#!/bin/sh

#
# cor_to_minc
#
#
# Copyright © 2021 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#


progname=`basename $0`

usage()
{

	echo "usage: $progname <cor directory> <minc file name>" >&2

	exit 1

} # end usage()

if [ $# -ne 2 ] ; then usage ; fi

if [ ! -d $1 ]
then
	echo "$progname: can't find directory $1" >&2
	exit 1
fi

cat $1/COR-[0-9]* | rawtominc -unsigned -byte -coronal -xstep -1 -ystep -1 -zstep -1 -xdircos 1 0 0 -ydircos 0 -1 0 -zdircos 0 0 1 -xstart 128 -ystart 128 -zstart 128 -mri -range 0 255 -scan_range $2 256 256 256

exit 0

# eof