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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 "algo/threaded_loop.h"
#include "image.h"
#include "adapter/jacobian.h"
#include "registration/warp/helpers.h"
#include "fixel/helpers.h"
#include "fixel/keys.h"
#include "fixel/loop.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";
SYNOPSIS = "Compute fixel-wise or voxel-wise metrics from a 4D deformation field";
REFERENCES
+ "Raffelt, D.; Tournier, JD/; Smith, RE.; Vaughan, DN.; Jackson, G.; Ridgway, GR. Connelly, A." // Internal
"Investigating White Matter Fibre Density and Morphology using Fixel-Based Analysis. "
"Neuroimage, 2017, 144, 58-73, doi: 10.1016/j.neuroimage.2016.09.029";
ARGUMENTS
+ Argument ("in", "the input deformation field").type_image_in();
OPTIONS
+ Option ("fc", "use an input template fixel image to define fibre orientations and output "
"a fixel image describing the change in fibre cross-section (FC) in the perpendicular "
"plane to the fixel orientation. e.g. warp2metric warp.mif -fc fixel_template_directory output_fixel_directory fc.mif")
+ Argument ("template_fixel_directory").type_image_in()
+ Argument ("output_fixel_directory").type_text()
+ Argument ("output_fixel_data").type_text()
+ Option ("jmat", "output a Jacobian matrix image stored in column-major order along the 4th dimension."
"Note the output jacobian describes the warp gradient w.r.t the scanner space coordinate system")
+ Argument ("output").type_image_out()
+ Option ("jdet", "output the Jacobian determinant instead of the full matrix")
+ Argument ("output").type_image_out();
}
using value_type = float;
void run ()
{
auto input = Image<value_type>::open (argument[0]).with_direct_io (3);
Registration::Warp::check_warp (input);
Image<value_type> jmatrix_output;
Image<value_type> jdeterminant_output;
Image<uint32_t> fixel_template_index;
Image<value_type> fixel_template_directions;
Image<value_type> fc_output_data;
auto opt = get_options ("fc");
if (opt.size()) {
std::string template_fixel_directory (opt[0][0]);
fixel_template_index = Fixel::find_index_header (template_fixel_directory).get_image<uint32_t>();
fixel_template_directions = Fixel::find_directions_header (template_fixel_directory).get_image<value_type>().with_direct_io();
std::string output_fixel_directory (opt[0][1]);
if (template_fixel_directory != output_fixel_directory) {
Fixel::copy_index_file (template_fixel_directory, output_fixel_directory);
Fixel::copy_directions_file (template_fixel_directory, output_fixel_directory);
}
fc_output_data = Image<value_type>::create (Path::join (output_fixel_directory, opt[0][2]), Fixel::data_header_from_index (fixel_template_index));
}
opt = get_options ("jmat");
if (opt.size()) {
Header output_header (input);
output_header.size(3) = 9;
jmatrix_output = Image<value_type>::create (opt[0][0], output_header);
}
opt = get_options ("jdet");
if (opt.size()) {
Header output_header (input);
output_header.ndim() = 3;
jdeterminant_output = Image<value_type>::create (opt[0][0], output_header);
}
if (!(jmatrix_output.valid() || jdeterminant_output.valid() || fc_output_data.valid()))
throw Exception ("Nothing to do; please specify at least one output image type");
Adapter::Jacobian<Image<value_type> > jacobian (input);
for (auto i = Loop ("outputting warp metric(s)", jacobian, 0, 3) (jacobian); i; ++i) {
auto jacobian_matrix = jacobian.value();
if (fc_output_data.valid()) {
assign_pos_of (jacobian, 0, 3).to (fixel_template_index);
for (auto f = Fixel::Loop (fixel_template_index) (fixel_template_directions, fc_output_data); f; ++f) {
Eigen::Vector3f fixel_direction = fixel_template_directions.row(1);
fixel_direction.normalize();
Eigen::Vector3f fixel_direction_transformed = jacobian_matrix * fixel_direction;
fc_output_data.value() = jacobian_matrix.determinant() / fixel_direction_transformed.norm();
}
}
if (jmatrix_output.valid()) {
assign_pos_of (jacobian, 0, 3).to (jmatrix_output);
for (size_t j = 0; j < 9; ++j) {
jmatrix_output.index(3) = j;
jmatrix_output.value() = jacobian_matrix.data()[j];
}
}
if (jdeterminant_output.valid()) {
assign_pos_of (jacobian, 0, 3).to (jdeterminant_output);
jdeterminant_output.value() = jacobian_matrix.determinant();
}
}
}
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