already installed, good" $log
else
echo " jq not installed, installing it with your help..." $log
sudo apt install jq
fi
# --- function kul_dcmtags (for reading specific parameters from dicom header & calculating missing BIDS parameters) ---
function kul_dcmtags {
local dcm_file=$1
local out=$final_dcm_tags_file
# 0/ Read out standard tags for logging
local seriesdescr=$(dcminfo "$dcm_file" -tag 0008 103E | cut -c 13-)
local manufacturer=$(dcminfo "$dcm_file" -tag 0008 0070 | cut -c 13-)
local software=$(dcminfo "$dcm_file" -tag 0018 1020 | cut -c 13-)
local imagetype=$(dcminfo "$dcm_file" -tag 0008 0008 2>/dev/null | cut -c 13- | head -n 1)
local patid=$(dcminfo "$dcm_file" -tag 0010 0020 | cut -c 13-)
local pixelspacing=$(dcminfo "$dcm_file" -tag 0028 0030 2>/dev/null | cut -c 13- | head -n 1)
local slicethickness=$(dcminfo "$dcm_file" -tag 0018 0088 2>/dev/null | cut -c 13- | head -n 1)
local acquisitionMatrix=$(dcminfo "$dcm_file" -tag 0018 1310 2>/dev/null | cut -c 13- | head -n 1)
local FovAP=$(dcminfo "$dcm_file" -tag 2005 1074 | cut -c 13-)
local FovFH=$(dcminfo "$dcm_file" -tag 2005 1075 | cut -c 13-)
local FovRL=$(dcminfo "$dcm_file" -tag 2005 1076 | cut -c 13-)
# local echonumber=$(dcminfo "$dcm_file" -tag 0018 0086 2>/dev/null | cut -c 13- | head -n 1)
# need to add local echonumber or something similar for mTE (0018,0086)
# Now we need to determine what vendor it is.
# Philips needs all the following calculations
# Siemens works out of the box
# GE most recent version also seem to work fine
#echo $manufacturer
if [ "$manufacturer" = "SIEMENS" ]; then
slicetime_provided_by_vendor=1
ees_trt_provided_by_vendor=1
#elif [ "$manufacturer" = 'GE ]
# need to be tested
else
slicetime_provided_by_vendor=0
ees_trt_provided_by_vendor=0
fi
# 1/ Calculate ess/trt; needed are : FieldStrength, WaterFatShift, EPIFactor
# Note: only calculate it when it is provided (sometimes this has been thrown away by anonymising the dicom-data)
# We check whether needed tags exist
tags_are_present=1
test_waterfatshift=$(dcminfo "$dcm_file" -tag 2001 1022)
if [ -z "$test_waterfatshift" ]; then
tags_are_present=0
local waterfatshift="empty"
else
local waterfatshift=$(dcminfo "$dcm_file" -tag 2001 1022 | awk '{print $(NF)}')
fi
test_fieldstrength=$(dcminfo "$dcm_file" -tag 0018 0087)
if [ -z "$test_fieldstrength" ]; then
tags_are_present=0
local fieldstrength="empty"
else
local fieldstrength=$(dcminfo "$dcm_file" -tag 0018 0087 | awk '{print $(NF)}')
fi
test_epifactor=$(dcminfo "$dcm_file" -tag 2001 1013)
if [ -z "$test_epifactor" ]; then
tags_are_present=0
local epifactor="empty"
else
local epifactor=$(dcminfo "$dcm_file" -tag 2001 1013 | awk '{print $(NF)}')
fi
if [ $tags_are_present -eq 0 ]; then
ees_sec="empty"
trt_sec="empty"
else
local water_fat_diff_ppm=3.3995
local resonance_freq_mhz_tesla=42.576
local water_fat_shift_hz=$(echo $fieldstrength $water_fat_diff_ppm $resonance_freq_mhz_tesla echo $fieldstrength $water_fat_diff_ppm | awk '{print $1 * $2 * $3}')
#effective_echo_spacing_msec = 1000 * WFS_PIXEL/(water_fat_shift_hz * (EPI_FACTOR + 1))
ees_sec=$(echo $waterfatshift $water_fat_shift_hz $epifactor | awk '{print $1 / ($2 * ($3 + 1))}')
#total_readout_time_fsl_msec = EPI_FACTOR * effective_echo_spacing_msec;
trt_sec=$(echo $epifactor $ees_sec | awk '{print $1 * $2 }')
fi
# 2/ Calculate slice SliceTiming
#function SliceTime=KUL_slicetiming(MB, NS, TR)
#%MB = 1; % Multiband factor
#%NS = 30; % Number of Slices
#%TR = 1.7; % TR in seconds
#st = repmat(0:TR/(NS/MB):TR-.0000001,1,MB);
#SliceTime = sprintf('%.8f,' , st);
#SliceTime = ['"SliceTiming": [' SliceTime(1:end-1) ']'];
#end
multiband_factor=$mb
# if mb is not found in the config file or is set to 0
# simply set it to 1 and run
if [[ -z ${multiband_factor} ]] || [[ ${multiband_factor} == 0 ]]; then
multiband_factor=1
fi
tags_are_present=1
test_number_of_slices=$(dcminfo "$dcm_file" -tag 2001 1018)
if [ -z "$test_number_of_slices" ]; then
tags_are_present=0
local number_of_slices="empty"
else
local number_of_slices=$(dcminfo "$dcm_file" -tag 2001 1018 | awk '{print $(NF)}')
fi
test_repetion_time_msec=$(dcminfo "$dcm_file" -tag 0018 0080 )
if [ -z "$test_repetion_time_msec" ]; then
tags_are_present=0
local repetion_time_msec="empty"
else
local repetion_time_msec=$(dcminfo "$dcm_file" -tag 0018 0080 | awk '{print $(NF)}')
fi
test_slice_scan_order=$(dcminfo "$dcm_file" -tag 2005 1081 )
if [ -z "$test_slice_scan_order" ]; then
#tags_are_present=0
local slice_scan_order="empty"
else
local slice_scan_order=$(dcminfo "$dcm_file" -tag 2005 1081 | head -n 1 | awk '{print $(NF)}')
fi
if [ $tags_are_present -eq 1 ]; then
if [ ! $multiband_factor = "" ];then
#single_slice_time (in seconds)
local single_slice_time=$(echo $repetion_time_msec $number_of_slices $multiband_factor | awk '{print $1 / ($2 / $3) / 1000}')
# clear variables
unset slit
unset slit1
unset slit2
# number of excitations given multiband
# e = n. of excitations/slices per band
local e=$(echo $number_of_slices $multiband_factor | awk '{print ($1 / $2) -1 }')
local spb=$((${e}+1));
#echo $e
#echo $spb
#echo "${slice_scan_order}"
# here we need to adapt to account for different slice orders
# e.g.
if [[ "${slice_scan_order}" == "rev. central" ]]; then
# this is a bit different from interleaved... namely we split it into 2 gps
# lower group is regular ascending and second group is regular descending
half_e=$(echo "scale=2;(${spb}/2)" | bc | awk '{print int($1+0.5)}')
for (( zc=0; zc<${half_e}; zc++ )); do
sl1=$(echo $zc $single_slice_time | awk '{print $1 * $2}')
if [[ -z ${slit1} ]]; then
slit1="${sl1}"
else
slit1="${slit1}, ${sl1}"
fi
done
for (( zx=${e}; zx>=${half_e}; zx-- )); do
sl2=$(echo $zx $single_slice_time | awk '{print $1 * $2}')
if [[ -z ${slit2} ]]; then
slit2="${sl2}"
else
slit2="${slit2}, ${sl2}"
fi
done
slit="${slit1}, ${slit2}"
echo "${slit}"
for iz in ${!tmp_order[@]}; do
sl=$(echo $((${tmp_order[$iz]})) ${single_slice_time} | awk '{print $1 * $2}');
echo ${sl}
if [[ -z ${slit} ]]; then
slit="${sl}"
echo ${slit}
else
slit="${slit}, ${sl}"
echo ${slit}
fi
done
# interleaved is ready!
elif [[ "${slice_scan_order}" == "interleaved" ]]; then
declare -a tmp_order
step=$(echo "sqrt(${spb})" | bc)
unset tmp_order curr bh ik slgp;
slgp=0;
declare -a tmp_order;
tmp_order[0]=0;
for ik in $(seq 1 ${e}); do
bh=$((${ik}-1));
curr=$((${tmp_order[$bh]}+${step}));
if [[ ${curr} -gt ${e} ]]; then
((slgp++));
curr=${slgp};
fi;
tmp_order[$ik]=${curr};
done;
for iz in ${!tmp_order[@]}; do
sl=$(echo $((${tmp_order[$iz]})) ${single_slice_time} | awk '{print $1 * $2}');
echo ${sl}
if [[ -z ${slit} ]]; then
slit="${sl}"
echo ${slit}
else
slit="${slit}, ${sl}"
echo ${slit}
fi
done
elif [[ "${slice_scan_order}" == "FH" ]]; then
for (( c=0; c<=$e; c++ )); do
sl=$(echo $c $single_slice_time | awk '{print $1 * $2}')
if [[ -z ${slit} ]]; then
slit="${sl}"
else
slit="${slit}, ${sl}"
fi
done
elif [[ "${slice_scan_order}" == "HF" ]]; then
for (( c=${e}; c>=0; c-- )); do
sl=$(echo $c $single_slice_time | awk '{print $1 * $2}')
if [[ -z ${slit} ]]; then
slit="${sl}"
else
slit="${slit}, ${sl}"
fi
done
elif [[ "${slice_scan_order}" == "default" ]]; then
echo ${slice_scan_order}
a=$((${spb} %2));
echo ${a}
# this is still untested
if [[ "${spb}" -le 6 ]]; then
step=2;
hlpp=$(($((${e}+1))/${step}));
lpsl=0;
lpal=${lpsl};
hpsl=${e};
hpal=${hpsl};
order=0;
for ii in $(seq 0 1 ${spb}); do
if [[ ${lpal} -lt $((${hlpp}-1)) ]]; then
tmp_order[${order}]=${lpal};
lpal=$((${lpal}+${step}));
((order++))
elif [[ ${hpal} -ge $((${hlpp}-1)) ]]; then
tmp_order[${order}]=${hpal};
hpal=$((${hpal}-${step}));
((order++))
else
lpal=$((${lpsl}+1))
hpal=$((${hpsl}-1))
fi
done
# We will not add a 1 as done in the matlab version but we iterate over spb not e also
for iz in ${!tmp_order[@]}; do
sl=$(echo $((${tmp_order[$iz]})) ${single_slice_time} | awk '{print $1 * $2}');
if [[ -z ${slit} ]]; then
slit="${sl}"
else
slit="${slit}, ${sl}"
fi
done
# this is still untested
elif [[ "${spb}" == 8 ]]; then
declare -a tmp_order
step=$(echo "sqrt(${spb})" | bc)
echo "step is ${step}"
unset tmp_order curr bh ik slgp;
slgp=0;
declare -a tmp_order;
tmp_order[0]=0;
echo ${tmp_order[@]};
for ik in $(seq 1 ${e}); do
echo " ik is ${ik}";
bh=$((${ik}-1));
echo "bh is ${bh}";
curr=$((${tmp_order[$bh]}+${step}));
echo "tmp_order of bh is ${tmp_order[$bh]};
echo "initially tmp_order of ik is ${tmp_order[$ik]};
echo "step is ${step}";
if [[ ${curr} -gt ${e} ]]; then
echo "slgp is ${slgp}";
((slgp++));
echo "inceremented slgp is ${slgp}";
curr=${slgp};
echo "now curr = ${slgp}";
fi;
tmp_order[$ik]=${curr};
echo "tmp_order of ik is ${tmp_order[$ik]}";
done;
echo ${tmp_order[@]}
for iz in ${!tmp_order[@]}; do
sl=$(echo $((${tmp_order[$iz]})) ${single_slice_time} | awk '{print $1 * $2}');
if [[ -z ${slit} ]]; then
slit="${sl}"
else
slit="${slit}, ${sl}"
fi
done
else
# if we have an odd no. of slices per band
if [[ ${a} == 1 ]]; then
for zc in $(seq 0 2 ${e} ); do
sl1=$(echo $zc $single_slice_time | awk '{print $1 * $2}')
if [[ -z ${slit1} ]]; then
slit1="${sl1}"
else
slit1="${slit1}, ${sl1}"
fi
done
for zx in $(seq 1 2 ${e} ); do
sl2=$(echo $zx $single_slice_time | awk '{print $1 * $2}')
if [[ -z ${slit2} ]]; then
slit2="${sl2}"
else
slit2="${slit2}, ${sl2}"
fi
done
slit="${slit1}, ${slit2}"
echo "${slit}"
# if we have an odd no. of slices per band
elif [[ ${a} == 0 ]]; then
step=2;
hlpp=$(($((${e}+1))/${step}));
lpsl=0;
lpal=${lpsl};
hpsl=${e};
hpal=${hpsl};
order=0;
for ii in $(seq 0 1 ${spb}); do
if [[ ${lpal} -lt $((${hlpp}-1)) ]]; then
tmp_order[${order}]=${lpal};
lpal=$((${lpal}+${step}));
((order++))
elif [[ ${hpal} -ge $((${hlpp}-1)) ]]; then
tmp_order[${order}]=${hpal};
hpal=$((${hpal}-${step}));
((order++))
else
lpal=$((${lpsl}+1))
hpal=$((${hpsl}-1))
fi
done
# We will not add a 1 as done in the matlab version but we iterate over spb not e also
for iz in ${!tmp_order[@]}; do
sl=$(echo $((${tmp_order[$iz]})) ${single_slice_time} | awk '{print $1 * $2}');
if [[ -z ${slit} ]]; then
slit="${sl}"
else
slit="${slit}, ${sl}"
fi
done
fi
fi
fi
slit2=$slit
rep=$(echo $multiband_factor | awk '{print $1 - 1}')
for (( c=1; c<=$rep; c++ )); do
slit2="$slit2, $slit"
done
slice_time=[$slit2]
fi
else
slice_time="empty"
fi
if [ $silent -eq 0 ]; then
echo " patid = $patid"
echo " the dicom file we are reading = $dcm_file"
echo " manufacturer = $manufacturer"
echo " software version = $software"
echo " imagetype = $imagetype"
echo " acquisitionMatrix = $acquisitionMatrix"
echo " FovAP = $FovAP"
echo " FovFH = $FovFH"
echo " FovRL = $FovRL"
echo " pixelspacing = $pixelspacing"
echo " slicethickness = $slicethickness"
echo " series = $seriesdescr"
echo " fieldstrength = $fieldstrength"
echo " waterfatshift = $waterfatshift"
echo " epifactor = $epifactor"
echo " calulated ees = $ees_sec"
echo " calculated trt = $trt_sec"
echo " number of slices = $number_of_slices"
echo " repetion_time_msec = $repetion_time_msec"
echo " slice_scan_order = $slice_scan_order"
if [ ! $multiband_factor = "" ];then
echo " multiband_factor = $mb"
echo " calculated single_slice_time = $single_slice_time"
echo " number of excitations - 1 = $e"
echo " for 1 multiband = $slit"
echo " complete slice_time = $slice_time"
fi
fi
if [ ! -f $out ]; then
echo -e "participant,session,dcm_file,manufacturer,software_version,series_descr,imagetype,fieldstrength,acquisitionMatrix,FovAP,FovFH,FovRL,pixelspacing,slicethickness,epifactor,wfs,ees_sec,trt_sec,nr_slices,slice_scan_order,repetion_time_msec,multiband_factor" > $out
fi
echo -e "$subj,${sess},$dcm_file,$manufacturer,$software,$seriesdescr,$imagetype,$fieldstrength,$acquisitionMatrix,$FovAP,$FovFH,$FovRL,$pixelspacing,$slicethickness,$epifactor,$waterfatshift,$ees_sec,$trt_sec,$number_of_slices,$slice_scan_order,$repetion_time_msec,$multiband_factor" >> $out
}
function kul_find_relevant_dicom_file {
kul_e2cl " Searching for ${identifier} using search_string $search_string" $log
# find the search_string in the dicom dump_file
# search for search_string in dump_file, find ORIGINAL, remove dicom tags, sort, take first line, remove trailing space
seq_file=$(grep "$search_string" $dump_file | grep ORIGINAL - | cut -f1 -d"[" | sort | head -n 1 | sed -e 's/[[:space:]]*$//')
if [ "$seq_file" = "" ]; then
kul_e2cl " ${identifier} dicoms are NOT FOUND" $log
seq_found=0
else
seq_found=1
kul_e2cl " a relevant ${identifier} dicom is $(basename "${seq_file}") " $log
fi
}
# END LOCAL FUNCTIONS --------------
# CHECK COMMAND LINE OPTIONS -------------
#
# Set defaults
sess=""
bids_output=BIDS
# Set flags
subj_flag=0
sess_flag=0
dcm_flag=0
conf_flag=0
bids_flag=0
tmp_flag=0
events_flag=0
n_sbref_tasks=0
silent=1
anon=0
if [ "$#" -lt 4 ]; then
Usage >&2
exit 1
else
while getopts "c:d:p:o:s:t:aveh" OPT; do
case $OPT in
d) #dicom_zip_file
dcm_flag=1
dcm=$OPTARG
;;
p) #participant
subj_flag=1
subj=$OPTARG
;;
c) #config_file
conf_flag=1
conf=$OPTARG
;;
o) #bids output directory
bids_flag=1
bids_output=$OPTARG
;;
s) #session
sess_flag=1
sess=$OPTARG
;;
a) #pydeface
anon=1
;;
v) #verbose
silent=0
;;
e) #events for task based fmri
events_flag=1
;;
t) #temporary directory
tmp_flag=1
tempo=$OPTARG
;;
h) #help
Usage >&2
exit 0
;;
\?)
echo "Invalid option: -$OPTARG" >&2
echo
Usage >&2
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
echo
Usage >&2
exit 1
;;
esac
done
fi
# check for required options
if [ $dcm_flag -eq 0 ] ; then
echo
echo "Option -d is required: give the file with your raw dicoms either .zip of tar.gz" >&2
echo
exit 2
fi
if [ $subj_flag -eq 0 ] ; then
echo
echo "Option -p is required: give the anonymised name of a subject this will create a directory subject_preproc with results." >&2
echo
exit 2
fi
if [ $conf_flag -eq 0 ] ; then
echo
echo "Option -c is required: give the path to the file that describes the sequences" >&2
echo
exit 2
elif [ ! -f $conf ] ; then
echo
echo "The config file $conf does not exist"
echo
exit 2
fi
# INITIATE ---
# main log file naming
d=$(date "+%Y-%m-%d_%H-%M-%S")
log=$log_dir/${subj}_main_log_${d}.txt
# file for initial dicom tags
dump_file=${log_dir}/${subj}_${sess}_initial_dicom_info.txt
# file with final dicom tags
final_dcm_tags_file=${log_dir}/${subj}_${sess}_final_dicom_info.csv
# location of bids_config_json_file
bids_config_json_file=${log_dir}/${subj}_${sess}_bids_config.json
# location of dcm2niix_log_file
dcm2niix_log_file=$log_dir/${subj}_${sess}_dcm2niix_log_file.txt
if [[ $tmp_flag -eq 1 ]] ; then
tmp=${cwd}/${tempo}
else
tmp="/tmp/${subj}"
fi
rm -fr ${tmp}
# exit
# remove previous existances to start fresh
rm -f $dump_file
rm -f $final_dcm_tags_file
rm -f $bids_config_json_file
# rm -fr ${cwd}/${tmp}/$subj
# ----------- SAY HELLO ----------------------------------------------------------------------------------
if [[ $silent -eq 0 ]]; then
echo " The script you are running has basename `basename "$0"`, located in dirname $kul_main_dir"
echo " The present working directory is `pwd`"
fi
# uncompress the zip file with dicoms or link the directory to tmp
# clear the /tmp directory
mkdir -p ${tmp}
if [[ -d "$dcm" ]]; then
# it is a directory
kul_e2cl " you gave the directory $dcm as input; linking to to $tmp/$subj" $log
ln -s "${cwd}/${dcm}" $tmp/$subj
else
kul_e2cl " uncompressing the zip file $dcm to $tmp/$subj" $log
# Check the extention of the archive
arch_ext="${dcm##*.}"
#echo $arch_ext
if [[ $arch_ext = "zip" ]]; then
unzip -q -o ${dcm} -d ${tmp}
elif [[] $arch_ext = "tar" ]]; then
tar --strip-components=5 -C ${tmp} -xzf ${dcm}
fi
fi
# if there is a Smartbrain, copy it to DICOM
if [ -d DICOM ]; then
IFS=$'\n'
sb=($(find -L $tmp -type d -name "SmartBrain*"))
n_sb=${#sb[@]}
if [ $n_sb -gt 0 ]; then
# find the largest .dcm
sb_dcm=$(find -L "${sb[0]}" -type f -printf '%s %p\n' | sort -nr | head -n 1 | awk -F/ '{ print $NF }')
cp -f "${sb[0]}/$sb_dcm" "DICOM/smartbrain.dcm"
fi
fi
# if there is a Localizer, copy it to DICOM
if [ -d DICOM ]; then
IFS=$'\n'
sb=($(find -L $tmp -type d -name "Localizers*"))
n_sb=${#sb[@]}
if [ $n_sb -gt 0 ]; then
# find the largest .dcm
sb_dcm=$(find -L "${sb[0]}" -type f -printf '%s %p\n' | sort -nr | head -n 1 | awk -F/ '{ print $NF }')
cp -f "${sb[0]}/$sb_dcm" "DICOM/localizer.dcm"
fi
fi
# dump the dicom tags of all dicoms in a file
kul_e2cl " brute force extraction of some relevant dicom tags of all dicom files of subject $subj into file $dump_file" $log
# check if a DICOMIR file exists and archive it (we do a brute force extraction and don't need the DICOMDIR file)
test_DICOMDIR=($(find -L ${tmp} -type f -name "DICOMDIR" ))
#echo "DICOMDIR = $test_DICOMDIR"
if [[ $test_DICOMDIR == "" ]]; then
echo " OK there is no DICOMDIR"
else
gzip $test_DICOMDIR
fi
# Do the bruce force extract
echo hello > $dump_file
task(){
dcm1=$(dcminfo "$dcm_file" -tag 0008 103E -tag 0008 0008 -tag 0008 0070 -nthreads 4 2>/dev/null | tr -s '\n' ' ')
echo "$dcm_file" $dcm1 >> $dump_file
}
(
find -L ${tmp} -type f |
while IFS= read -r dcm_file; do
task
done
)
kul_e2cl " done reading dicom tags of $dcm" $log
# create empty bids description
# bids=""
# we read the config file
declare -a sub_bids
while IFS=, read identifier search_string task mb pe_dir acq_label; do
bs=$(( $bs + 1))
if [[ ! ${identifier} == \#* ]]; then
if [[ ${identifier} == "T1w" ]]; then
kul_find_relevant_dicom_file
if [ $seq_found -eq 1 ]; then
# read the relevant dicom tags
kul_dcmtags "${seq_file}"
sub_bids_T1='{"dataType": "anat", "modalityLabel": "T1w", "criteria": {
"SeriesDescription": "*'${search_string}'*"}}'
sub_bids_[$bs]=$(echo ${sub_bids_T1} | python -m json.tool )
fi
fi
if [[ ${identifier} == "cT1w" ]]; then
kul_find_relevant_dicom_file
if [ $seq_found -eq 1 ]; then
# read the relevant dicom tags
kul_dcmtags "${seq_file}"
sub_bids_T1='{"dataType": "anat", "modalityLabel": "T1w", "criteria": {
"SeriesDescription": "*'${search_string}'*"},
"customLabels": "ce-gadolinium",
"sidecarChanges": {"KUL_dcm2bids": "yes","ContrastBolusIngredient": "gadolinium"}
}'
sub_bids_[$bs]=$(echo ${sub_bids_T1} | python -m json.tool )
fi
fi
if [[ ${identifier} == "T2w" ]]; then
kul_find_relevant_dicom_file
if [ $seq_found -eq 1 ]; then
# read the relevant dicom tags
kul_dcmtags "${seq_file}"
sub_bids_T2='{"dataType": "anat", "modalityLabel": "T2w", "criteria": {
"SeriesDescription": "*'${search_string}'*"}'
# add an acq_label if any
echo $acq_label
if [ "$acq_label" = "" ];then
sub_bids_T2b='}'
else
sub_bids_T2b=', "customLabels": "acq-'${acq_label}'"}'
fi
echo ${sub_bids_T2}${sub_bids_T2b}
sub_bids_[$bs]=$(echo ${sub_bids_T2}${sub_bids_T2b} | python -m json.tool)
fi
fi
if [[ ${identifier} == "PDw" ]]; then
kul_find_relevant_dicom_file
if [ $seq_found -eq 1 ]; then
# read the relevant dicom tags
kul_dcmtags "${seq_file}"
sub_bids_PD='{"dataType": "anat", "modalityLabel": "PDw", "criteria": {
"SeriesDescription": "*'${search_string}'*"}}'
sub_bids_[$bs]=$(echo ${sub_bids_PD} | python -m json.tool)
fi