ibic_birthdaycard

#!/bin/bash
# Program to generate birthday card from a structural MRI image

#the help function
function HELP {
    echo ""
    echo "  Usage"
    echo ""
    echo "  Input format: -t /filepathway/<T1 image> -s /filepathway/<T1 skullstrip image> -n <name of patient> -o <output file name> -[d]"
    echo ""
    echo "  Example: ibic_birthdaycard  -s ~/Subject19_skstrip.nii.gz -t ~/Subject19_T1.nii.gz -n Elizabeth -o finalimage"
    echo ""
    echo "  T1 files must be in standard orientation. "
    echo ""
    echo "  Output file name should not have a suffix"
    echo ""
    echo "  Input has four required parameters and one optional:" 
    echo "  -t for the T1 image"
    echo "  -s for skullstripped image"
    echo "  -n for name of patient"
    echo "  -o for name of the output file"
    echo "  [-d] for how many centimeters away from the center of the brain to take the sagittal slice. This parameter is optional. Default is 1 cm."
    echo ""
}


opterr=0;

#initializing the variables
T1=1
T1_skstrip=1
Name=1
output=1
distance=1

if (( $# == 0 )); then
    echo "No arguments. Refer to help menu."
    HELP
    exit 1
elif [ "$1" == "-h" ]; then
    HELP
    exit
fi

while getopts ":ht:s:o:n:d:" opt; do
    case $opt in
      t)
        T1=$OPTARG;
        if [ ! -f "$T1" ]
        then
            echo "NiFTI file does not exist."
            exit 1
        else
            echo "T1 image: $T1"
        fi
        ;;
    s)
        T1_skstrip=$OPTARG
        if [ ! -f "$T1_skstrip" ]
        then
            echo "File $T1_skstrip does not exist."
            exit 1
        else
           echo "Skullstrip image: $T1_skstrip"
        fi
        ;;
    n)
        Name=$OPTARG
        echo "Name of patient: $Name"
        ;;
    o)
        output=$(basename $OPTARG .png)
        echo "Name of output file: $output"
        ;;
    d)
        distance=$OPTARG
        echo "Distance of sagittal: $distance"
        ;;
    h)
        HELP
        exit
        ;;
    \?)
        echo "Invalid option: $OPTARG" 1>&2
        exit 1
        ;;
    :)
        echo "Option $OPTARG requires an argument" 1>&2
        exit 1
        ;;
      esac
done


# File to create artwork for card located in lib directory along with artwork
## for this file
## By default the enviroment variable is set to $LIB_IBIC_BIRTHDAYCARD
## By default, if you cd into the `birthdaycard` directory and run the `ibic_birthdaycard` program, everything will work correctly.
## If the enviroment variable is not set, or the lib is installed elsewhere on the system, then edit the LIB=$(pwd)/lib to the correct location

if [[ -z "{$LIB_IBIC_BIRTHDAYCARD}" ]]
then
    #The enviroment variable can be set in the terminal, such as LIB_IBIC_BIRTHDAYCARD=~/birthdaycard/lib
    LIB=$LIB_IBIC_BIRTHDAYCARD
else
    #edit this variable to be the library location if you change it
    #otherwise it will use the lib directory in the current location
    LIB=$(pwd)/lib
fi

       
# Temp directory generated for intermediate file
tmpdir=$(mktemp -d /tmp/bdayXXXX)


# Remove spaces from name for file names
namenospaces=$(echo ${Name} | sed 's/ //g')

# Creates the subject name label
convert \
    -background none \
    -fill red \
    -font Utopia \
    -gravity center \
    -size 700x250 \
    label:"$Name" \
    ${tmpdir}/${namenospaces}.png

echo "Generating Image..."

# Finds Dimensions of T1 image
dim1=$(fslval $T1 dim1)
dim2=$(fslval $T1 dim2)
dim3=$(fslval $T1 dim3)
pixdim2=$(fslval $T1 pixdim2)
pixdim=$(echo "($pixdim2+0.5)/1" | bc)

# Cutting the neck
## Starting from 0 along the z axis, iterates through the length of dim3 and
## takes a slice using fslroi and determines the mean using fslstats.
## The first slice with a mean greater than zero defines the lower limit of the
## brain. Slice taken 8 cm down from this lower limit (so some neck is visible
## after slice)
sliced_neck=${tmpdir}/$(basename ${T1} .nii.gz)_sliced_neck.nii.gz
MMtoCM=10
cm=$(( $MMtoCM / $pixdim ))
offset=$(($cm * 8))
for index in $(seq $dim3)
do
    tempfile=$tmpdir/$(basename ${T1_skstrip} .nii.gz)_index.nii.gz
    fslroi $T1_skstrip ${tempfile} 0 $dim1 0 $dim2 $index 1
    z=$(fslstats ${tempfile} -m)
    stat="$(echo $z | bc)"
    if (( $(echo "$stat > 0" | bc -l) ))
    then
        slice=$(echo $index - $offset | bc)
        if (( ${slice} < 0 )) ; then slice=0 ; fi
        fslroi $T1 ${sliced_neck} 0 $dim1 0 $dim2 $slice $dim3
        
        break	
    fi
done

## Finding the y upper limit
## iterates through each dimension starting from 0 along the y-axis, taking a
## 1 voxel slice and determining the mean
## the slice with a mean greater than 0 defines the boundary of the brain
## this limit moved 2 cm and recorded as y_lim
## $brainy_lim is used for calculating the placement of the hat image
## $index is the first voxel in the y direction (left to right) from the left that contains brain
y_lim=1
offsetY=$(($cm*2))

for index in $(seq 1 1 $dim2)
do
    tempfile=$tmpdir/$(basename ${T1_skstrip} .nii.gz)_index1.nii.gz
    fslroi $T1_skstrip ${tempfile} 0 $dim1 $index 1 0 $dim3
    y=$(fslstats ${tempfile} -m)
    stat="$(echo $y | bc)"
    if (( $(echo "$stat > 0" | bc -l) ))
    then
        y_lim="$(echo $index -$offsetY | bc)"
	brainy_lim=$index
        break
	
    fi
done


# Finding the z upper limit
## iterates through each dimension starting from the top along the z-axis,
## taking a 1 voxel slice and determining the mean
## the slice with a mean greater than 0 defines the upper boundary of the brain
## this limit is move up 2 cm and recorded as z_lim
## $brainz_lim is used for calculating the placement of the hat image
## $index is the first voxel in the z direction (up and down) from the top where brain is found
z_lim=1
offsetZ=$(($cm * 2))
for index in $(seq $dim3 -1 1)
do
    tempfile=$tmpdir/$(basename ${T1_skstrip}_index2 .nii.gz).nii.gz
    fslroi $T1_skstrip ${tempfile} 0 $dim1 0 $dim2 $index 1
    z=$(fslstats ${tempfile} -m)
    stat="$(echo $z | bc)"
    if (( $(echo "$stat > 0" | bc -l) ))
    then
        z_lim="$(echo $index -$offsetZ | bc)"
        brainz_lim="$(echo $dim3 -$index | bc)"
        break
    fi
done



chmod ug+rwx $tmpdir/*

# Takes a Sagittal Slice of the Brain
## slice taken 1 cm (default) off the center of the brain
## A different distance can be specified in the parameters.
## the offset moves the slice off from the center by 1 cm

offset=$(($cm * $distance))
middle=$(($dim1/2-$offset))
#middle=$(($dim1/2-$cm))
slicer ${sliced_neck} -x -$middle $tmpdir/final.png


# Adds Hat and Labels to brain
# offset=$(($dim3 / 2))
# ydim="$(echo $y_lim + $offset| bc)"

# zdim="$(echo $dim3 - 2 | bc)"

# dots per inch are 300 
dpi=300
# width should be 4 inches
width_in=4
#height should be 6 inches
height_in=6
width_pix=$(echo $dpi $width_in| awk '{print $1*$2}')
#upper left hand corner is 0,0

# These hat variables are finding the top and left limits of the brain for hat placement
## If neccesary, these can be edited for better fit.
## To adjust, change the constant number. Increments of 10 work best, and each is changed in their respective x and y coordinates.
hatx=$(echo 95 -$brainy_lim | bc)
haty=$(echo 65 -$brainz_lim | bc)

 convert \
    ${LIB}/background.png -resize 900x700 -threshold 100% -alpha off  \
    $tmpdir/final.png                       -geometry 500x500+175+25  \
    -composite $LIB/Rotated_Hat_none3.png   -geometry 250x250+${hatx}+${haty}   \
    -composite $LIB/Happy_Birthday.png      -geometry 600x600+100+10  \
    -composite $LIB/We_Lobe_You.png         -geometry 400x400+210+520 \
    -composite $tmpdir/${namenospaces}.png  -geometry 380x380+230+570 \
    -composite \
    -density ${dpi} -resize ${width_pix}x1800 -background black -gravity center  \
        -extent ${width_pix}x1800 \
    ${output}.jpg


# convert
# Load background image, resize to 900x700 and turn all black
# Load T1 image and place it slightly off center


echo "$(pwd)/${output}.jpg generated"
rm -R $tmpdir