procGradCorrect

#!/bin/bash


#function for unwarping and generating warp files
function usage {
 echo "Performs gradient unwarping and saves relevant output"
 echo ""
 echo "Required args:"
 echo "  -i input_nii"
 echo "  -g input_grad_coeff"
 echo ""
 echo "Optional args:"
 echo "  -u output_unwarped_nii"
 echo "  -c output_unwarped_intcorr_nii"
 echo "  -w output_warp_nii (apply with FSL applywarp --abs)"
 echo "  -j output_jacobian_determinant_nii (multiply for intensity correction)"
 echo "  -d output_grad_dev_nii (for DWI)"
 echo "  -s scratch_dir (default `pwd`/gradcorr)"
 echo "  -k     (keep scratch directory , default removed afterwards)"
 echo ""
 echo "Grad-unwarp options"
 echo "  -I interporder"
 echo "  -N numpoints"
 echo "  -F fovmin (from -fovmin to +fovmin)"


}

if [ "$#" -lt 3 ]
then
 usage
 exit 1
fi

in_nii=
grad_coeff=
scratch_dir=`pwd`/gradcorr
unwarped_nii=
unwarped_intcorr_nii=
warp_nii=
detjac_nii=
grad_dev_nii=
keep_scratch=0
fovmin=0.2 #in metres
numpoints=150 
interporder=3 #cubic


while getopts "i:g:s:kw:u:c:j:d:I:N:F:" options; do
 case $options in
     i ) echo "  Input nii $OPTARG"
         in_nii=$OPTARG;;
     g ) echo "  Input grad_coeff $OPTARG"
         grad_coeff=$OPTARG;;
     s ) echo "  Using scratch dir $OPTARG"
         scratch_dir=$OPTARG;;
     k ) echo "  Keeping scratch dir"
         keep_scratch=1;;
     w ) echo "  Saving warp  nii to $OPTARG "
         warp_nii=$OPTARG;;
     u ) echo "  Saving unwarped nii to $OPTARG"
         unwarped_nii=$OPTARG;;
     c ) echo "  Saving unwarped, intensity-corrected nii to $OPTARG"
         unwarped_intcorr_nii=$OPTARG;;
     j ) echo "  Saving warp detjac nii to $OPTARG"
         detjac_nii=$OPTARG;;
     d ) echo "  Saving warp grad_dev nii to $OPTARG"
         grad_dev_nii=$OPTARG;;
     I ) echo "  Interp order $OPTARG"
         interporder=$OPTARG;;
     N ) echo "  Numpoints $OPTARG"
         numpoints=$OPTARG;;
     F ) echo "  fovmin $OPTARG"
         fovmin=$OPTARG;;

    * ) usage
	exit 1;;
 esac
done

if [ ! -n "$in_nii" -o ! -n "$grad_coeff" ]
then
    usage
    exit 1
fi

#CAVEAT -- works only for nii.gz, not nii

if [ ! -e $in_nii ]
then
 echo "Input image $in_nii does not exist!"
 exit 1
fi

if [ ! -e $grad_coeff ]
then
 echo "Input grad coeff $grad_coeff does not exist!"
 exit 1
fi

   

if [ ! -e $scratch_dir ]
then
    mkdir -p $scratch_dir
fi

in=input.nii.gz
coeff=coeff.grad
unwarped=input_unwarped.nii.gz
unwarped_intcorr=input_unwarped_intcorr.nii.gz
detjac=detjac.nii.gz
warp=fullWarp_abs.nii.gz
grad_dev=grad_dev.nii.gz
grad_dev_prefix=grad_dev

ext=${in_nii##*.}
if [ "$ext" = "nii" ]
then
    cp -v --no-preserve mode $in_nii $scratch_dir/input.nii
    gzip $scratch_dir/input.nii

elif [ "$ext" = "gz" ]
then
    cp -v --no-preserve mode $in_nii $scratch_dir/$in
else
     echo "Unknown file extension, $ext, for $in_nii" 
     exit 1
fi

cp -v --no-preserve mode $grad_coeff $scratch_dir/$coeff

pushd $scratch_dir

 
  #run gradunwarp
  gradient_unwarp.py $in $unwarped siemens -g $coeff  -n --fovmin -$fovmin --fovmax $fovmin --numpoints $numpoints --interp_order $interporder --verbose 

  #get jacobian determinant
  reg_jacobian  -ref $unwarped -def $warp -jac $detjac
  fslmaths $detjac -mul -1 -abs $detjac

  #modulate by det jac (intensity correction)
  fslmaths $unwarped -mul $detjac $unwarped_intcorr

 if [ -n "$grad_dev_nii" ]
 then
  #gen grad_dev (for dwi)
  calc_grad_perc_dev --fullwarp=$warp --out=$grad_dev_prefix
  fslmerge -t $grad_dev ${grad_dev_prefix}_x ${grad_dev_prefix}_y ${grad_dev_prefix}_z
  fslmaths $grad_dev -div 100 $grad_dev 
fi
popd 

#copy files to output paths
if [ -n "$unwarped_nii" ]
then
cp -v $scratch_dir/$unwarped $unwarped_nii
fi

if [ -n "$unwarped_intcorr_nii" ]
then
cp -v $scratch_dir/$unwarped_intcorr $unwarped_intcorr_nii
fi

if [ -n "$warp_nii" ]
then
cp -v $scratch_dir/$warp $warp_nii
fi

if [ -n "$detjac_nii" ]
then
cp -v $scratch_dir/$detjac $detjac_nii
fi

if [ -n "$grad_dev_nii" ]
then
cp -v $scratch_dir/$grad_dev $grad_dev_nii
fi

if [ -n "$unwarped_nii" ]
then
cp -v $scratch_dir/$unwarped $unwarped_nii
fi

if [ "$keep_scratch" = 0 ]
then
  rm -f $scratch_dir/*
  rmdir $scratch_dir
fi