fslchpixdim

#!/bin/sh

#   fslchpixdim - change pixel dimensions, but keep everything else the same
#
#   Mark Jenkinson and Matthew Webster, FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2010 University of Oxford
#
#   SHCOPYRIGHT

if [ $# -lt 4 ] ; then
  echo "Usage: $0 <hdrfile> <xdim> <ydim> <zdim> [tdim]      (in mm, or seconds for tdim)"
  echo "WARNING: This will set default s/q-form values for NIFTI files"
  exit 1;
fi

if [ `${FSLDIR}/bin/imtest $1` = 0 ] ; then
  echo "Cannot find image $1";
  exit 1;
fi

xsz=`$FSLDIR/bin/fslval $1 dim1`;
ysz=`$FSLDIR/bin/fslval $1 dim2`;
zsz=`$FSLDIR/bin/fslval $1 dim3`;
tsz=`$FSLDIR/bin/fslval $1 dim4`;
dt=`$FSLDIR/bin/fslval $1 datatype`;
xor=`$FSLDIR/bin/fslval $1 origin1`;
yor=`$FSLDIR/bin/fslval $1 origin2`;
zor=`$FSLDIR/bin/fslval $1 origin3`;
tr=`$FSLDIR/bin/fslval $1 pixdim4`;

if [ x$xor = x ] ; then
xor=0
fi 

if [ x$yor = x ] ; then
yor=0
fi

if [ x$zor = x ] ; then
zor=0
fi


flag=`$FSLDIR/bin/fslhd $1 | cat -v | grep swapping | wc -w`;
if [ $flag -eq 0 ] ; then
  flag='';
else
  flag='-r';
fi

if [ $# -eq 5 ] ; then
  tr=$5
fi

echo $FSLDIR/bin/fslcreatehd $xsz $ysz $zsz $tsz $2 $3 $4 $tr $xor $yor $zor $dt $1 $flag
$FSLDIR/bin/fslcreatehd $xsz $ysz $zsz $tsz $2 $3 $4 $tr $xor $yor $zor $dt $1 $flag