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KUL_FWT_make_VOIs.sh
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#!/bin/bash
# set -x
# the point of this one is to make my life easier!
# when it comes to VOI gen
cwd="$(pwd)"
# function Usage
function Usage {
cat <<USAGE
`basename $0` generates all inclusion and exclusion VOIs for fully automated fiber tractography according to an input config file
Usage:
`basename $0` -p pat001 -s 01 -F /path_to/FS_dir/aparc+aseg.mgz -M /path_to/MSBP_dir/sub-pat001_label-L2018_desc-scale3_atlas.nii.gz -d /path_to/dMRI_dir -c /path_to/KUL_FWT_tracks_list.txt -o /fullpath/output
Examples:
`basename $0` -p pat001 -s 01 -F /path_to/FS_dir/aparc+aseg.mgz -M /path_to/MSBP_dir/sub-pat001_label-L2018_desc-scale3_atlas.nii.gz -d /path_to/dMRI_dir -c /path_to/KUL_FWT_tracks_list.txt -o /fullpath/output -n 6
Purpose:
This workflow generates the VOIs needed for fiber tracking by KUL_FWT_make_TCKs.sh from input FS and MSBP for all bundles specified in the input config file for single subject data
Required arguments:
-p: BIDS participant name (anonymised name of the subject without the "sub-" prefix)
-s: BIDS participant session (session no. without the "ses-" prefix)
-M: full path and file name of scale 3 MSBP parcellation
-F: full path and file name of aparc+aseg.mgz from FreeSurfer
-c: path to config file with list of tracks to segment from the whole brain tractogram
-d: path to directory with diffusion data (specific to subject and run)
-o: full path to output dir (if not set reverts to default output ./sub-*_ses-*_KUL_FWT_output)
Optional arguments:
-n: number of cpu for parallelisation (default is 6)
-h: prints help menu
USAGE
exit 1
}
# add this later
# -b: if using BIDS and all data is in BIDS/derivatives
# CHECK COMMAND LINE OPTIONS -------------
#
# Set defaults
# Set required options
p_flag=0
s_flag=0
F_flag=0
M_flag=0
c_flag=0
d_flag=0
o_flag=0
# b_flag=0
if [ "$#" -lt 1 ]; then
Usage >&2
exit 1
else
while getopts "p:s:t:M:F:c:d:o:n:h" OPT; do
case $OPT in
p) #participant
p_flag=1
subj=$OPTARG
;;
s) #session
s_flag=1
ses=$OPTARG
;;
M) #MSBP scale parcellation
M_flag=1
MS_sc3_in=$OPTARG
;;
F) #FS aparc+aseg.mgz
F_flag=1
FS_apas_in=$OPTARG
;;
c) #config file
c_flag=1
conf_f=$OPTARG
;;
d) #diffusion dir
d_flag=1
d_dir=$OPTARG
;;
o) #output
o_flag=1
out_dir=$OPTARG
;;
n) #parallel
n_flag=1
ncpu=$OPTARG
;;
h) #help
Usage >&2
exit 0
;;
\?)
echo "Invalid option: -$OPTARG" >&2
echo
Usage >&2
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
echo
Usage >&2
exit 1
;;
esac
done
fi
# deal with ncpu and itk ncpu
# MRTRIX verbose or not?
# if [ $silent -eq 1 ] ; then
# export MRTRIX_QUIET=1
# fi
# REST OF SETTINGS ---
# timestamp
start=$(date +%s)
d=$(date "+%Y-%m-%d_%H-%M-%S")
# check for required inputs
# config file
srch_conf_str=($(basename ${conf_f})) ; conf_dir=($(dirname ${conf_f}))
srch_conf_c=($(find ${conf_dir} -type f | grep ${srch_conf_str}))
# diffusion data dir
srch_ddir_str=($(basename ${d_dir})) ; diff_dir=($(dirname ${d_dir}))
srch_ddir_c=($(find ${diff_dir} -type d | grep ${srch_ddir_str}))
# FS dirs
srch_FS_str=($(basename ${FS_apas_in})) ; FS_dir=($(dirname ${FS_apas_in}))
srch_FS_c=($(find ${FS_dir} -type f | grep ${srch_FS_str}))
# MSBP dirs
srch_MS_str=($(basename ${MS_sc3_in})) ; MS_dir=($(dirname ${MS_sc3_in}))
srch_MS_c=($(find ${MS_dir} -type f | grep ${srch_MS_str}))
if [[ ${p_flag} -eq 0 ]] || [[ ${F_flag} -eq 0 ]] || [[ ${M_flag} -eq 0 ]] || [[ ${c_flag} -eq 0 ]] || [[ ${d_flag} -eq 0 ]]; then
echo
echo "Inputs to -s -f -d and -c must be set." >&2
echo
exit 2
else
if [[ -z "${srch_FS_c}" ]]; then
echo
echo " Incorrect path to the FS aparc+aseg, please check the path and name "
echo
exit 2
fi
if [[ -z "${srch_MS_c}" ]]; then
echo
echo " Incorrect path MSBP parcellation, please check the path and name "
echo
exit 2
fi
if [[ -z "${srch_ddir_c}" ]]; then
echo
echo " Incorrect path to the diffusion data dir, please check the dir path and name "
echo
exit 2
fi
if [[ -z "${srch_conf_c}" ]]; then
echo
echo " Incorrect config file, please check the path and name "
echo
exit 2
fi
if [[ ! ${d_dir} == *"${subj}"* ]] || [[ ! ${FS_dir} == *"${subj}"* ]] || [[ ! ${MS_dir} == *"${subj}"* ]]; then
echo
echo " Subject string does not match input files, please double check your inputs "
echo
exit 2
else
if [[ ! -z ${ses} ]]; then
if [[ ! ${d_dir} == *"ses-${ses}"* ]] || [[ ! ${FS_dir} == *"ses-${ses}"* ]] || [[ ! ${MS_dir} == *"ses-${ses}"* ]]; then
echo
echo " Session string does not match input files, please double check your inputs "
echo
exit 2
fi
fi
fi
echo "Inputs are -p ${subj} -s ${ses} -c ${conf_f} -d ${d_dir} -F ${FS_dir} -M ${MS_dir} "
fi
# set this manually for debugging
# this is now searching for the genVOIs script
function_path=($(which KUL_FWT_make_VOIs.sh | rev | cut -d"/" -f2- | rev))
mrtrix_path=($(which mrmath | rev | cut -d"/" -f3- | rev))
if [[ -z ${function_path} ]]; then
echo "update function path to reflect function name line 215"
# exit 2
else
echo " KUL_FWT lives in ${function_path} "
fi
# deal with scan sessions
if [[ -z ${s_flag} ]]; then
# no session flag defined
ses_str="";
ses_str_dir="";
elif [[ ${s_flag} -eq 1 ]]; then
# this is fine
ses_str="_ses-${ses}";
ses_str_dir="/ses-${ses}/";
fi
# REST OF SETTINGS ---
# Some parallelisation
if [[ "$n_flag" -eq 0 ]]; then
ncpu=6
echo " -n flag not set, using default 6 threads. "
else
echo " -n flag set, using " ${ncpu} " threads."
fi
FSLPARALLEL=$ncpu; export FSLPARALLEL
OMP_NUM_THREADS=$ncpu; export OMP_NUM_THREADS
# Priors dir and check
## change the temps dir name later
pr_d="${function_path}/KUL_FWT_templates"
if [[ ! -d ${pr_d} ]]; then
echo "KUL_FWT priors directory not found where expected, exiting"
exit 2
fi
# handle the dirs
cd ${cwd}
# handle output and processing dirs
if [[ "$o_flag" -eq 1 ]]; then
output_d="${out_dir}"
else
output_d="${cwd}/sub-${subj}${ses_str}_KUL_FWT_output"
fi
# output sub-dirs
ROIs_d="${output_d}/sub-${subj}${ses_str}_VOIs"
prep_d="${output_d}/sub-${subj}${ses_str}_prep"
# make your dirs
mkdir -p ${output_d} >/dev/null 2>&1
mkdir -p ${prep_d} >/dev/null 2>&1
mkdir -p ${ROIs_d} >/dev/null 2>&1
mkdir -p "${ROIs_d}/custom_VOIs" >/dev/null 2>&1
# make your log file
prep_log2="${output_d}/KUL_FWT_VOIs_log_${subj}_${d}.txt";
if [[ ! -f ${prep_log2} ]] ; then
touch ${prep_log2}
else
echo "${prep_log2} already created"
fi
# set mrtrix tmp dir to prep_d
rm -rf ${prep_d}/tmp_ims_*
tmpo_d=($(find ${prep_d} -type d -name *"tmp_ims_"*))
if [[ -z ${tmpo_d} ]]; then
tmpo_d="${prep_d}/tmp_ims_${d}"
fi
mkdir -p "${tmpo_d}" >/dev/null 2>&1
export MRTRIX_TMPFILE_DIR="${tmpo_d}"
# report pid
processId=$(ps -ef | grep 'ABCD' | grep -v 'grep' | awk '{ printf $2 }')
echo $processId
echo "KUL_FWT_make_VOIs.sh @ ${d} with parent pid $$ and process pid $BASHPID " | tee -a ${prep_log2}
echo "Inputs are -p sub-${subj} -s ses-${ses} -c ${conf_f} -d ${d_dir} -F ${FS_dir} -M ${MS_dir} " | tee -a ${prep_log2}
# read the config file
# if a hash is found this cell is populated with ##
declare -a tck_lst1
declare -a tck_list
declare -a nosts_list
# tck_lst1=($(cat ${conf_f}))
IFS=$'\n' read -d '' -r -a tck_lst1 < ${conf_f}
for i in ${!tck_lst1[@]}; do
if [[ ${tck_lst1[$i]} == *"#"* ]]; then
tck_list[$i]="none"
else
# tck_list[$i]=${tck_lst1[$i]}
tck_list[$i]=$(echo ${tck_lst1[$i]} | cut -d ',' -f1)
# test to make sure tck_list[$i] contains a string
if [[ ${tck_list[$i]} =~ ^[+-]?[0-9]+$ ]]; then
echo " there is a problem with config file, first column does not contain a string"
exit 2
fi
nosts_list[$i]=$(echo ${tck_lst1[$i]} | cut -d ',' -f2)
# test to make sure nosts_list[$i] contains a number
if [[ ! ${nosts_list[$i]} =~ ^[+-]?[0-9]+$ ]]; then
echo " there is a problem with config file, second column does not contain numbers"
exit 2
fi
fi
done
# unset tcks_lst1
# now echo this
echo "You have asked to segment the following bundles from whole brain TCK ${tck_list[@]}" | tee -a ${prep_log2}
# Exec_all function
# need to recreate this function to include proc. control
function task_exec {
echo "-------------------------------------------------------------" | tee -a ${prep_log2}
echo ${task_in} | tee -a ${prep_log2}
echo " Started @ $(date "+%Y-%m-%d_%H-%M-%S")" | tee -a ${prep_log2}
eval ${task_in} 2>&1 | tee -a ${prep_log2} &
# echo " pid = $! basicPID = $BASHPID " | tee -a ${prep_log2}
echo " pid = $! " | tee -a ${prep_log2}
wait ${pid}
sleep 5
echo "exit status $?" | tee -a ${prep_log2}
# if [ $? -eq 0 ]; then
# echo Success >> ${prep_log2}
# else
# echo Fail >> ${prep_log2}
# exit 1
# fi
echo " Finished @ $(date "+%Y-%m-%d_%H-%M-%S")" | tee -a ${prep_log2}
echo "-------------------------------------------------------------" | tee -a ${prep_log2}
echo "" | tee -a ${prep_log2}
unset task_in
}
# script start here
# part 1 of this workflow is general purpose and should be run for all bundles
# use processing control
# find your priors
# all priors are in MNI space
UKBB_temp=($(find ${pr_d} -type f -name "T1_preunbiased.nii.gz"))
UKBB_temp_mask=($(find ${pr_d} -type f -name "T1_UKBB_brain_mask.nii.gz"))
UKBB_labels="${pr_d}/UKBB_BStem_VOIs_comb.nii.gz" # done
# these would benefit from a propagate labels step probably
JHU_labels="${pr_d}/JHU_WM_labels.nii.gz" # done
JuHA_labels="${pr_d}/Juelich_GNs_inMNI.nii.gz" # done
Man_VOIs="${pr_d}/Manual_VOIs.nii.gz" # done
PD25="${pr_d}/PD25_hist_1mm_RLinMNI.nii.gz" # done
SUIT="${pr_d}/SUIT_atlas_inMNI.nii.gz" # done
RL_VOIs="${pr_d}/RL_hemi_masks.nii.gz" # done
####
# these we create
# will probably need some for the tckseg script
sub_FA_in_T1="${prep_d}/sub-${subj}${ses_str}_FA2T1brainMS_Warped.nii.gz"
sub_T1inFA="${prep_d}/sub-${subj}${ses_str}_T1brain_MSinFA_Warped.nii.gz"
T1_brain_mask_inFA="${prep_d}/sub-${subj}${ses_str}_T1bm_MSinFA_Warped.nii.gz"
MSBP_csf_mask="${prep_d}/sub-${subj}${ses_str}_MSBP_CSF_mask.nii.gz"
MSBP_csf_mask_binv="${ROIs_d}/custom_VOIs/sub-${subj}${ses_str}_MSBP_CSF_mask_binv.nii.gz"
T1_BM_inFA_minCSF="${prep_d}/sub-${subj}${ses_str}_T1bm_MSinFA_minCSF.nii.gz"
RL_in_FA="${prep_d}/sub-${subj}${ses_str}_RL_masks_inFA.nii.gz"
PD25_in_FA="${prep_d}/sub-${subj}${ses_str}_PD25_histological_inFA.nii.gz"
SUIT_in_FA="${prep_d}/sub-${subj}${ses_str}_SUIT_cerebellar_atlas_inFA.nii.gz"
UKBB_in_FA="${prep_d}/sub-${subj}${ses_str}_UKBB_Bstem_VOIs_inFA.nii.gz"
JuHA_in_FA="${prep_d}/sub-${subj}${ses_str}_Juelich_VOIs_inFA.nii.gz"
JHU_in_FA="${prep_d}/sub-${subj}${ses_str}_JHU_VOIs_inFA.nii.gz"
Man_VOIs_in_FA="${prep_d}/sub-${subj}${ses_str}_Manual_VOIs_inFA.nii.gz"
subj_aparc_inFA="${prep_d}/sub-${subj}${ses_str}_aparc_inFA.nii.gz"
subj_aseg_inFA="${prep_d}/sub-${subj}${ses_str}_aseg_inFA.nii.gz"
subj_FS_WMaparc_inFA="${prep_d}/sub-${subj}${ses_str}_WMaparc_inFA.nii.gz"
subj_MSsc3_inFA="${prep_d}/sub-${subj}${ses_str}_MSBP_scale3_inFA.nii.gz"
CFP_aparc_inFA="${prep_d}/sub-${subj}${ses_str}_LC+spine_inFA.nii.gz"
# subj_MSsc1_inFA_uint8="${prep_d}/sub-${subj}${ses_str}_MSBP_scale1_inFA_uint8.nii.gz"
subj_FS_lobes_inFA="${prep_d}/sub-${subj}${ses_str}_FS_lobes_inFA.nii.gz"
subj_FS_2009_inFA="${prep_d}/sub-${subj}${ses_str}_FS_2009_inFA.nii.gz"
subj_FS_Fx_inFA="${prep_d}/sub-${subj}${ses_str}_FS_fornix_inFA.nii.gz"
# subj_T1MSregrid="${tmpo_d}/sub-${subj}${ses_str}_MS_T1w_regridded.nii.gz"
subj_MS_brain="${prep_d}/sub-${subj}${ses_str}_MS_T1w_brain.nii.gz"
##
# parallel breaks
qo=4;
function PD25_lab_gen {
PD25_labels_LT=("PD25_DM_LT" "PD25_DL_LT" "PD25_VA_LT" "PD25_VL_LT" "PD25_VPL_LT" "PD25_VPM_LT" "PD25_Pulvi_LT" \
"PD25_MG_LT" "PD25_RN_LT");
PD25_labels_RT=("PD25_DM_RT" "PD25_DL_RT" "PD25_VA_RT" "PD25_VL_RT" "PD25_VPL_RT" "PD25_VPM_RT" "PD25_Pulvi_RT" \
"PD25_MG_RT" "PD25_RN_RT");
PD25_vals_RT=("37" "40" "53" "26" "28" "36" "89" \
"86" "87" "88" "90" "91" "92" "93" "94" "104" \
"111" "112" "114" "120" "123" "96" "97" "98" \
"115" "117" "118" "95" "113" \
"102" "103" "105" "106" "107" "116" "119" "68" "48");
PD25_vals_LT=("3700" "4000" "5300" "2600" "2800" "3600" "8900" \
"8600" "8700" "8800" "9000" "9100" "9200" "9300" "9400" "10400" \
"11100" "11200" "11400" "12000" "12300" "9600" "9700" "9800" \
"11500" "11700" "11800" "9500" "11300" \
"10200" "10300" "10500" "10600" "10700" "11600" "11900" "6800" "4800");
# this should be 36 entries per side + RNs
# vals outnumber labels, as each nucleus (label) constitutes
# multiple ROIs from the atlas
srch_PD25Ls=($(find ${ROIs_d}/custom_VOIs -type f | grep "PD25_VPALPLPM_RT_custom.nii.gz"))
if [[ ! ${srch_PD25Ls} ]]; then
qs=0;
for hl in ${!PD25_vals_LT[@]}; do
((qs++))
((qs=${qs}%${qo}))
echo " separating PD25_LT ROIs" >> ${prep_log2}
# isolate rois
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${PD25_in_FA} ${MSBP_csf_mask_binv} -mult ${PD25_vals_LT[$hl]} \
-eq ${tmpo_d}/PD25_ROI_${PD25_vals_LT[$hl]}_LT_custom.nii.gz"
task_exec &
if [[ ${qs} == 0 ]]; then
wait
fi
done
# sleep 200
wait
# unset hl
qs=0;
for hr in ${!PD25_vals_RT[@]}; do
((qs++))
((qs=${qs}%${qo}))
echo " separating PD25_RT ROIs" >> ${prep_log2}
# isolate rois
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${PD25_in_FA} ${MSBP_csf_mask_binv} -mult ${PD25_vals_RT[$hr]} \
-eq ${tmpo_d}/PD25_ROI_${PD25_vals_RT[$hr]}_RT_custom.nii.gz"
task_exec &
if [[ ${qs} == 0 ]]; then
wait
fi
done
wait
sleep 50
# unset hr
# make nuclei
echo " Creating PD25 derived thalamic VOIs " >> ${prep_log2}
##################
VA_rois_RT=("26" "28" "36" "89");
VA_rois_LT=("2600" "2800" "3600" "8900");
VL_rois_RT=("86" "87" "88" "90" "91" "92" "93" "94" "104" \
"111" "112" "114" "120" "123");
VL_rois_LT=("8600" "8700" "8800" "9000" "9100" "9200" "9300" "9400" "10400" \
"11100" "11200" "11400" "12000" "12300");
VPL_rois_RT=("96" "97" "98" "115" "117" "118");
VPL_rois_LT=("9600" "9700" "9800" "11500" "11700" "11800");
VPM_rois_RT=("95" "113");
VPM_rois_LT=("9500" "11300");
PUL_rois_RT=("102" "103" "105" "106" "107" "116" "119");
PUL_rois_LT=("10200" "10300" "10500" "10600" "10700" "11600" "11900");
# Isolate the thalamus from the aparc
# We use this to refine PD25 thalamic VOIs
task_in="mrcalc -force -datatype uint16 -force -nthreads ${ncpu} ${subj_aparc_inFA} 10 -eq 0 -gt ${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz \
&& mrcalc -force -datatype uint16 -force -nthreads ${ncpu} ${subj_aparc_inFA} 49 -eq 0 -gt ${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz"
task_exec
# DM
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_37_RT_custom.nii.gz ${tmpo_d}/PD25_ROI_40_RT_custom.nii.gz \
-add 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_DM_RT_custom.nii.gz -force"
task_exec &
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_3700_LT_custom.nii.gz ${tmpo_d}/PD25_ROI_4000_LT_custom.nii.gz \
-add 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_DM_LT_custom.nii.gz -force"
task_exec &
#################################
# DL
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_53_RT_custom.nii.gz 0.5 -gt - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - \
0.5 -gt ${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_DL_RT_custom.nii.gz"
task_exec &
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_5300_LT_custom.nii.gz 0.5 -gt - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - \
0.5 -gt ${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_DL_LT_custom.nii.gz"
task_exec &
#################################
# VA
VA_adds_RT=$(printf " ${tmpo_d}/PD25_ROI_%s_RT_custom.nii.gz -add" "${VA_rois_RT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_26_RT_custom.nii.gz ${tmpo_d}/PD25_ROI_28_RT_custom.nii.gz -add \
${VA_adds_RT} 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VA_RT_custom.nii.gz -force"
task_exec
VA_adds_LT=$(printf " ${tmpo_d}/PD25_ROI_%s_LT_custom.nii.gz -add" "${VA_rois_LT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_2600_LT_custom.nii.gz ${tmpo_d}/PD25_ROI_2800_LT_custom.nii.gz -add \
${VA_adds_LT} 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VA_LT_custom.nii.gz -force"
task_exec
#################################
# VL
VL_adds_RT=$(printf " ${tmpo_d}/PD25_ROI_%s_RT_custom.nii.gz -add" "${VL_rois_RT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_86_RT_custom.nii.gz ${tmpo_d}/PD25_ROI_87_RT_custom.nii.gz -add \
${VL_adds_RT} 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VL_RT_custom.nii.gz -force"
task_exec &
VL_adds_LT=$(printf " ${tmpo_d}/PD25_ROI_%s_LT_custom.nii.gz -add" "${VL_rois_LT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_8600_LT_custom.nii.gz ${tmpo_d}/PD25_ROI_8700_LT_custom.nii.gz -add \
${VL_adds_LT} 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VL_LT_custom.nii.gz -force"
task_exec &
#################################
# VPL
VPL_adds_RT=$(printf " ${tmpo_d}/PD25_ROI_%s_RT_custom.nii.gz -add" "${VPL_rois_RT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_96_RT_custom.nii.gz ${tmpo_d}/PD25_ROI_97_RT_custom.nii.gz -add \
${VPL_adds_RT} 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VPL_RT_custom.nii.gz -force"
task_exec &
VPL_adds_LT=$(printf " ${tmpo_d}/PD25_ROI_%s_LT_custom.nii.gz -add" "${VPL_rois_LT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_9600_LT_custom.nii.gz ${tmpo_d}/PD25_ROI_9700_LT_custom.nii.gz -add \
${VPL_adds_LT} 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VPL_LT_custom.nii.gz -force"
task_exec &
#################################
# VPM
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_95_RT_custom.nii.gz ${tmpo_d}/PD25_ROI_113_RT_custom.nii.gz -add \
0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VPM_RT_custom.nii.gz -force"
task_exec
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_9500_LT_custom.nii.gz ${tmpo_d}/PD25_ROI_11300_LT_custom.nii.gz -add \
0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_VPM_LT_custom.nii.gz -force"
task_exec
#################################
# Pulvi
# switched to -npass 2 dilation with maskfilter from mriflter only for the pulvies
PUL_adds_RT=$(printf " ${tmpo_d}/PD25_ROI_%s_RT_custom.nii.gz -add" "${PUL_rois_RT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_102_RT_custom.nii.gz ${tmpo_d}/PD25_ROI_103_RT_custom.nii.gz -add \
${PUL_adds_RT} 0.5 -gt - | maskfilter - dilate -npass 1 - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_Pulvi_RT_custom.nii.gz -force"
task_exec &
PUL_adds_LT=$(printf " ${tmpo_d}/PD25_ROI_%s_LT_custom.nii.gz -add" "${PUL_rois_LT[@]:2}")
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_10200_LT_custom.nii.gz ${tmpo_d}/PD25_ROI_10300_LT_custom.nii.gz -add \
${PUL_adds_LT} 0.5 -gt - | maskfilter - dilate -npass 1 - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_Pulvi_LT_custom.nii.gz -force"
task_exec &
#################################
# # MG
# task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_68_RT_custom.nii.gz 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
# ${ROIs_d}/custom_VOIs/Thalamus_RT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_MG_RT_custom.nii.gz -force"
# task_exec &
# task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_6800_LT_custom.nii.gz 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
# ${ROIs_d}/custom_VOIs/Thalamus_LT_FS_custom.nii.gz -mult ${ROIs_d}/custom_VOIs/PD25_MG_LT_custom.nii.gz -force"
# task_exec &
#################################
# Red Nucleus
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_48_RT_custom.nii.gz 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/PD25_RN_RT_custom.nii.gz -force"
task_exec
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${tmpo_d}/PD25_ROI_4800_LT_custom.nii.gz 0.5 -gt - | mrfilter - smooth - | maskfilter - connect -largest -connectivity - | mrcalc -force -datatype uint16 - 0.5 -gt \
${ROIs_d}/custom_VOIs/PD25_RN_LT_custom.nii.gz -force"
task_exec
###
# this will be used for the ORs, ML and the thalamic radiations
task_in="mrcalc -force -datatype uint16 -force -nthreads 1 ${ROIs_d}/custom_VOIs/PD25_VA_LT_custom.nii.gz ${ROIs_d}/custom_VOIs/PD25_VL_LT_custom.nii.gz -add 0.5 -gt ${ROIs_d}/custom_VOIs/PD25_VA_VL_LT_custom.nii.gz && \
mrcalc -force -datatype uint16 -force -nthreads 1 ${ROIs_d}/custom_VOIs/PD25_VPL_LT_custom.nii.gz ${ROIs_d}/custom_VOIs/PD25_VPM_LT_custom.nii.gz -add 0.5 -gt ${ROIs_d}/custom_VOIs/PD25_VPL_VPM_LT_custom.nii.gz && \
mrcalc -force -datatype uint16 -force -nthreads 1 ${ROIs_d}/custom_VOIs/PD25_VA_VL_LT_custom.nii.gz ${ROIs_d}/custom_VOIs/PD25_VPL_VPM_LT_custom.nii.gz -add 0.5 -gt ${ROIs_d}/custom_VOIs/PD25_VPALPLPM_LT_custom.nii.gz \
&& mrcalc -force -datatype uint16 -force -nthreads 1 ${ROIs_d}/custom_VOIs/PD25_VA_RT_custom.nii.gz ${ROIs_d}/custom_VOIs/PD25_VL_RT_custom.nii.gz -add 0.5 -gt ${ROIs_d}/custom_VOIs/PD25_VA_VL_RT_custom.nii.gz && \
mrcalc -force -datatype uint16 -force -nthreads 1 ${ROIs_d}/custom_VOIs/PD25_VPL_RT_custom.nii.gz ${ROIs_d}/custom_VOIs/PD25_VPM_RT_custom.nii.gz -add 0.5 -gt ${ROIs_d}/custom_VOIs/PD25_VPL_VPM_RT_custom.nii.gz && \
mrcalc -force -datatype uint16 -force -nthreads 1 ${ROIs_d}/custom_VOIs/PD25_VA_VL_RT_custom.nii.gz ${ROIs_d}/custom_VOIs/PD25_VPL_VPM_RT_custom.nii.gz -add 0.5 -gt ${ROIs_d}/custom_VOIs/PD25_VPALPLPM_RT_custom.nii.gz"
task_exec
else
echo "PD25 labels already warped to subject space, skipping " >> ${prep_log2}
fi
}
# initial vars
subj_dwi=($(find ${d_dir} -type f -name "dwi_preproced_reg2T1w.mif"))
subj_fod=($(find ${d_dir} -type f -name "dhollander_wmfod_reg2T1w.mif"))
subj_dt=($(find ${d_dir} -type f -name "dwi_dt_reg2T1w.mif"))
subj_FA=($(find ${d_dir}/qa -type f -name "fa_reg2T1w.nii.gz"))
subj_ADC=($(find ${d_dir}/qa -type f -name "adc_reg2T1w.nii.gz"))
subj_dwi_bm=($(find ${d_dir} -type f -name "dwi_preproced_reg2T1w_mask.nii.gz"))
# find label images
subj_aparc_nii=($(find ${MS_dir} -type f -name "*_desc-aparcaseg_dseg.nii.gz"))
subj_aseg_nii=($(find ${MS_dir} -type f -name "*_desc-aseg_dseg.nii.gz"))
subj_aparc_mgz=($(find ${FS_dir} -type f -name "aparc+aseg.mgz"))
subj_MS_sc3=($(find ${MS_dir} -type f -name "*_label-L2018_desc-scale3_atlas.nii.gz"))
subj_MS_sc1=($(find ${MS_dir} -type f -name "*_label-L2018_desc-scale1_atlas.nii.gz"))
subj_FS_lobes=($(find ${FS_dir} -type f -name "sub-${subj}${ses}_lobes.mgz"))
subj_FS_2009=($(find ${FS_dir} -type f -name "aparc.a2009s+aseg.mgz"))
subj_FS_Fx=($(find ${FS_dir} -type f -name "sub-${subj}${ses_str}_Fx_aseg.mgz"))
subj_FS_WMaparc=($(find ${FS_dir} -type f -name "wmparc.mgz"))
subj_FS_brain=($(find ${FS_dir} -type f -name "brain.nii.gz"))
subj_FS_bm=($(find ${FS_dir} -type f -name "brainmask.nii.gz"))
subj_MS_bm=($(find ${MS_dir} -type f -name "*_desc-brain_mask.nii.gz"))
subj_MS_T1=($(find ${MS_dir} -type f -name "*_desc-cmp_T1w.nii.gz"))
##
temp2subj_str="FS_2_UKBB_${subj}${ses_str}"
temp2subj="${prep_d}/${temp2subj_str}"
MS2FS_str="MS_2_FS_${subj}"
MS2FS="${prep_d}/${MS2FS_str}"
FA2FS_str="${prep_d}/fa_2_UKBB_vFS_${subj}${ses_str}"
FA2MS_str="${prep_d}/fa_2_UKBB_vMS_${subj}${ses_str}"
# split the JuHA labels apart already
GNs=("LGN_RT" "LGN_LT" "MGN_RT" "MGN_LT");
# find your dwis
if [[ ! -f ${subj_dwi} ]]; then
subj_dwi=($(find ${d_dir} -type f -name "*dwi_prep*"))
if [[ ! -f ${subj_dwi} ]]; then
subj_dwi=($(find ${d_dir} -type f -name "*dwi_pp*"))
if [[ ! -f ${subj_dwi} ]]; then
subj_dwi=($(find ${d_dir} -type f -name "*dwi*"))
if [[ ! -f ${subj_dwi} ]]; then
echo "no DWI found, quitting" | tee -a ${prep_log2}
exit 2
else
echo "Potentially unprocessed dwi being used -> ${subj_dwi}, results can be suboptimal" | tee -a ${prep_log2}
fi
else
echo "preprocessed dwi found ${subj_dwi}" | tee -a ${prep_log2}
fi
fi
fi
# find FODs
if [[ -z ${subj_fod} ]]; then
subj_fod=($(find ${d_dir} -type f -name "*wmfod_reg2T1w.mif"))
if [[ -z ${subj_fod} ]]; then
subj_fod=($(find ${d_dir} -type f -name "*wmfod*"))
if [[ -z ${subj_fod} ]]; then
echo "no FODs found, quitting" | tee -a ${prep_log2}
exit 2
fi
fi
fi
# find diff brain mask
if [[ ! -f ${subj_dwi_bm} ]]; then
subj_dwi_bm=($(find ${d_dir} -type f -name "dwi_mask.nii.gz"))
if [[ ! -f ${subj_dwi_bm} ]]; then
subj_dwi_bm=($(find ${d_dir} -type f -name "*brain_mask*"))
if [[ ! -f ${subj_dwi_bm} ]]; then
echo "no dwi brain mask found, quitting" | tee -a ${prep_log2}
exit 2
fi
fi
fi
pt1_done="${ROIs_d}/Part1.done"
srch_pt1_done=($(find ${ROIs_d} -not -path '*/\.*' -type f | grep "Part1.done"))
if [[ -z ${srch_pt1_done} ]]; then
echo " general purpose steps "
# subject dwi inputs
# find dwis, fods, and make dt, and derivatives if not found
# these strings are currently hardcoded to work with KUL_NITs output
# and the HCP data we've preproced
# right now the FA being used is not the right one
# must handle multiple instances, in case KUL_dwiprep_2_MNI has been applied - on it
# we assume the T1s and dMRIs are already registered right?
if [[ ! -f ${subj_MS_brain} ]]; then
task_in="mrgrid -force -nthreads ${ncpu} -template ${subj_MS_bm} ${subj_MS_T1} \
regrid - | mrcalc - ${subj_MS_bm} -mult ${subj_MS_brain} -force -nthreads ${ncpu}"
task_exec
fi
if [[ ! -f ${subj_dt} ]]; then
subj_dt=($(find ${d_dir} -type f -name "*_tensor*"))
if [[ ! -f ${subj_dt} ]]; then
subj_dt="${prep_d}/sub-${subj}_tensor.mif"
subj_FA="${prep_d}/fa.nii.gz"
subj_ADC="${prep_d}/adc.nii.gz"
echo "no Diffusion tensor found, we will make it and its derivatives" | tee -a ${prep_log2}
task_in="dwi2tensor -force -nthreads ${ncpu} -mask ${subj_dwi_bm} ${subj_dwi} ${subj_dt} \
&& tensor2metric -force -nthreads ${ncpu} -mask ${subj_dwi_bm} -fa ${subj_FA} -adc ${subj_ADC} \
${subj_dt}"
task_exec
else
echo " Diffusion tensor found, this data is not preprocessed using KUL_NITs " | tee -a ${prep_log2}
subj_FA=($(find ${d_dir} -type f -name "FA.nii.gz"));
subj_ADC=($(find ${d_dir} -type f -name "ADC.nii.gz"));
if [[ -z ${subj_FA} ]] || [[ -z ${subj_ADC} ]]; then
subj_FA="${prep_d}/fa.nii.gz"
subj_ADC="${prep_d}/adc.nii.gz"