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/* Copyright (c) 2008-2025 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#include "command.h"
#include "datatype.h"
#include "header.h"
#include "image.h"
#include "registration/warp/helpers.h"
#include "registration/warp/invert.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au) and David Raffelt (david.raffelt@florey.edu.au)";
SYNOPSIS = "Invert a non-linear warp field";
DESCRIPTION
+ "By default, this command assumes that the input warp field is a deformation field, i.e. each voxel "
"stores the corresponding position in the other image (in scanner space), and the calculated output "
"warp image will also be a deformation field. If the input warp field is instead a displacment field, "
"i.e. where each voxel stores an offset from which to sample the other image (but still in scanner "
"space), then the -displacement option should be used; the output warp field will additionally be "
"calculated as a displacement field in this case.";
ARGUMENTS
+ Argument ("in", "the input warp image.").type_image_in ()
+ Argument ("out", "the output warp image.").type_image_out ();
OPTIONS
+ Option ("template", "define a template image grid for the output warp")
+ Argument ("image").type_image_in ()
+ Option ("displacement", "indicates that the input warp field is a displacement field; the output will also be a displacement field");
}
void run ()
{
const bool displacement = get_options ("displacement").size();
Header header_in (Header::open (argument[0]));
Registration::Warp::check_warp (header_in);
Header header_out (header_in);
auto opt = get_options ("template");
if (opt.size()) {
header_out = Header::open (opt[0][0]);
if (displacement) {
header_out.ndim() = 3;
} else {
header_out.ndim() = 4;
header_out.size(3) = 3;
}
header_out.datatype() = DataType::Float32;
header_out.datatype().set_byte_order_native();
}
Image<default_type> image_in (header_in.get_image<default_type>());
Image<default_type> image_out (Image<default_type>::create (argument[1], header_out));
if (displacement) {
Registration::Warp::invert_displacement (image_in, image_out);
} else {
Registration::Warp::invert_deformation (image_in, image_out);
}
}
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