generate_b0calc

#!/bin/sh

#   POSSUM
#
#   Tejas Pendse	12.12.12
#
#   Wrapper script for b0calc. To used primarily by the GUI (B0 field -> Make B0 file)

#################################
#$ -l h_rt=5:0:0
#$ -l h_vmem=2.5G,tmem=2.5G
#$ -S /bin/bash
#$ -cwd
#$ -N makeb0
#$ -V
#################################


usage()
{
	echo "makeb0.sh  --  Tejas Pendse 14.12.12"
	echo
	echo "Compulsory Options:"
	echo "  -i <input-file>    -   Input Air-tissue segmentation"
	echo "  -o <output-file>   -   Output B0 file(s) basename"
	echo
	echo "Optional Options:"
	echo "  -f <field-str>     -   Field Strength (in Tesla)"
	echo "  -m                 -   Motion (generates 9 volumes)"
	echo
}


## Get input options
motion="no"
verbose="yes"
fieldstr=1
compset=0
while [ ! -z "$1" ]
do
  case "$1" in
      -i) input="$2";compset=$((compset+1));shift;;
      -o) output="$2";compset=$((compset+1));shift;;
      -f) fieldstr="$2";shift;;
      -m) motion="yes";shift;;
      *) break;;
  esac
  shift
done

if [ $compset != "2" ]
then
	usage
	exit
fi

if [ ! -z $verbose ]
then 
	echo "Input: $input;   Output: $output;"
	echo "FieldStrength: ${fieldstr}T;   Motion: $motion"
fi

if [ ! -e $input ]; then echo "Error: Can't find '$input'!" >&2; exit; fi

date
hostname

outwd=$(dirname $output)
output=$(basename $output)
output=$(echo $output | sed -e 's/.nii.gz//')

if [ $motion == "yes" ]
then
	## b0x
	if [ ! -z $verbose ];then echo "------B0X------";fi
	b0calc -i $input -o $outwd/b0x --b0x=1 --b0y=0 --b0=0 --xyz
	fslsplit $outwd/b0x $outwd/b0x -t
	
	## b0y
	if [ ! -z $verbose ];then echo "------B0Y------";fi
	b0calc -i $input -o $outwd/b0y --b0x=0 --b0y=1 --b0=0 --xyz
	fslsplit $outwd/b0y $outwd/b0y -t

	## b0z
	if [ ! -z $verbose ];then echo "------B0Z------";fi
	b0calc -i $input -o $outwd/b0z --b0x=0 --b0y=0 --b0=1 --xyz
	fslsplit $outwd/b0z $outwd/b0z -t

	if [ ! -z $verbose ];then echo "------Merging------";fi
	fslmerge -t $outwd/$output $outwd/b0z0002 $outwd/b0z0001 $outwd/b0z0000 $outwd/b0y0002 $outwd/b0y0001 $outwd/b0y0000 $outwd/b0x0002 $outwd/b0x0001 $outwd/b0x0000

	## Multiply by the field strength if other than 1T
	if [ $fieldstr -ne 1 ]
	then
		fslmaths $outwd/$output -mul $fieldstr $outwd/$output
	fi

	## Clean up
	rm -rv $outwd/b0x.nii.gz $outwd/b0y.nii.gz $outwd/b0z.nii.gz $outwd/b0z0002.nii.gz $outwd/b0z0001.nii.gz $outwd/b0z0000.nii.gz $outwd/b0y0002.nii.gz $outwd/b0y0001.nii.gz $outwd/b0y0000.nii.gz $outwd/b0x0002.nii.gz $outwd/b0x0001.nii.gz $outwd/b0x0000.nii.gz
else
	if [ ! -z $verbose ];then echo "------B0CALC SINGLE------";fi
	b0calc -i $input -o $outwd/$output

	## Multiply by the field strength if other than 1T
	if [ $fieldstr -ne 1 ]
	then
		fslmaths $outwd/$output -mul $fieldstr $outwd/$output
	fi
fi

echo "Files generated at $outwd/$output"