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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 "image.h"
#include "stride.h"
#include "transform.h"
#include "algo/threaded_loop.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Create an initial warp image, representing an identity transformation";
DESCRIPTION
+ "This is useful to obtain the warp fields from other normalisation "
"applications, by applying the transformation of interest to the "
"warp field generated by this program."
+ "The image generated is a 4D image with the same spatial characteristics as "
"the input template image. It contains 3 volumes, with each voxel containing "
"its own x,y,z coordinates."
+ "Note that this command can be used to create 3 separate X,Y,Z images "
"directly (which may be useful to create images suitable for use in the "
"registration program) using the following syntax:"
+ " $ warpinit template.mif warp-'[]'.nii";
ARGUMENTS
+ Argument ("template", "the input template image.").type_image_in ()
+ Argument ("warp", "the output warp image.").type_image_out ();
}
void run ()
{
auto header = Header::open (argument[0]);
header.datatype() = DataType::Float32;
header.ndim() = 4;
header.size(3) = 3;
Stride::set (header, Stride::contiguous_along_axis (3, header));
auto warp = Image<float>::create(argument[1], header);
Transform transform (header);
auto func = [&transform](Image<float>& image) {
Eigen::Vector3d voxel_pos ((float)image.index(0), (float)image.index(1), (float)image.index(2));
Eigen::Vector3f scanner_pos = (transform.voxel2scanner * voxel_pos).cast<float>();
for (auto l = Loop (3) (image); l; ++l)
image.value() = scanner_pos[image.index(3)];
};
ThreadedLoop ("generating identity warp", warp, 0, 3)
.run (func, warp);
}
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