#! /bin/sh
#
# fix_OCMR_fieldmaps - script to hopefully fix the OCMR fieldmap conversion errors, mainly caused by dicom2ana or dicom2nifti
#
# Mark Jenkinson, Johannes Klein and Karla Miller, FMRIB Centre
#
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# V1 2005_07_28 Johannes Klein/Mark Jenkinson, FMRIB Centre
# V2 2007_07_05 KLM: added input for TE time (seems to be 2.46 now??)
# V2 2007_07_06 KLM: added detection of magnitude image dimensions
# V4 2007_09_15 KLM: changed to work with new fsltools
# V5 2008_03_19 MJ: subsantially modified to do sanity checking and work with VARIAN - first supported version in FMRIB
#

usage() {
 echo "Usage: `basename $0` <phase_image> <magnitude_image>"
 echo " "
 echo "  Attempts to fix two specific conversion errors in OCMR fieldmap scans"
 echo "  - the z voxel-size and interleaved slices for magnitude scans"
 echo "  - writes corrected images with *_fixed filenames"
}



if [ $# -lt 2 ] ; then
  usage
  exit 1
fi

if [ `$FSLDIR/bin/imtest $1` -ne 1 ]; then
 echo "$1 not found/not an image file"
 exit 1
fi

if [ `$FSLDIR/bin/imtest $2` -ne 1 ]; then
 echo "$2 not found/not an image file"
 exit 1
fi

phaseroot=`$FSLDIR/bin/remove_ext $1`
absroot=`$FSLDIR/bin/remove_ext $2`

# copy and change filetype
$FSLDIR/bin/fslmaths ${phaseroot} ${phaseroot}_fixed
$FSLDIR/bin/fslmaths ${absroot} ${absroot}_fixed

fix=no;

# check if voxel sizes seem sensible
nt=`$FSLDIR/bin/fslval ${absroot}_fixed dim3`;
ny=`$FSLDIR/bin/fslval ${absroot}_fixed dim2`;
nx=`$FSLDIR/bin/fslval ${absroot}_fixed dim1`;
dz=`$FSLDIR/bin/fslval ${absroot}_fixed pixdim3`;
dy=`$FSLDIR/bin/fslval ${absroot}_fixed pixdim2`;
dx=`$FSLDIR/bin/fslval ${absroot}_fixed pixdim1`;
if [ `echo "$dz / $dx < 0.9" | bc -l` -eq 1 ] ; then
    pdz=`$FSLDIR/bin/fslval ${phaseroot}_fixed pixdim3`
    echo "Detected unusual z-voxel size of $dz mm in magnitude image"
    echo "Making it equal to the z-voxel size of the phase image: $pdz mm" 
    $FSLDIR/bin/fslhd -x ${absroot}_fixed > ${absroot}_hdr.txt
    cat ${absroot}_hdr.txt | sed "s/dz =.*/dz = \'$pdz\'/" > ${absroot}_newhdr.txt
    $FSLDIR/bin/fslcreatehd ${absroot}_newhdr.txt ${absroot}_fixed
    fix=yes;
fi

# determine if we need to decimate magnitude image 
#   (should not be needed if reconstruction from dicom was OK)
nabs=`$FSLDIR/bin/fslval ${absroot}_fixed dim3`
nphs=`$FSLDIR/bin/fslval ${phaseroot}_fixed dim3`
nphs2=`echo "$nphs * 2" | bc`
tmpnm=`$FSLDIR/bin/tmpnam`
if [ $nabs -eq $nphs2 ]; then
    echo "Detected dual echo magnitude image in single file - correcting..."
    $FSLDIR/bin/fslslice ${absroot}_fixed ${tmpnm}_tmp_abs
    $FSLDIR/bin/fslmerge -z ${tmpnm}_tmp_abs_echo1 ${tmpnm}_tmp_abs_slice_0*[02468].*
    rm -rf ${tmpnm}_tmp_abs_slice*
    $FSLDIR/bin/imrm ${absroot}_fixed
    $FSLDIR/bin/fslmaths ${tmpnm}_tmp_abs_echo1 ${absroot}_fixed
    fix=yes;
fi

rm -rf ${tmpnm}_tmp_ph* ${tmpnm}_tmp_abs*  ${absroot}_*hdr.txt

# report if fix has been done
if [ $fix = yes ] ; then
    echo " "
    echo "Corrected phase image written as ${phaseroot}_fixed"
    echo "Corrected magnitude image written as ${absroot}_fixed"
else
    echo " "
    echo "Finished"
fi