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KUL_lesion_fs_recall.sh
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KUL_lesion_fs_recall.sh
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#!/bin/bash
set -x
# Ahmed Radwan ahmed.radwan@kuleuven.be
# Stefan Sunaert stefan.sunaert@kuleuven.be
# # v 1.0 - dd 20/03/2019 - dev Alpha
v="1.0 - dd 20/03/2019"
# This script is meant for allowing a decent recon-all output in the presence of a large brain lesion
# It is not a final end-all solution but a rather crude and simplistic work around
# The main idea is to replace the lesion with a hole and fill the hole with information from normal hemisphere # maintains subject specificity and diseased hemisphere information but replaces lesion tissue with sham brain
# should be followed by a loop calculating overlap between fake labels resulting from sham brain with actual lesion
# To do: #
# - A similar approach for bilateral lesions could still work, using a population template perhaps ?
# - improve lesion fill patch ( elastic registration ?)
# - Use also MNI space images in recon-all
# - add N4 bias correction to MNI space images
# - test -a -t -f and -s flags
# - Add QC step similarity measure as follows:
# MeasureImageSimilarity -d 3 --metric MI[../../../BIDS/sub-PT01/anat/sub-PT01_T1w.nii.gz,../../../lesion_wf/lesion_wf_output/sub-PT01/sub-PT01_T1nat_T1_sim_lesionless_Warped.nii.gz,1,64] \
# --masks [../../../lesion_wf/lesion_wf_preproc/sub-PT01/sub-PT01_MNI_brain_mask_in_T1nat_minlesion.nii.gz,../../../lesion_wf/lesion_wf_preproc/sub-PT01/sub-PT01_MNI_mask_min_lesion.nii.gz] \
# -o ./test_im_sim_MI.nii.gz -v
# - add a sharpening step to the hemispheres before generating the lesion_fill
# also do a sharpening step to the image before making the hole and replacing the lesion with the fill patch.
# Description:
# Info and Instructions:
# This functiona in its current state is a WIP for S61759 AR,SK,EC,TT,PD,SS
# - KUL_Lesion_FSrecall takes as input T1, T2, FLAIR and a lesion mask
# - The end result is running Freesurfer recon-all on lesioned brains
# - We start with unprocessed data
# - At least 2 modalities (T1 + * ) are required plus a lesion mask
# - The idea is to use warped healthy subject specific brain tissue to fill the lesioned area.
# - Takes as input: subject_label, BIDS_dir, lesion mask file path & name
# Steps:
# - The input images are rigidly aligned to the T1, T1 affine 2 MNI, then all to MNI
# - The MNI images are flipped in LR # % - The lesion mask in binarized and inverted in MNI + either smoothed or dilated
# - This is followed by a rough brain extraction in MNI
# - The lesion & brain masks are combined with apriori left right split masks in MNI
# - Left & right hemispheres are split from the rough BET in MNI images
# - Determine if lesion is R or L, and warp as follows
# - Use lesioned_side-lesion_mask as target mask (fixed image MNI unflip brain)
# - Use lesioned_side_w_lesion mask as input mask (source image MNI flip brain)
# - Lesion fill is created out of the warped healthy to unhealthy brain tissue
# - Lesion fill is inserted in place of lesion in original MNI images
# - Inverse warp to native space T1
# - Use both native T1&T2 and MNIT1&T2 to run recon-all as if we have two sessions with two modalities each.
# - Calculate percentage volume overlap with each lobe.
# - Move results to KUL_NITs location # % @ Ahmed Radwan (ahmed.radwan@kuleuven.be) 07/03/2019
# Requires: FSL, Freesurfer, T1 and T2 WIs and lesion mask out of itk-snap
# to add a lesion argument later
# - lesion mask name should include space, modality, and adhere to BIDS naming scheme
# ----------------------------------- MAIN ---------------------------------------------
# this script uses "preprocessing control", i.e. if some steps are already processed it will skip these
kul_lesion_dir=`dirname "$0"`
script=`basename "$0"`
# source $kul_main_dir/KUL_main_functions.sh
cwd=($(pwd))
# FUNCTIONS --------------
# function Usage
function Usage {
cat <<USAGE
`basename $0` preps structural images with lesions and runs recon-all.
Usage:
`basename $0` -p subject <OPT_ARGS> -l <OPT_ARGS> -z <OPT_ARGS> -b
or
`basename $0` -p subject <OPT_ARGS> -a <OPT_ARGS> -b <OPT_ARGS> -c <OPT_ARGS> -l <OPT_ARGS> -z <OPT_ARGS>
Examples:
`basename $0` -p pat001 -b -n 6 -l /fullpath/lesion_T1w.nii.gz -z T1 -o /fullpath/output
`basename $0` -p pat001 -n 6 -a /fullpath/T1w.nii.gz -b /fullpath/T2w.nii.gz -l /fullpath/lesion_T2w.nii.gz -z T2
`basename $0` -p pat001 -n 6 -a /fullpath/T1w.nii.gz -c /fullpath/flair.nii.gz -l /fullpath/lesion_flair.nii.gz -z FLAIR
Required arguments:
-p: BIDS participant name (anonymised name of the subject without the "sub-" prefix)
-b: if data is in BIDS
-l: full path and file name to lesion mask file per session
-z: space of the lesion mask used (T1, T2, or FLAIR)
-a: full path and file name to T1
-t: full path and file name to T2
-f: full path and file name to T2 FLAIR
-m: full path to intermediate output dir
-o: full path to output dir (if not set reverts to default output ./lesion_wf_output)
(This workflow require at least 2 modalities T1 + T2 or FLAIR)
Optional arguments:
-s: session (of the participant)
-n: number of cpu for parallelisation
-v: show output from mrtrix commands
-h: prints help menu
USAGE
exit 1
}
# CHECK COMMAND LINE OPTIONS -------------
#
# Set defaults
ncpu=6
silent=1
# Set required options
p_flag=0
bids_flag=0
s_flag=0
l_flag=0
l_spaceflag=0
t1_flag=0
t2_flag=0
flair_flag=0
o_flag=0
m_flag=0
n_flag=0
if [ "$#" -lt 1 ]; then
Usage >&2
exit 1
else
while getopts "p:a:t:f:l:z:s:o:m:n:bvh" OPT; do
case $OPT in
p) #subject
p_flag=1
subj=$OPTARG
;;
b) #BIDS or not ?
bids_flag=1
;;
a) #T1 WIs
t1_flag=1
t1_orig=$OPTARG
;;
t) #T2 WIs
t2_flag=1
t2_orig=$OPTARG
;;
f) #Flair WIs
flair_flag=1
flair_orig=$OPTARG
;;
s) #session
s_flag=1
ses=$OPTARG
;;
l) #lesion_mask
l_flag=1
L_mask=$OPTARG
;;
z) #lesion_mask
l_spaceflag=1
L_mask_space=$OPTARG
;;
m) #intermediate output
m_flag=1
wf_dir=$OPTARG
;;
o) #output
o_flag=1
out_dir=$OPTARG
;;
n) #parallel
n_flag=1
ncpu=$OPTARG
;;
v) #verbose
silent=0
;;
h) #help
Usage >&2
exit 0
;;
\?)
echo "Invalid option: -$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 inputs and define your workflow accordingly
if [[ $p_flag -eq 0 || $l_flag -eq 0 || $l_spaceflag -eq 0 ]]; then
echo
echo "Inputs -p -lesion -lesion_space must be set." >&2
echo
exit 2
else
echo "Inputs are -p " $subj " -lesion " $L_mask " -lesion_space " $L_mask_space
fi
if [[ $bids_flag -eq 1 && $s_flag -eq 0 ]]; then
# bids flag defined but not session flag
search_sessions=($(find ${cwd}/BIDS/sub-${subj} -type d | grep anat));
num_sessions=${#search_sessions[@]};
ses_long="";
if [[ $num_sessions -eq 1 ]]; then
echo " we have one session in the BIDS dir, this is good."
# now we need to search for the images
# here we also need to search for the images
# then also find which modalities are available and set wf accordingly
search_T1=($(find $search_sessions -type f | grep T1w.nii.gz));
search_T2=($(find $search_sessions -type f | grep T2w.nii.gz));
search_FLAIR=($(find $search_sessions -type f | grep FLAIR.nii.gz));
if [[ $search_T1 ]]; then
T1_orig=$search_T1
echo " We found T1 WIs " $T1_orig
else
echo " no T1 WIs found in BIDS dir, exiting"
exit 2
fi
if [[ $search_T2 && ! $search_FLAIR ]]; then
wf=1;
T2_orig=$search_T2;
echo " We found also T2 WIs, but no FLAIR WIs "
elif [[ ! $search_T2 && $search_FLAIR ]]; then
wf=2;
FLAIR_orig=$search_FLAIR;
echo " We found also FLAIR WIs, but no T2 WIs "
elif [[ $search_T2 && $search_FLAIR ]]; then
wf=3;
T2_orig=$search_T2;
FLAIR_orig=$search_FLAIR;
echo " We found also T2 WIs, and FLAIR WIs "
else
echo " This script requires at least T1 WIs + either T2 or FLAIR WIs, exiting."
exit 2
fi
else
echo " There's a problem with sessions in BIDS dir. "
echo " Please double check your data structure &/or specify one session with -s if you have multiple ones. "
exit 2
fi
elif [[ $bids_flag -eq 1 && $s_flag -eq 1 ]]; then
# this is fine
search_sessions=($(find ${cwd}/BIDS/sub-${subj}_ses-${ses} -type d | grep anat));
num_sessions=1;
ses_long=_ses-0${num_sessions};
# here we also need to search for the images
# then also find which modalities are available and set wf accordingly
if [[ $num_sessions -eq 1 ]]; then
echo " One session " $ses " specified in BIDS dir, good."
# now we need to search for the images
# here we also need to search for the images
# then also find which modalities are available and set wf accordingly
search_T1=($(find $search_sessions -type f | grep T1w.nii.gz));
search_T2=($(find $search_sessions -type f | grep T2w.nii.gz));
search_FLAIR=($(find $search_sessions -type f | grep flair.nii.gz));
if [[ $search_T1 ]]; then
T1_orig=$search_T1;
echo " We found T1 WIs " $T1_orig
else
echo " no T1 WIs found in BIDS dir, exiting "
exit 2
fi
if [[ $search_T2 && ! $search_FLAIR ]]; then
wf=1;
T2_orig=$search_T2;
echo " We found also T2 WIs, but no FLAIR WIs "
elif [[ ! $search_T2 && $search_FLAIR ]]; then
wf=2;
FLAIR_orig=$search_FLAIR;
echo " We found also FLAIR WIs, but no T2 WIs "
elif [[ $search_T2 && $search_FLAIR ]]; then
wf=3;
T2_orig=$search_T2;
FLAIR_orig=$search_FLAIR;
echo " We found also T2 WIs, and FLAIR WIs "
else
echo " This script requires at least T1 WIs + either T2 or FLAIR WIs, exiting."
exit 2
fi
elif [[ $bids_flag -eq 0 && $s_flag -eq 0 ]]; then
# this is fine if T1 and T2 and/or flair are set
# find which ones are set and define wf accordingly
ses_long="";
if [[ $t1_flag ]]; then
T1_orig=$t1_orig
else
echo " No T1 WIs specified, exiting. "
exit 2
fi
if [[ $seach_T1 && $search_T2 && ! $search_FLAIR ]]; then
wf=1;
T2_orig=$search_T2;
echo " We also have T2 WIs, but no FLAIR WIs "
elif [[ $seach_T1 && ! $search_T2 && $search_FLAIR ]]; then
wf=2;
FLAIR_orig=$search_FLAIR;
echo " We also have FLAIR WIs, but no T2 WIs "
elif [[ $seach_T1 && $search_T2 && $search_FLAIR ]]; then
wf=3;
T2_orig=$search_T2;
FLAIR_orig=$search_FLAIR;
echo " We also have T2 WIs, and FLAIR WIs "
else
echo " This script requires at least T1 WIs + either T2 or FLAIR WIs, exiting."
exit 2
fi
elif [[ $bids_flag -eq 0 && $s_flag -eq 1 ]]; then
echo " Wrong optional arguments, we can't have sessions without BIDS, exiting."
exit 2
fi
fi
function_path=($(which KUL_lesion_fs_recall.sh | rev | cut -d"/" -f2- | rev))
# REST OF SETTINGS ---
# timestamp
start_t=$(date +%s)
# 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=$ncpu; export OMP_NUM_THREADS
d=$(date "+%Y-%m-%d_%H-%M-%S");
log=log/log_${d}.txt;
# --- MAIN ----------------
# here we give session invariate variables (e.g. template images)
# only in for WIP - R 09-03-2019
# subj=BAC
# The necessary priors
# need to use multiple templates here...
# will need to include a folder with priors
MNI_T1=${function_path}/atlasses/Templates/MNI_T1.nii.gz
MNI_T1_brain=${function_path}/atlasses/Templates/MNI_T1_brain.nii.gz
# MNI_T2=${function_path}/atlasses/Templates/MNI_T2.nii.gz
MNI_T2_brain=${function_path}/atlasses/Templates/MNI_T2_brain.nii.gz
# MNI_FLAIR=${function_path}/atlasses/Templates/MNI_FLAIR.nii.gz
MNI_FLAIR_brain=${function_path}/atlasses/Templates/MNI_FLAIR_brain.nii.gz
MNI_brain_mask=${function_path}/atlasses/Templates/MNI_brain_mask.nii.gz
MNI_rl=${function_path}/atlasses/Templates/MNI_RL1c_labels.nii.gz
# Either a session is given on the command line
# If not the session(s) need to be determined.
# ---- BIG LOOP for processing each session
#
for current_session in `seq 0 $(($num_sessions-1))`; do
cd $cwd
long_bids_subj=${search_sessions[$current_session]}
echo $long_bids_subj
bids_subj=${long_bids_subj%anat}
echo $bids_subj
lesion_wf=${cwd}/lesion_wf
# output
if [[ $o_flag -eq 1 ]]; then
output=$out_dir
else
output=${lesion_wf}/lesion_wf_output/sub-${subj}${ses_long}
fi
# intermediate folder
if [[ $m_flag -eq 1 ]]; then
preproc=$wf_dir
else
preproc=${lesion_wf}/lesion_wf_preproc/sub-${subj}${ses_long}
fi
echo $lesion_wf
ROIs=${output}/ROIs
overlap=${output}/overlap
# make your dirs
mkdir -p ${preproc}
mkdir -p ${output}
mkdir -p ${ROIs}
mkdir -p ${overlap}
# The lesion as provided (this depends on the session)
L_mask_bin=${L_mask::${#L_mask}-7}.nii.gz
fslmaths $L_mask -bin $L_mask_bin
L_mask_orig=${L_mask_bin}
L_mask_binv_in_T1=${preproc}/sub-${subj}${ses_long}_L_mask_binv_T1.nii.gz
L_mask_in_MNI=${preproc}/sub-${subj}${ses_long}_L_mask_in_MNI.nii.gz
L_mask_in_MNI_dil=${preproc}/sub-${subj}${ses_long}_L_mask_dil_in_MNI.nii.gz
L_mask_in_MNI_dil_binv=${preproc}/sub-${subj}${ses_long}_L_mask_dil_binv_in_MNI.nii.gz
MNI_mask_min_lesion=${preproc}/sub-${subj}${ses_long}_MNI_mask_min_lesion.nii.gz
lesion_left_hemi_overlap=${preproc}/sub-${subj}${ses_long}_lesion_left_hemi_overlap.nii.gz
lesion_right_hemi_overlap=${preproc}/sub-${subj}${ses_long}_lesion_right_hemi_overlap.nii.gz
# vars for images
T2_in_T1=${preproc}/sub-${subj}${ses_long}_T2_in_T1_Warped.nii.gz
FLAIR_in_T1=${preproc}/sub-${subj}${ses_long}_FLAIR_in_T1_Warped.nii.gz
T2_to_T1_affine=${preproc}/sub-${subj}${ses_long}_T2_in_T1_0GenericAffine.mat
FLAIR_to_T1_affine=${preproc}/sub-${subj}${ses_long}_FLAIR_in_T1_0GenericAffine.mat
T1_in_MNI=${preproc}/sub-${subj}${ses_long}_T1_in_MNI_Warped.nii.gz
T1_N4BFC=${preproc}/sub-${subj}${ses_long}_T1_N4BFC.nii.gz
T2_N4BFC=${preproc}/sub-${subj}${ses_long}_T2_N4BFC.nii.gz
FLAIR_N4BFC=${preproc}/sub-${subj}${ses_long}_FLAIR_N4BFC.nii.gz
MNI_brain_mask_in_nat=${preproc}/sub-${subj}${ses_long}_MNI_brain_mask_in_T1nat.nii.gz
MNI_brain_mask_in_nat_min_lesion=${preproc}/sub-${subj}${ses_long}_MNI_brain_mask_in_T1nat_minlesion.nii.gz
T1_in_MNI_brain=${preproc}/sub-${subj}${ses_long}_T1_in_MNI_BrainExtractionBrain.nii.gz
subj_brain_mask_in_MNI=${preproc}/sub-${subj}${ses_long}_T1_in_MNI_BrainExtractionMask.nii.gz
T1_in_MNI_brain_flip=${preproc}/sub-${subj}${ses_long}_flip_T1_in_MNI_brain.nii.gz
T1_in_MNI_SyN_brain_flip=${preproc}/sub-${subj}${ses_long}_flip_T1_brain_in_MNI_SyN_Warped.nii.gz
T2_in_MNI=${preproc}/sub-${subj}${ses_long}_T2_in_MNI_Warped.nii.gz
T2_in_MNI_brain=${preproc}/sub-${subj}${ses_long}_T2_in_MNI_brain.nii.gz
T2_in_MNI_brain_flip=${preproc}/sub-${subj}${ses_long}_flip_T2_in_MNI_brain.nii.gz
T2_in_MNI_SyN_brain_flip=${preproc}/sub-${subj}${ses_long}_flip_T2_brain_in_MNI_SyN_Warped.nii.gz
FLAIR_in_MNI=${preproc}/sub-${subj}${ses_long}_FLAIR_in_MNI_Warped.nii.gz
FLAIR_in_MNI_brain=${preproc}/sub-${subj}${ses_long}_FLAIR_in_MNI_brain.nii.gz
FLAIR_in_MNI_brain_flip=${preproc}/sub-${subj}${ses_long}_flip_FLAIR_in_MNI_brain.nii.gz
FLAIR_in_MNI_SyN_brain_flip=${preproc}/sub-${subj}${ses_long}_flip_FLAIR_brain_in_MNI_SyN_Warped.nii.gz
T1_to_MNI_affine=${preproc}/sub-${subj}${ses_long}_T1_in_MNI_0GenericAffine.mat
T1_with_lesion_fill_MNI=${output}/sub-${subj}${ses_long}_MNI_T1_sim_lesionless.nii.gz
T2_with_lesion_fill_MNI=${output}/sub-${subj}${ses_long}_MNI_T2_sim_lesionless.nii.gz
FLAIR_with_lesion_fill_MNI=${output}/sub-${subj}${ses_long}_MNI_FLAIR_sim_lesionless.nii.gz
T1_with_lesion_fill_T1nat=${output}/sub-${subj}${ses_long}_T1nat_T1_sim_lesionless_Warped.nii.gz
T2_with_lesion_fill_T1nat=${output}/sub-${subj}${ses_long}_T1nat_T2_sim_lesionless_Warped.nii.gz
FLAIR_with_lesion_fill_T1nat=${output}/sub-${subj}${ses_long}_T1nat_FLAIR_sim_lesionless_Warped.nii.gz
MNI_left=${preproc}/MNI_left_bin.nii.gz
MNI_right=${preproc}/MNI_right_bin.nii.gz
# kul_e2cl " Start processing $bids_subj" ${preproc}/${log}
cd $preproc
# determine which workflow we need to apply and run it.
# this is distributed in nested if loops
# processing control flags are called wf_mark, listed below.
wf_mark1=${preproc}"/first_part_done.done"
wf_mark2=${preproc}"/second_part_done.done"
wf_mark3=${preproc}"/third_part_done.done"
search_wf_mark1=($(find ${preproc} -type f | grep first_part_done.done));
search_wf_mark2=($(find ${preproc} -type f | grep second_part_done.done));
search_wf_mark3=($(find ${preproc} -type f | grep third_part_done.done));
if [[ ! $search_wf_mark1 ]] ; then
N4BiasFieldCorrection -d 3 -i $T1_orig -o $T1_N4BFC
antsRegistrationSyNQuick.sh -d 3 -f $MNI_T1 -m $T1_N4BFC -t a -o ${preproc}/sub-${subj}${ses_long}_T1_in_MNI_ -n ${ncpu}
# This screws me over big time! let's do a respectable BET
# fslmaths $T1_in_MNI -mas $subj_brain_mask_in_MNI $T1_in_MNI_brain
antsBrainExtraction.sh -d 3 -a ${T1_in_MNI} -e ${MNI_T1} -m ${MNI_brain_mask} -o ${preproc}/sub-${subj}${ses_long}_T1_in_MNI_ -u 1
sleep 2
WarpImageMultiTransform 3 $subj_brain_mask_in_MNI $MNI_brain_mask_in_nat -R $T1_orig -i $T1_to_MNI_affine
fslmaths $MNI_brain_mask_in_nat -bin $MNI_brain_mask_in_nat
fslswapdim $T1_in_MNI_brain -x y z $T1_in_MNI_brain_flip
fslorient -swaporient $T1_in_MNI_brain_flip
echo " first part done. " >> $wf_mark1
else
echo " fist part already done, skipping. "
fi
if [[ ! $search_wf_mark2 ]] ; then
if [[ $wf -eq 1 ]]; then
N4BiasFieldCorrection -d 3 -i $T2_orig -o $T2_N4BFC
antsRegistrationSyNQuick.sh -d 3 -f $T1_orig -m $T2_N4BFC -t a -o $preproc/sub-${subj}${ses_long}_T2_in_T1_ -n ${ncpu}
WarpImageMultiTransform 3 $T2_in_T1 $T2_in_MNI -R $MNI_T1 $T1_to_MNI_affine
fslmaths $T2_in_MNI -mas $subj_brain_mask_in_MNI $T2_in_MNI_brain
if [[ $L_mask_space == "T1" ]] ; then
L_mask_in_T1=$L_mask_orig
elif [[ $L_mask_space == "T2" ]] ; then
L_mask_in_T2=$L_mask_orig
L_mask_in_T1=$preproc/sub-${subj}${ses_long}_L_mask_in_T2_to_T1.nii.gz
WarpImageMultiTransform 3 $L_mask_in_T2 $L_mask_in_T1 -R $T1_orig $T2_to_T1_affine
fslmaths $L_mask_in_T1 -bin $L_mask_in_T1
fi
# flip T2 in MNI
fslswapdim $T2_in_MNI_brain -x y z $T2_in_MNI_brain_flip
fslorient -swaporient $T2_in_MNI_brain_flip
WarpImageMultiTransform 3 $L_mask_in_T1 $L_mask_in_MNI -R $MNI_T1 $T1_to_MNI_affine
fslmaths $L_mask_in_MNI -dilM -bin $L_mask_in_MNI_dil
fslmaths $L_mask_in_MNI_dil -binv $L_mask_in_MNI_dil_binv
fslmaths $subj_brain_mask_in_MNI -mas $L_mask_in_MNI_dil_binv $MNI_mask_min_lesion
# SyN warp the flipped brains to the respective MNI template
antsRegistrationSyNQuick.sh -d 3 -f $MNI_T1_brain -m $T1_in_MNI_brain_flip -t s \
-x $MNI_brain_mask,$MNI_mask_min_lesion -o $preproc/sub-${subj}${ses_long}_flip_T1_brain_in_MNI_SyN_ -n ${ncpu}
antsRegistrationSyNQuick.sh -d 3 -f $MNI_T2_brain -m $T2_in_MNI_brain_flip -t s \
-x $MNI_brain_mask,$MNI_mask_min_lesion -o $preproc/sub-${subj}${ses_long}_flip_T2_brain_in_MNI_SyN_ -n ${ncpu}
elif [[ $wf -eq 2 ]] ; then
N4BiasFieldCorrection -d 3 -i $FLAIR_orig -o $FLAIR_N4BFC
antsRegistrationSyNQuick.sh -d 3 -f $T1_orig -m $FLAIR_N4BFC -t a -o $preproc/sub-${subj}${ses_long}_FLAIR_in_T1_ -n ${ncpu}
WarpImageMultiTransform 3 $FLAIR_in_T1 $FLAIR_in_MNI -R $MNI_T1 $T1_to_MNI_affine
fslmaths $FLAIR_in_MNI -mas $subj_brain_mask_in_MNI $FLAIR_in_MNI_brain
if [[ $L_mask_space == "T1" ]] ; then
L_mask_in_T1=$L_mask_orig
elif [[ $L_mask_space == "FLAIR" ]] ; then
L_mask_in_FLAIR=$L_mask_orig
L_mask_in_T1=$preproc/sub-${subj}${ses_long}_L_mask_in_FLAIR_to_T1.nii.gz
WarpImageMultiTransform 3 $L_mask_in_FLAIR $L_mask_in_T1 -R $T1_orig $FLAIR_to_T1_affine
fslmaths $L_mask_in_T1 -bin $L_mask_in_T1
fi
# flip FLAIR in MNI
fslswapdim $FLAIR_in_MNI_brain -x y z $FLAIR_in_MNI_brain_flip
fslorient -swaporient $FLAIR_in_MNI_brain_flip
WarpImageMultiTransform 3 $L_mask_in_T1 $L_mask_in_MNI -R $MNI_T1 $T1_to_MNI_affine
fslmaths $L_mask_in_MNI -dilM -bin $L_mask_in_MNI_dil
fslmaths $L_mask_in_MNI_dil -binv $L_mask_in_MNI_dil_binv
fslmaths $subj_brain_mask_in_MNI -mas $L_mask_in_MNI_dil_binv $MNI_mask_min_lesion
# SyN warp the flipped brains to the respective MNI template
antsRegistrationSyNQuick.sh -d 3 -f $MNI_T1_brain -m $T1_in_MNI_brain_flip -t s \
-x $MNI_brain_mask,$MNI_mask_min_lesion -o $preproc/sub-${subj}${ses_long}_flip_T1_brain_in_MNI_SyN_ -n ${ncpu}
antsRegistrationSyNQuick.sh -d 3 -f $MNI_FLAIR_brain -m $FLAIR_in_MNI_brain_flip -t s \
-x $MNI_brain_mask,$MNI_mask_min_lesion -o $preproc/sub-${subj}${ses_long}_flip_FLAIR_brain_in_MNI_SyN_ -n ${ncpu}
elif [[ $wf -eq 3 ]] ; then
N4BiasFieldCorrection -d 3 -i $T2_orig -o $T2_N4BFC
N4BiasFieldCorrection -d 3 -i $FLAIR_orig -o $FLAIR_N4BFC
antsRegistrationSyNQuick.sh -d 3 -f $T1_orig -m $FLAIR_N4BFC -t a -o $preproc/sub-${subj}${ses_long}_FLAIR_in_T1_ -n ${ncpu}
antsRegistrationSyNQuick.sh -d 3 -f $T1_orig -m $T2_N4BFC -t a -o $preproc/sub-${subj}${ses_long}_T2_in_T1_ -n ${ncpu}
WarpImageMultiTransform 3 $T2_in_T1 $T2_in_MNI -R $MNI_T1 $T1_to_MNI_affine
WarpImageMultiTransform 3 $FLAIR_in_T1 $FLAIR_in_MNI -R $MNI_T1 $T1_to_MNI_affine
fslmaths $T1_in_MNI -mas $subj_brain_mask_in_MNI $T1_in_MNI_brain
fslmaths $T2_in_MNI -mas $subj_brain_mask_in_MNI $T2_in_MNI_brain
fslmaths $FLAIR_in_MNI -mas $subj_brain_mask_in_MNI $FLAIR_in_MNI_brain
if [[ $L_mask_space == "T1" ]] ; then
L_mask_in_T1=$L_mask_orig
elif [[ $L_mask_space == "T2" ]] ; then
L_mask_in_T2=$L_mask_orig
L_mask_in_T1=$preproc/sub-${subj}${ses_long}_L_mask_in_T2_to_T1.nii.gz
WarpImageMultiTransform 3 $L_mask_in_T2 $L_mask_in_T1 -R $T1_orig $T2_to_T1_affine
fslmaths $L_mask_in_T1 -bin $L_mask_in_T1
elif [[ $L_mask_space == "FLAIR" ]] ; then
L_mask_in_FLAIR=$L_mask_orig
L_mask_in_T1=$preproc/sub-${subj}${ses_long}_L_mask_in_FLAIR_to_T1.nii.gz
WarpImageMultiTransform 3 $L_mask_in_FLAIR $L_mask_in_T1 -R $T1_orig $FLAIR_to_T1_affine
fslmaths $L_mask_in_T1 -bin $L_mask_in_T1
fi
# flip T2 and FLAIR in MNI
fslswapdim $T2_in_MNI_brain -x y z $T2_in_MNI_brain_flip
fslorient -swaporient $T2_in_MNI_brain_flip
fslswapdim $FLAIR_in_MNI_brain -x y z $FLAIR_in_MNI_brain_flip
fslorient -swaporient $FLAIR_in_MNI_brain_flip
WarpImageMultiTransform 3 $L_mask_in_T1 $L_mask_in_MNI -R $MNI_T1 $T1_to_MNI_affine
fslmaths $L_mask_in_MNI -dilM -bin $L_mask_in_MNI_dil
fslmaths $L_mask_in_MNI_dil -binv $L_mask_in_MNI_dil_binv
fslmaths $subj_brain_mask_in_MNI -mas $L_mask_in_MNI_dil_binv $MNI_mask_min_lesion
# SyN warp the flipped brains to the respective MNI template
antsRegistrationSyNQuick.sh -d 3 -f $MNI_T1_brain -m $T1_in_MNI_brain_flip -t s \
-x $MNI_brain_mask,$MNI_mask_min_lesion -o $preproc/sub-${subj}${ses_long}_flip_T1_brain_in_MNI_SyN_ -n ${ncpu}
antsRegistrationSyNQuick.sh -d 3 -f $MNI_T2_brain -m $T2_in_MNI_brain_flip -t s \
-x $MNI_brain_mask,$MNI_mask_min_lesion -o $preproc/sub-${subj}${ses_long}_flip_T2_brain_in_MNI_SyN_ -n ${ncpu}
antsRegistrationSyNQuick.sh -d 3 -f $MNI_FLAIR_brain -m $FLAIR_in_MNI_brain_flip -t s \
-x $MNI_brain_mask,$MNI_mask_min_lesion -o $preproc/sub-${subj}${ses_long}_flip_FLAIR_brain_in_MNI_SyN_ -n ${ncpu}
fi
echo " second part done " >> $wf_mark2
else
echo " second part already done, skipping. "
L_mask_in_T1=($(find ${preproc} -type f | grep _to_T1.nii.gz));
fi
# all workflows collapse to this same step at this point
T1_fake_left_hemi=${preproc}/T1_fake_left_hemi.nii.gz
T2_fake_left_hemi=${preproc}/T2_fake_left_hemi.nii.gz
FLAIR_fake_left_hemi=${preproc}/FLAIR_fake_left_hemi.nii.gz
T1_fake_right_hemi=${preproc}/T1_fake_right_hemi.nii.gz
T2_fake_right_hemi=${preproc}/T2_fake_right_hemi.nii.gz
FLAIR_fake_right_hemi=${preproc}/FLAIR_fake_right_hemi.nii.gz
T1_fake_left_hemi_mask=${preproc}/T1_fake_left_hemi_mask.nii.gz
T2_fake_left_hemi_mask=${preproc}/T2_fake_left_hemi_mask.nii.gz
FLAIR_fake_left_hemi_mask=${preproc}/FLAIR_fake_left_hemi_mask.nii.gz
T1_fake_right_hemi_mask=${preproc}/T1_fake_right_hemi_mask.nii.gz
T2_fake_right_hemi_mask=${preproc}/T2_fake_right_hemi_mask.nii.gz
FLAIR_fake_right_hemi_mask=${preproc}/FLAIR_fake_right_hemi_mask.nii.gz
T1_real_left_hemi=${preproc}/T1_real_left_hemi.nii.gz
T2_real_left_hemi=${preproc}/T2_real_left_hemi.nii.gz
FLAIR_real_left_hemi=${preproc}/FLAIR_real_left_hemi.nii.gz
T1_real_right_hemi=${preproc}/T1_real_right_hemi.nii.gz
T2_real_right_hemi=${preproc}/T2_real_right_hemi.nii.gz
FLAIR_real_right_hemi=${preproc}/FLAIR_real_right_hemi.nii.gz
T1_real_left_hemi_mask_min_lesion=${preproc}/T1_real_left_hemi_mask_min_lesion.nii.gz
T2_real_left_hemi_mask_min_lesion=${preproc}/T2_real_left_hemi_mask_min_lesion.nii.gz
FLAIR_real_left_hemi_mask_min_lesion=${preproc}/FLAIR_real_left_hemi_mask_min_lesion.nii.gz
T1_real_right_hemi_mask_min_lesion=${preproc}/T1_real_right_hemi_mask_min_lesion.nii.gz
T2_real_right_hemi_mask_min_lesion=${preproc}/T2_real_right_hemi_mask_min_lesion.nii.gz
FLAIR_real_right_hemi_mask_min_lesion=${preproc}/FLAIR_real_right_hemi_mask_min_lesion.nii.gz
T1_left_fake_2_real_hemi_SyN=${preproc}/sub-${subj}${ses_long}_T1_left_fake_2_real_hemiWarped.nii.gz
T2_left_fake_2_real_hemi_SyN=${preproc}/sub-${subj}${ses_long}_T2_left_fake_2_real_hemiWarped.nii.gz
FLAIR_left_fake_2_real_hemi_SyN=${preproc}/sub-${subj}${ses_long}_FLAIR_left_fake_2_real_hemiWarped.nii.gz
T1_right_fake_2_real_hemi_SyN=${preproc}/sub-${subj}${ses_long}_T1_right_fake_2_real_hemiWarped.nii.gz
T2_right_fake_2_real_hemi_SyN=${preproc}/sub-${subj}${ses_long}_T2_right_fake_2_real_hemiWarped.nii.gz
FLAIR_right_fake_2_real_hemi_SyN=${preproc}/sub-${subj}${ses_long}_FLAIR_right_fake_2_real_hemiWarped.nii.gz
T1_lesion_fill=${preproc}/sub-${subj}${ses_long}_lesion_fill_T1.nii.gz
T2_lesion_fill=${preproc}/sub-${subj}${ses_long}_lesion_fill_T2.nii.gz
FLAIR_lesion_fill=${preproc}/sub-${subj}${ses_long}_lesion_fill_FLAIR.nii.gz
# determine lesion side
if [[ ! $search_wf_mark3 ]]; then
fslmaths $MNI_rl -thr 100 -uthr 100 -bin $MNI_left
fslmaths $MNI_left -mas $L_mask_in_MNI_dil $lesion_left_hemi_overlap
overlap_left="$(fslstats $lesion_left_hemi_overlap -V | head -c 1)"
fslmaths $MNI_rl -thr 1 -uthr 1 -bin $MNI_right
fslmaths $MNI_right -mas $L_mask_in_MNI_dil $lesion_right_hemi_overlap
overlap_right="$(fslstats $lesion_right_hemi_overlap -V | head -c 1)"
fslmaths $L_mask_in_T1 -binv $L_mask_binv_in_T1
fslmaths $MNI_brain_mask_in_nat -mas $L_mask_binv_in_T1 $MNI_brain_mask_in_nat_min_lesion
# generate lesion fill and inject it into images in MNI, the hemisphere we manipulate depends on lesion laterality
if [[ ! $overlap_left -eq 0 ]]; then
echo "it's a left sided lesion"
fslmaths $T1_in_MNI_SyN_brain_flip -mas $MNI_left $T1_fake_left_hemi
fslmaths $T1_fake_left_hemi -bin $T1_fake_left_hemi_mask
fslmaths $T1_in_MNI_brain -mas $MNI_left $T1_real_left_hemi
fslmaths $T1_real_left_hemi -bin -mas $L_mask_in_MNI_dil_binv $T1_real_left_hemi_mask_min_lesion
antsRegistrationSyN.sh -d 3 -f $T1_real_left_hemi -m $T1_fake_left_hemi -t s \
-x $T1_real_left_hemi_mask_min_lesion,$T1_fake_left_hemi_mask -o ${preproc}/sub-${subj}${ses_long}_T1_left_fake_2_real_hemi -n ${ncpu}
fslmaths $T1_left_fake_2_real_hemi_SyN -mas $L_mask_in_MNI_dil $T1_lesion_fill
fslmaths $T1_in_MNI -mas $L_mask_in_MNI_dil_binv -add $T1_lesion_fill $T1_with_lesion_fill_MNI
antsRegistrationSyN.sh -d 3 -f $T1_orig -m $T1_with_lesion_fill_MNI -t a \
-x $MNI_brain_mask_in_nat_min_lesion,$MNI_mask_min_lesion -o ${output}/sub-${subj}${ses_long}_T1nat_T1_sim_lesionless_ -n ${ncpu}
if [[ $wf -eq 1 ]] ; then
fslmaths $T2_in_MNI_SyN_brain_flip -mas $MNI_left $T2_fake_left_hemi
fslmaths $T2_fake_left_hemi -bin $T2_fake_left_hemi_mask
fslmaths $T2_in_MNI_brain -mas $MNI_left $T2_real_left_hemi
fslmaths $T2_real_left_hemi -bin -mas $L_mask_in_MNI_dil_binv $T2_real_left_hemi_mask_min_lesion
antsRegistrationSyN.sh -d 3 -f $T2_real_left_hemi -m $T2_fake_left_hemi -t s \
-x $T2_real_left_hemi_mask_min_lesion,$T2_fake_left_hemi_mask -o ${preproc}/sub-${subj}${ses_long}_T2_left_fake_2_real_hemi -n ${ncpu}
fslmaths $T2_left_fake_2_real_hemi_SyN -mas $L_mask_in_MNI_dil $T2_lesion_fill
fslmaths $T2_in_MNI -mas $L_mask_in_MNI_dil_binv -add $T2_lesion_fill $T2_with_lesion_fill_MNI
antsRegistrationSyN.sh -d 3 -f $T2_in_T1 -m $T2_with_lesion_fill_MNI -t a \
-x $MNI_brain_mask_in_nat_min_lesion,$MNI_mask_min_lesion -o ${output}/sub-${subj}${ses_long}_T1nat_T2_sim_lesionless_ -n ${ncpu}
elif [[ $wf -eq 2 ]] ; then
fslmaths $FLAIR_in_MNI_SyN_brain_flip -mas $MNI_left $FLAIR_fake_left_hemi
fslmaths $FLAIR_fake_left_hemi -bin $FLAIR_fake_left_hemi_mask
fslmaths $FLAIR_in_MNI_brain -mas $MNI_left $FLAIR_real_left_hemi
fslmaths $FLAIR_real_left_hemi -bin -mas $L_mask_in_MNI_dil_binv $FLAIR_real_left_hemi_mask_min_lesion
antsRegistrationSyN.sh -d 3 -f $FLAIR_real_left_hemi -m $FLAIR_fake_left_hemi -t s \
-x $FLAIR_real_left_hemi_mask_min_lesion,$FLAIR_fake_left_hemi_mask -o ${preproc}/sub-${subj}${ses_long}_FLAIR_left_fake_2_real_hemi -n ${ncpu}
fslmaths $FLAIR_left_fake_2_real_hemi_SyN -mas $L_mask_in_MNI_dil $FLAIR_lesion_fill
fslmaths $FLAIR_in_MNI -mas $L_mask_in_MNI_dil_binv -add $FLAIR_lesion_fill $FLAIR_with_lesion_fill_MNI
antsRegistrationSyN.sh -d 3 -f $FLAIR_in_T1 -m $FLAIR_with_lesion_fill_MNI -t a \
-x $MNI_brain_mask_in_nat_min_lesion,$MNI_mask_min_lesion -o ${output}/sub-${subj}${ses_long}_T1nat_FLAIR_sim_lesionless_ -n ${ncpu}
elif [[ $wf -eq 3 ]] ; then
fslmaths $T2_in_MNI_SyN_brain_flip -mas $MNI_left $T2_fake_left_hemi
fslmaths $T2_fake_left_hemi -bin $T2_fake_left_hemi_mask
fslmaths $T2_in_MNI_brain -mas $MNI_left $T2_real_left_hemi
fslmaths $T2_real_left_hemi -bin -mas $L_mask_in_MNI_dil_binv $T2_real_left_hemi_mask_min_lesion
antsRegistrationSyN.sh -d 3 -f $T2_real_left_hemi -m $T2_fake_left_hemi -t s \
-x $T2_real_left_hemi_mask_min_lesion,$T2_fake_left_hemi_mask -o ${preproc}/sub-${subj}${ses_long}_T2_left_fake_2_real_hemi -n ${ncpu}
fslmaths $T2_left_fake_2_real_hemi_SyN -mas $L_mask_in_MNI_dil $T2_lesion_fill
fslmaths $T2_in_MNI -mas $L_mask_in_MNI_dil_binv -add $T2_lesion_fill $T2_with_lesion_fill_MNI
antsRegistrationSyN.sh -d 3 -f $T2_in_T1 -m $T2_with_lesion_fill_MNI -t a \
-x $MNI_brain_mask_in_nat_min_lesion,$MNI_mask_min_lesion -o ${output}/sub-${subj}${ses_long}_T1nat_T2_sim_lesionless_ -n ${ncpu}
fslmaths $FLAIR_in_MNI_SyN_brain_flip -mas $MNI_left $FLAIR_fake_left_hemi
fslmaths $FLAIR_fake_left_hemi -bin $FLAIR_fake_left_hemi_mask
fslmaths $FLAIR_in_MNI_brain -mas $MNI_left $FLAIR_real_left_hemi
fslmaths $FLAIR_real_left_hemi -bin -mas $L_mask_in_MNI_dil_binv $FLAIR_real_left_hemi_mask_min_lesion
antsRegistrationSyN.sh -d 3 -f $FLAIR_real_left_hemi -m $FLAIR_fake_left_hemi -t s \