#!/bin/sh

#   reorientation script
#
#   Matthew Webster
#   FMRIB Image Analysis Group
#
#   Copyright (C) 2012 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
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#   Imaging of the Brain), Department of Clinical Neurology, Oxford
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#   
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if [ $# -lt 1 ] ; then 
  echo "Usage: `basename $0` <input_image> [output_image]"
  echo " "
  echo "`basename $0` is a tool for reorienting the image to match the"
  echo "approximate orientation of the standard template images (MNI152)."
  echo "It only applies 0, 90, 180 or 270 degree rotations."
  echo "It is not a registration tool."
  echo "It requires NIfTI images with valid orientation information"
  echo "in them (seen by valid labels in FSLView).  This tool"
  echo "assumes the labels are correct - if not, fix that before using this."
  echo "If the output name is not specified the equivalent transformation"
  echo " matrix is written to the standard output"
  echo " "
  exit 1
fi

img=`$FSLDIR/bin/remove_ext $1`;
outimg=$2;

if [ `$FSLDIR/bin/imtest $img` = 0 ] ; then
  echo "ERROR: Could not find image $1"
  exit 2
fi

scode=`$FSLDIR/bin/fslval $img sform_code`;
qcode=`$FSLDIR/bin/fslval $img qform_code`;
if [ $scode = 0 -a $qcode = 0 ] ; then
  echo "ERROR: Orientation information not stored in ${1}!"
  echo "Cannot reslice without orientation information (i.e. need valid labels in FSLView)"
  echo "The NIfTI image must contain a non-zero code for either the sform or the qform"
  echo " - check your reconstruction/conversion software to try and fix this"
  exit 3
fi

pattern=sto_xyz
if [ $scode = 0 ] ; then
  pattern=qto_xyz
fi
$FSLDIR/bin/fslhd $img | grep $pattern | awk '{ print $2 " " $3 " " $4 " " $5  }' > ${outimg}_nii.mat
det=`$FSLDIR/bin/avscale ${outimg}_nii.mat | grep Determinant | awk '{ print $3 }'`;
if [ X`echo "if ( $det < 0 ) { 1 }" | bc -l` = X1 ] ; then
    # radiological case (negative determinant)
    $FSLDIR/bin/fslswapdim $img RL PA IS $outimg
else
    $FSLDIR/bin/fslswapdim $img LR PA IS $outimg
fi

# clean up
rm -f ${outimg}_nii.mat