#!/bin/sh
#### What could be done ##################################################################
# - add a preprocessing step in order to intensity normalise all the input images ???
# - Any other ?
##########################################################################################
if [ $# -lt 1 ]
then
echo ""
echo "*******************************************************************************"
echo "One argument is expected to run this script:"
echo "- File with contains the altas creation parameters"
echo "example: $0 param_groupwise_niftyreg.sh "
echo "*******************************************************************************"
echo ""
exit
fi
#############################################################################
# read the input parameters
. $1
#############################################################################
## the argument value are checked
if [ ${#IMG_INPUT[@]} -lt 2 ]
then
echo "Less than 2 images have been specified"
echo "Exit ..."
exit
fi
if [ ! -e ${TEMPLATE} ]
then
echo "The template image (${TEMPLATE}) does not exist"
echo "Exit ..."
exit
fi
if [ "${TEMPLATE_MASK}" != "" ] && [ ! -f ${TEMPLATE_MASK} ]
then
echo "The template image mask (${TEMPLATE_MASK}) does not exist"
echo "Exit ..."
fi
IMG_NUMBER=${#IMG_INPUT[@]}
MASK_NUMBER=${#IMG_INPUT_MASK[@]}
if [ ${MASK_NUMBER} -gt 0 ] && [ ! -f ${IMG_INPUT_MASK[0]} ] \
&& [ ${MASK_NUMBER} != ${IMG_NUMBER} ]
then
echo "The number of images is different from the number of floating masks"
echo "Exit ..."
exit
fi
#############################################################################
## SET UP THE NIFTYREG EXECUTABLES
AFFINE=reg_aladin
NRR=reg_f3d
RES=reg_resample
AVERAGE=reg_average
TRANS=reg_transform
TOOLS=reg_tools
#############################################################################
echo ""
echo "************************************************************"
echo ">>> There are ${IMG_NUMBER} input images to groupwise register <<<"
echo ">>> The template image to initialise the registration is ${TEMPLATE} <<<"
echo "************************************************************"
echo ""
#############################################################################
# CREATE THE RESULT FOLDER
if [ ! -d ${RES_FOLDER} ]
then
echo "The output image folder (${RES_FOLDER}) does not exist"
mkdir ${RES_FOLDER}
if [ ! -d ${RES_FOLDER} ]
then
echo "Unable to create the ${RES_FOLDER} folder"
echo "Exit ..."
exit
else
echo "The output image folder (${RES_FOLDER}) has been created"
fi
fi
#############################################################################
#############################################################################
# PERFORM THE RIGID/AFFINE REGISTRATION
# The initial average image is as specified by the user
averageImage=${TEMPLATE}
# Loop over all iterations
for (( CUR_IT=1; CUR_IT<=${AFF_IT_NUM}; CUR_IT++ ))
do
# Check if the iteration has already been performed
if [ ! -f ${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz ]
then
#############################
# Create a folder to store the result
if [ ! -d ${RES_FOLDER}/aff_${CUR_IT} ]
then
mkdir ${RES_FOLDER}/aff_${CUR_IT}
fi
#############################
# Run the rigid or affine registration
if [ "`which sbatch 2> /dev/null`" == "" ]
then
# All registration are performed serially
for (( i=0 ; i<${IMG_NUMBER}; i++ ))
do
name=`basename ${IMG_INPUT[${i}]} .gz`
name=`basename ${name} .nii`
name=`basename ${name} .hdr`
name=`basename ${name} .img`
# Check if the registration has already been performed
if [ ! -f ${RES_FOLDER}/aff_${CUR_IT}/aff_mat_${name}_it${CUR_IT}.txt ]
then
aladin_args=""
# Registration is forced to be rigid for the first step
if [ ${CUR_IT} == 1 ]
then
aladin_args="-rigOnly"
else
# Check if a previous affine can be use for initialisation
if [ -f ${RES_FOLDER}/aff_`expr ${CUR_IT} - 1`/aff_mat_${name}_it`expr ${CUR_IT} - 1`.txt ]
then
aladin_args="-inaff \
${RES_FOLDER}/aff_`expr ${CUR_IT} - 1`/aff_mat_${name}_it`expr ${CUR_IT} - 1`.txt"
fi
fi
# Check if a mask has been specified for the reference image
if [ "${TEMPLATE_MASK}" != "" ]
then
aladin_args="${aladin_args} -rmask ${TEMPLATE_MASK}"
fi
# Check if a mask has been specified for the floating image
if [ ${MASK_NUMBER} == ${IMG_NUMBER} ]
then
aladin_args="${aladin_args} -fmask ${IMG_INPUT_MASK[${i}]}"
fi
result="/dev/null"
if [ "${CUR_IT}" == "${AFF_IT_NUM}" ]
then
result="${RES_FOLDER}/aff_${CUR_IT}/aff_res_${name}_it${CUR_IT}.nii.gz"
fi
# Perform the registration
reg_aladin ${AFFINE_args} ${aladin_args} \
-ref ${averageImage} \
-flo ${IMG_INPUT[${i}]} \
-aff ${RES_FOLDER}/aff_${CUR_IT}/aff_mat_${name}_it${CUR_IT}.txt \
-res ${result} > ${RES_FOLDER}/aff_${CUR_IT}/aff_log_${name}_it${CUR_IT}.txt
if [ ! -f ${RES_FOLDER}/aff_${CUR_IT}/aff_mat_${name}_it${CUR_IT}.txt ]
then
echo "Error when creating \
${RES_FOLDER}/aff_${CUR_IT}/aff_mat_${name}_it${CUR_IT}.txt"
exit
fi
fi
done
else
# Create shell script to run all jobs in an array
echo \#\!/bin/bash > ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
if [ $[avg_aff_`expr ${CUR_IT} - 1`_${$}] -ne 0 ]; then
echo "#SBATCH --dependency=afterok:$[avg_aff_`expr ${CUR_IT} - 1`_${$}]" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
fi
# Define the current image index
echo "img_number=\`expr \$SLURM_ARRAY_TASK_ID - 1\`" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo ". `readlink -f $1`" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
# Extract the name of the file without the path and the extension
echo "name=\`basename \${IMG_INPUT[\$img_number]} .gz\`" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo "name=\`basename \$name .nii\`" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo "name=\`basename \$name .hdr\`" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo "name=\`basename \$name .img\`" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
# Check that the registration has not already been performed
echo "if [ ! -e ${RES_FOLDER}/aff_${CUR_IT}/aff_mat_\${name}_it${CUR_IT}.txt ]" >> \
${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo "then" >> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
# Check if an input affine is available
echo "trans_affine=${RES_FOLDER}/aff_`expr ${CUR_IT} - 1`/aff_mat_\${name}_it`expr ${CUR_IT} - 1`.txt" >> \
${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
# Set up the registration argument
echo "${AFFINE} ${AFFINE_args} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo "-ref ${averageImage} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo "-flo \${IMG_INPUT[img_number]} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
echo "-aff ${RES_FOLDER}/aff_${CUR_IT}/aff_mat_\${name}_it${CUR_IT}.txt \\" >> \
${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
result="/dev/null"
if [ "${CUR_IT}" == "${AFF_IT_NUM}" ]
then
result="${RES_FOLDER}/aff_${CUR_IT}/aff_res_\${name}_it${CUR_IT}.nii.gz"
fi
echo "-res ${result} \\" >> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
if [ "${TEMPLATE_MASK}" != "" ]; then
echo "-rmask ${TEMPLATE_MASK} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
fi
if [ ${MASK_NUMBER} == ${IMG_NUMBER} ]; then
echo "-fmask \${IMG_INPUT_MASK[\$img_number]} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
fi
# If this is the first iteration. The registration is forced to be rigid
# Otherwise the previous affine is used for initialisation
if [ ${CUR_IT} == 1 ]
then
echo "-rigOnly" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
else
echo "-inaff \${trans_affine}" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
fi
echo "fi" >> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh
## Run the rigid/affine registration - Submit the job array
# Wait to see if the previous iteration average has been created
ID=$(${SBATCH_CMD} \
--output=${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.out \
--job-name=aladin_${CUR_IT}_${$} \
--array=1-${IMG_NUMBER} \
${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_aladin_${CUR_IT}_${$}.sh)
echo $ID
declare "aladin_${CUR_IT}_${$}=${ID##* }"
fi
#############################
if [ "${CUR_IT}" != "${AFF_IT_NUM}" ]
then
# The transformation are demean'ed to create the average image
# Note that this is not done for the last iteration step
list_average=""
for img in ${IMG_INPUT[@]}
do
name=`basename ${img} .gz`
name=`basename ${name} .nii`
name=`basename ${name} .hdr`
name=`basename ${name} .img`
list_average="${list_average} \
${RES_FOLDER}/aff_${CUR_IT}/aff_mat_${name}_it${CUR_IT}.txt ${img}"
done
if [ "`which sbatch 2> /dev/null`" == "" ]
then
# The average is created on the host
echo "reg_average \
${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz \
-demean ${averageImage} \
${list_average}"
reg_average \
${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz \
-demean ${averageImage} \
${list_average}
if [ ! -f ${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz ]
then
echo "Error when creating \
${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz"
exit
fi
else # if [ "`which qsub 2> /dev/null`" == "" ]
# The average is performed through the cluster
echo \#\!/bin/bash > ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
echo "${AVERAGE} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
echo "${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
echo "-demean ${averageImage} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
echo "${list_average}" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
ID=$(${SBATCH_CMD} \
--dependency=afterok:$[aladin_${CUR_IT}_${$}] \
--output=${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.out \
--job-name=avg_aff_${CUR_IT}_${$} \
${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh)
echo $ID
declare "avg_aff_${CUR_IT}_${$}=${ID##* }"
fi # if [ "`which qsub 2> /dev/null`" == "" ]
else # if [ "${CUR_IT}" != "${AFF_IT_NUM}" ]
# All the result images are directly averaged during the last step
if [ "`which sbatch 2> /dev/null`" == "" ]
then
reg_average \
${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz \
-avg \
`ls ${RES_FOLDER}/aff_${CUR_IT}/aff_res_*_it${CUR_IT}.nii*`
if [ ! -f ${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz ]
then
echo "Error when creating \
${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz"
exit
fi
else # if [ "`which qsub 2> /dev/null`" == "" ]
# The average is performed through the cluster
echo \#\!/bin/bash > ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
echo "${AVERAGE} \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
echo "${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz \\" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
echo "-avg ${RES_FOLDER}/aff_${CUR_IT}/aff_res_*_it${CUR_IT}.nii*" \
>> ${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh
ID=$(${SBATCH_CMD} \
--dependency=afterok:$[aladin_${CUR_IT}_${$}] \
--output=${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.out \
--job-name=avg_aff_${CUR_IT}_${$} \
${RES_FOLDER}/aff_${CUR_IT}/run_gw_niftyReg_avg_aff_${CUR_IT}_${$}.sh)
echo $ID
declare "avg_aff_${CUR_IT}_${$}=${ID##* }"
fi # if [ "`which qsub 2> /dev/null`" == "" ]
fi # if [ "${CUR_IT}" != "${AFF_IT_NUM}" ]
else # if [ ! -f ${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz ]
echo "${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz already exists"
fi # if [ ! -f ${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz ]
# Update the average image used as a reference
averageImage=${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz
done # Loop over affine iteration
#############################################################################
#############################################################################
### Non rigid registration loop
for (( CUR_IT=1; CUR_IT<=${NRR_IT_NUM}; CUR_IT++ ))
do
#############################
# Check if the current average image has already been created
if [ ! -f ${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz ]
then
#############################
# Create a folder to store the current results
if [ ! -d ${RES_FOLDER}/nrr_${CUR_IT} ]
then
mkdir ${RES_FOLDER}/nrr_${CUR_IT}
fi
#############################
# Run the nonrigid registrations
if [ "`which sbatch 2> /dev/null`" == "" ]
then
for (( i=0 ; i<${IMG_NUMBER}; i++ ))
do
name=`basename ${IMG_INPUT[${i}]} .gz`
name=`basename ${name} .nii`
name=`basename ${name} .hdr`
name=`basename ${name} .img`
# Check if the registration has already been performed
if [ ! -f ${RES_FOLDER}/nrr_${CUR_IT}/nrr_cpp_${name}_it${CUR_IT}.nii* ]
then
f3d_args=""
# Check if a mask has been specified for the reference image
if [ "${TEMPLATE_MASK}" != "" ]
then
f3d_args="${f3d_args} -rmask ${TEMPLATE_MASK}"
fi
# Check if a mask has been specified for the floating image
if [ ${MASK_NUMBER} == ${IMG_NUMBER} ]
then
f3d_args="${f3d_args} -fmask ${IMG_INPUT_MASK[${i}]}"
fi
if [ ${AFF_IT_NUM} -gt 0 ]
then
f3d_args="${f3d_args} -aff \
${RES_FOLDER}/aff_${AFF_IT_NUM}/aff_mat_${name}_it${AFF_IT_NUM}.txt"
fi
result="/dev/null"
if [ "${CUR_IT}" == "${NRR_IT_NUM}" ]
then
result="${RES_FOLDER}/nrr_${CUR_IT}/nrr_res_${name}_it${CUR_IT}.nii.gz"
fi
# Perform the registration
reg_f3d ${NRR_args} ${f3d_args} \
-ref ${averageImage} \
-flo ${IMG_INPUT[${i}]} \
-cpp ${RES_FOLDER}/nrr_${CUR_IT}/nrr_cpp_${name}_it${CUR_IT}.nii.gz \
-res ${result} > ${RES_FOLDER}/nrr_${CUR_IT}/nrr_log_${name}_it${CUR_IT}.txt
fi
done
else
echo \#\!/bin/bash > ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
if [ $[avg_nrr_`expr ${CUR_IT} - 1`_${$}] -ne 0 ]
then
echo "#SBATCH --dependency=afterok:$[avg_aff_${AFF_IT_NUM}_${$}],$[avg_nrr_`expr ${CUR_IT} - 1`_${$}]" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
else
echo "#SBATCH --dependency=afterok:$[avg_aff_${AFF_IT_NUM}_${$}]" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
fi
# Define the current image index
echo "img_number=\`expr \$SLURM_ARRAY_TASK_ID - 1\`" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
echo ". `readlink -f $1`" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
# Extract the name of the file without the path and the extension
echo "name=\`basename \${IMG_INPUT[\$img_number]} .gz\`" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
echo "name=\`basename \$name .nii\`" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
echo "name=\`basename \$name .hdr\`" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
echo "name=\`basename \$name .img\`" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
# Check that the registration has not already been performed
echo "if [ ! -e ${RES_FOLDER}/nrr_${CUR_IT}/nrr_cpp_\${name}_it${CUR_IT}.nii* ]" >> \
${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
echo "then" >> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
# Set up the registration argument
echo "${NRR} ${NRR_args} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
echo "-ref ${averageImage} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
if [ "${TEMPLATE_MASK}" != "" ]; then
echo "-rmask ${TEMPLATE_MASK} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
fi
echo "-flo \${IMG_INPUT[\$img_number]} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
if [ ${AFF_IT_NUM} -gt 0 ]
then
echo "-aff ${RES_FOLDER}/aff_${AFF_IT_NUM}/aff_mat_\${name}_it${AFF_IT_NUM}.txt \\" >> \
${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
fi
if [ ${MASK_NUMBER} == ${IMG_NUMBER} ]; then
echo "-fmask \${IMG_INPUT_MASK[\$img_number]} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
fi
echo "-cpp ${RES_FOLDER}/nrr_${CUR_IT}/nrr_cpp_\${name}_it${CUR_IT}.nii.gz \\" >> \
${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
result="/dev/null"
if [ "${CUR_IT}" == "${NRR_IT_NUM}" ]
then
result="${RES_FOLDER}/nrr_${CUR_IT}/nrr_res_\${name}_it${CUR_IT}.nii.gz"
fi
echo "-res ${result}" >> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
echo "fi" >> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh
## Run the nonrigid registrations - Submit the job array
ID=$(${SBATCH_CMD} \
--output=${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.out \
--job-name=f3d_${CUR_IT}_${$} \
--array=1-${IMG_NUMBER} \
${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_f3d_${CUR_IT}_${$}.sh)
echo $ID
declare "f3d_${CUR_IT}_${$}=${ID##* }"
fi
#############################
# The transformation are demean'ed to create the average image
# Note that this is not done for the last iteration step
if [ "${CUR_IT}" != "${NRR_IT_NUM}" ]
then
list_average=""
for img in ${IMG_INPUT[@]}
do
name=`basename ${img} .gz`
name=`basename ${name} .nii`
name=`basename ${name} .hdr`
name=`basename ${name} .img`
list_average="${list_average} \
${RES_FOLDER}/aff_${AFF_IT_NUM}/aff_mat_${name}_it${AFF_IT_NUM}.txt \
${RES_FOLDER}/nrr_${CUR_IT}/nrr_cpp_${name}_it${CUR_IT}.nii.gz ${img}"
done
if [ "`which sbatch 2> /dev/null`" == "" ]
then
# The average is created on the host
reg_average \
${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz \
-demean_noaff ${averageImage} \
${list_average}
if [ ! -f ${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz ]
then
echo "Error when creating \
${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz"
exit
fi
else # if [ "`which qsub 2> /dev/null`" == "" ]
# The average is performed through the cluster
echo \#\!/bin/bash > ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
echo "${AVERAGE} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
echo "${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
echo "-demean_noaff ${averageImage} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
echo "${list_average}" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
ID=$(${SBATCH_CMD} \
--dependency=afterok:$[f3d_${CUR_IT}_${$}] \
--output=${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.out \
--job-name=avg_nrr_${CUR_IT}_${$} \
${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh)
echo $ID
declare "avg_nrr_${CUR_IT}_${$}=${ID##* }"
fi # if [ "`which qsub 2> /dev/null`" == "" ]
else # if [ "${CUR_IT}" != "${NRR_IT_NUM}" ]
# All the result images are directly averaged during the last step
if [ "`which sbatch 2> /dev/null`" == "" ]
then
reg_average \
${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz \
-avg \
`ls ${RES_FOLDER}/nrr_${CUR_IT}/nrr_res_*_it${CUR_IT}.nii*`
if [ ! -f ${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz ]
then
echo "Error when creating \
${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz"
exit
fi
else # if [ "`which qsub 2> /dev/null`" == "" ]
# The average is performed through the cluster
echo \#\!/bin/bash > ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
echo "${AVERAGE} \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
echo "${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz \\" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
echo "-avg ${RES_FOLDER}/nrr_${CUR_IT}/nrr_res_*_it${CUR_IT}.nii*" \
>> ${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh
ID=$(${SBATCH_CMD} \
--dependency=afterok:$[f3d_${CUR_IT}_${$}] \
--output=${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.out \
--job-name=avg_nrr_${CUR_IT}_${$} \
${RES_FOLDER}/nrr_${CUR_IT}/run_gw_niftyReg_avg_nrr_${CUR_IT}_${$}.sh)
echo $ID
declare "avg_nrr_${CUR_IT}_${$}=${ID##* }"
fi # if [ "`which qsub 2> /dev/null`" == "" ]
fi # if [ "${CUR_IT}" != "${NRR_IT_NUM}" ]
else # if [ ! -f ${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz ]
echo "${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz already exists"
fi # if [ ! -f ${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz ]
# Update the average image
averageImage=${RES_FOLDER}/nrr_${CUR_IT}/average_nonrigid_it_${CUR_IT}.nii.gz
done
#############################################################################
