#!/bin/bash
##########################
# Multi-Brain-Seperation #
# Author: Da MA #
# da_ma@sfu.ca #
# d.ma.11@ucl.ac.uk #
##########################
source MASHelperFunctions.sh > /dev/null 2>&1
function getOrientation(){
#gets orientation string using mri_info
if [ "$#" -lt "1" ]; then
return 1
else
IMG=$1
fi
ORIENT=`mri_info $IMG | grep Orientation`
ORIENT=${ORIENT##*\ }
echo $ORIENT
}
function convert_dcm_to_nifti_batch(){
local function_name=${FUNCNAME[0]}
if [[ $# -lt 3 ]]; then
echo "Usage: $function_name [input_dir] [dcm_nii_dir]"
return 1
fi
local input_dir=$1
local dcm_nii_dir=$2
local line
for line in $(cat $targetlist_raw); do
local id=$(echo $line | cut -d',' -f1)
local input_dir=$(echo $line | cut -d',' -f2)
dcm2niix_afni -9 -f $id -t -o $dcm_nii_dir -v 1 -z i $input_dir
mv $input_dir/$id.nii.gz $dcm_nii_dir
done
}
function multi_brain_seperation(){
local function_name=${FUNCNAME[0]}
if [[ $# -lt 3 ]]; then
echo "Usage: $function_name [target_dir] [target_id] [result_dir] (Optional) [brain_no] [threshold]"
return 1
fi
local target_dir=$1
local target_id=$2
local result_dir=$3
## Number of brain to separate
local brain_no
if [[ ! -z $4 ]]; then
brain_no=$4
else
# default number of brain = 3
brain_no=3
fi
## Threshold value to extract the brain region
if [[ ! -z $5 ]]; then
local thr=$5
else
# default threshold = 5000
local thr=5000
fi
echo "target_dir=$target_dir"
echo "target_id=$target_id"
echo "result_dir=$result_dir"
local ero=2
local dil=4
local ero2=2
local tmp_dir=$result_dir/tmp_${RANDOM}
mkdir -p $tmp_dir
# create multi-brain mask
seg_maths $target_dir/$target_id -thr $thr -bin -ero $ero -dil $dil -fill -ero $ero2 $tmp_dir/${target_id}_multimask_1.nii.gz
local i=1
while [[ i -le $brain_no ]]; do
echo "extract ${i}th brain"
# extract ${i}th mask out
seg_maths $tmp_dir/${target_id}_multimask_$i.nii.gz -lconcomp $tmp_dir/${target_id}_mask_$i.nii.gz
# using mask
seg_maths $tmp_dir/${target_id}_mask_$i.nii.gz -dil 1 -mul $target_dir/$target_id $result_dir/${target_id}_${i}.nii.gz
# substract ${i}th extracted mask
if [[ i -lt $brain_no ]]; then
# echo "substract ${i}th extracted mask (-sub)"
seg_maths $tmp_dir/${target_id}_multimask_$i.nii.gz -sub $tmp_dir/${target_id}_mask_$i.nii.gz $tmp_dir/${target_id}_multimask_$(( i + 1 )).nii.gz
fi
i=$(( $i + 1 ))
done
rm -rf $tmp_dir
}
function multi_brain_seperation_batch(){
local function_name=${FUNCNAME[0]}
if [[ $# -lt 3 ]]; then
echo "Usage: $function_name [target_dir] [targetlist] [result_dir]"
return 1
fi
local target_dir=$1
local targetlist=$2
local result_dir=$3
# local thr=5000
# local ero=2
# local dil=6
# local ero2=4
# local tmp_dir=$result_dir/tmp_${RANDOM}
# mkdir -p $tmp_dir
# brain_no=3
for target_id in $(cat $targetlist); do
multi_brain_seperation $target_dir $target_id $result_dir # $brain_no
# seg_maths $target_dir/$target_id -thr $thr -bin -ero $ero -dil $dil -fill -ero $ero2 $tmp_dir/${target_id}_mask_multi.nii.gz
done
}
function fix_header_info(){
local function_name=${FUNCNAME[0]}
if [[ $# -lt 3 ]]; then
echo "$function_name Usage: $function_name [Input_file with wrong header] [orientation] [Output_file] [(Optional) output_type (analyze/nii)]"
return 1
fi
local input_file=$1
local orientation=$2
local output_file=$3
local output_type
if [[ ! -z $4 ]]; then
output_type=$4
else
output_type=nii
fi
mri_convert --in_orientation $orientation --out_orientation $orientation -ot $output_type $input_file $3 # -odt float
}
function reorder_brain(){
# not working properly
local function_name=${FUNCNAME[0]}
if [[ $# -lt 2 ]];then
echo "Usage: $function_name [input_nii] [output_nii] [out_orientation (Optional,default=RAS)]"
return 1
fi
local input_nii=$1
local output_nii=$2
local orient_out=$3 #RAS
local orient_in=$(getOrientation $input_nii)
mri_convert --in_orientation $orient_in $input_nii $output_nii $orient_out
fix_header_info $output_nii $orient_out $output_nii
}
function reorient_brain(){
local function_name=${FUNCNAME[0]}
if [[ $# -lt 4 ]]; then
echo "Usage: $function_name [target_dir] [target_id] [location (L/R/S)] [result_dir] [(Optional) convert_RAS]"
echo " convert_RAS: 0) skip (not) convert to LAS MNI152 standatd orientation (no resampling) [Default]"
echo " Otherwise) convert to LAS MNI152 standatd orientation (involve resampling)"
return 1
fi
local target_dir=$1
local target_id=$2
local location=$3
local result_dir=$4
local convert_RAS=$5
local out_orientation="LR PA IS" # = RAS
if [[ "$location" = "S" ]]; then
# orientation=RSA
orientation=RSP
elif [[ "$location" = "R" ]]; then
# orientation=ILA
orientation=ILP
elif [[ "$location" = "L" ]]; then
# orientation=SRA
orientation=SRP
fi
# local
target_file=$(ls $target_dir/${target_id}* | cut -d' ' -f1)
# Fix nifti hearder info using FreeSurfer
fix_header_info $target_file $orientation $result_dir/$target_id.nii.gz
# If FSL is installed, reorient into LAS MNI152 space
# check if FSL is installed (by checking variable $FSLDIR)
if [[ -z $convert_RAS ]]; then convert_RAS=1; fi
echo "convert_RAS = $convert_RAS"
if [[ $convert_RAS -eq 1 ]] && [[ ! -z $FSLDIR ]]; then
echo "using fslswapdim to convert data to RAS"
fslswapdim $result_dir/$target_id.nii.gz $out_orientation $result_dir/$target_id.nii.gz
fi
}
function reorient_brain_batch_3brain(){
local function_name=${FUNCNAME[0]}
if [[ $# -lt 3 ]]; then
echo "Usage: $function_name [target_dir] [scan_list] [result_dir]"
return 1
fi
local target_dir=$1
local scan_list=$2
local result_dir=$3
echo "target_dir=$target_dir"
echo "scan_list=$scan_list"
echo "result_dir=$result_dir"
local scan_id
local target_id
local target_id_oriented
local convert_RAS=1
local location
local orientation
local qc_orientation="LAS"
for scan_id in $(cat $scan_list); do
for brain_id in 1 2 3; do
target_id=${scan_id}_$brain_id
# make three orientation guess
for location in L R S; do
if [[ "$location" = "S" ]]; then
# orientation=RSA
orientation=RSP
elif [[ "$location" = "R" ]]; then
# orientation=ILA
orientation=ILP
elif [[ "$location" = "L" ]]; then
# orientation=SRA
orientation=SRP
fi
echo ".......... reorienting: $target_id to $orientation (guessing location: $location) .........."
if [[ -e $target_dir/$target_id.nii.gz ]]; then
echo ".......... reorienting ......"
reorient_brain $target_dir $target_id $location $result_dir
# rename to add orientation guess behind
target_id_oriented=${target_id}_$location
mv $result_dir/$target_id.nii.gz $result_dir/$target_id_oriented.nii.gz
# generate quickcheck (not working as expected yet, due to the limitation of FSL's slicer command)
# echo ".......... generating quickcheck ......"
# mas_quickcheck $result_dir/$target_id_oriented.nii.gz '' $result_dir $target_id_oriented $qc_orientation
fi
done
done
done
}
function extract_label(){
local function_name=$[FUNCNAME[0]]
if [[ $# -lt 4 ]]; then
echo "Usage: $function_name [target_dir] [target_id] [label] [result_dir]"
return 1
fi
local target_dir=$1
local target_list=$2
local label=$3
local result_dir=$4
seg_maths $target_dir/$target_id.nii.gz -thr $(($label-0.5)) -uthr $(($label+0.5)) $result_dir/$target_id.nii.gz
}
# function masking_batch_nii(){
# local function_name=${FUNCNAME[0]}
# if [[ $# -lt 3 ]]; then
# echo "Usage: $function_name [target_dir] [target_list] [result_dir] [(optional) atlas_dir]"
# return 1
# fi
# local target_dir=$1
# local target_list=$2
# local result_dir=$3
# local atlas_dir=$4
# echo "target_dir=$target_dir"
# echo "target_list=$target_list"
# echo "result_dir=$result_dir"
# echo "atlas_dir=$atlas_dir"
# local target_id
# for target_id in $(cat $target_list); do
# # $$AtlasListFileName=template_list.cfg
# for atlas_id in $(cat $atlas_dir/$AtlasListFileName); do
# # cloud process need to run on rcg-queen
# # local target_result_dir=$result_dir/$target_id
# # mkdir -p $target_result_dir
# mas_masking -T $target_dir -t $target_id -A $atlas_dir -a $atlas_id -r $result_dir
# done
# done
# }
