nii2streams.sh

#!/bin/bash

reset="\e[0m" # reset color
color="\e[1;33m" # yellow

help(){
  echo -e "\n      ${color}Usage:${reset} `basename $0` inline_roi outline_roi ref_image [out_dir] [side] [prefix]"
  echo -e "\n       ${color}Info:${reset} Generates columnar & laminar cortical streamlines within"
  echo -e "             the area between the provided ROIs."
  echo -e "\n ${color}Parameters:${reset}  inline_roi - Cortical inline (nifti format)"
  echo -e "             outline_roi - Interior (nifti format)"
  echo -e "               ref_image - reference subject image to get the affine transform (nifti format)"
  echo -e "                 out_dir - Output dirctory (default = 'inline_roi' directory)"
  echo -e "                    side - hemisphere side of the given ROIs (MANDATORY if 'prefix' is set)"
  echo -e "                  prefix - string to prefix created filenames (default = prefix of 'inline_roi') "
  echo -e "\n    ${color}Returns:${reset} '*_out_resampled.tck' & '*_out_resampled_h.tck' streamlines files.\n"
}

if [ "$1" == "-h" -o "$1" == "--help" -o "$1" == "" ]; then help; exit 0; fi


#out_folder=${3:-$(dirname $grid_in)}

inline=$1
outline=$2
ref_image=$3
dir_name=${4:-`dirname $inline`} # output directory
#no_ext=`basename ${inline%%.*}` # 'inline_roi' basename without file extension
#IFS='_' read -ra split_inline <<< "$no_ext"
#prefix_default=${no_ext::-9} # 'inline_roi' subject ID with path
#prefix=${6:-$prefix_default}
IFS='_' read -ra split_inline <<< `basename $inline`
side=${5:-${split_inline[-2]}} # gets 'side' from the 'inline_roi' filename
prefix=${6:-${split_inline[-3]}}
script_dir=`dirname $0`

# print parameters
#echo -e "\n    Parameters: " $inline $outline $ref_image $dir_name $side $prefix"\n"

# Masks construction:
echo -e "\n  Running: mask_closing.py $inline $outline $dir_name ${prefix} -s ${side}"
$script_dir/mask_closing.py $inline $outline $dir_name $prefix -s ${side}

# Dilate cortical mask (9 pixels):
input1=$dir_name/${prefix}_${side}_grid_mid.nii.gz; voxels_dilated=9
echo -e "\n  Running: mask_dilation.py ${input1} $voxels_dilated"
$script_dir/mask_dilation.py $input1 $voxels_dilated

# Create grid for mincLaplace input:
input1=$dir_name/${prefix}_${side}_grid_in_short.nii.gz
input2=$dir_name/${prefix}_${side}_grid_mid_dilatedx${voxels_dilated}.nii.gz
echo -e "\n  Running: make_grid.sh $input1 $input2"
$script_dir/make_grid.sh $input1 $input2


# Run 'mincLaplace' to generate `*_minc_thick_*.nii`:
input1=$dir_name/${prefix}_${side}_grid_123.mnc
echo -e "\n  Running: run_grid.sh $input1 '_thick'"
$script_dir/run_grid.sh $input1 '_thick'

# Apply cortical mask `*_mid.nii.gz*` to `*_Grad[X-Z].nii`:
input1=$dir_name/${prefix}_${side}_grid_mid.nii.gz
for a in GradX GradY GradZ RGB
do
  input2=$dir_name/${prefix}_${side}_minc_thick_${a}.nii.gz
  output=$dir_name/${prefix}_${side}_minc_${a}.nii.gz
  echo -e "\n  Applying cortical mask '$input1' to '$input2':"
	mrcalc $input1 $input2 -mult $output
done


# Generate seed points for streamlines
#input1=$dir_name/${prefix}_${side}_outline.nii.gz
echo -e "\n  Running: get_seeds.py $outline $dir_name"
$script_dir/get_seeds.py $outline $dir_name $prefix

# Create streamlines
mkdir $dir_name/tck
input1=$dir_name/${prefix}_${side}_minc_RGB.nii.gz
for seed_file in $dir_name/${prefix}_${side}_??_seeds_smooth_resampled.txt;
do
  IFS='_' read -ra split_name <<< "$seed_file"
  j=${split_name[-4]}   # <- slice_n
  #input2=$seed_file
  input2=$dir_name/${prefix}_${side}_${j}_seeds_smooth_resampled.txt
  output=$dir_name/tck/${prefix}_${side}_${j}_out
  echo -e "\n  Running: vector2streams.py $input1 $input2 $ref_image $output \n"
  $script_dir/vector2streams.py $input1 $input2 $ref_image $output
done

# zip .txt files (-v to verbose)
tar -czf $dir_name/tck/${prefix}_${side}_${j}_out.tar.gz $dir_name/tck/${prefix}_${side}_${j}_out_*.txt

# remove '*.txt'
rm $dir_name/tck/${prefix}_${side}_${j}_out_???.txt

# Check streamlines:
echo -e "\n  ${color}To check created streamlines run:\n${reset}"
echo -e "    mrview $ref_image -tractography.load $dir_name/tck/${prefix}_${side}_${j}_out_resampled.tck -plane 2 -fullscreen & \n"

printf \\a; sleep 0.1; printf \\a # sound in bash