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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 "progressbar.h"
#include "algo/loop.h"
#include "image.h"
#include "fixel/helpers.h"
#include "fixel/keys.h"
#include "fixel/types.h"
#include "dwi/tractography/file.h"
#include "dwi/tractography/scalar_file.h"
#include "dwi/tractography/streamline.h"
#include "dwi/tractography/mapping/loader.h"
#include "dwi/tractography/mapping/mapper.h"
using namespace MR;
using namespace App;
using Fixel::index_type;
#define DEFAULT_ANGULAR_THRESHOLD 45.0
void usage ()
{
AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";
SYNOPSIS = "Map fixel values to a track scalar file based on an input tractogram";
DESCRIPTION
+ "This command is useful for visualising all brain fixels (e.g. the output from fixelcfestats) in 3D.";
ARGUMENTS
+ Argument ("fixel_in", "the input fixel data file (within the fixel directory)").type_image_in ()
+ Argument ("tracks", "the input track file ").type_tracks_in ()
+ Argument ("tsf", "the output track scalar file").type_file_out ();
OPTIONS
+ Option ("angle", "the max anglular threshold for computing correspondence "
"between a fixel direction and track tangent "
"(default = " + str(DEFAULT_ANGULAR_THRESHOLD, 2) + " degrees)")
+ Argument ("value").type_float (0.001, 90.0);
}
using SetVoxelDir = DWI::Tractography::Mapping::SetVoxelDir;
void run ()
{
auto in_data_image = Fixel::open_fixel_data_file<float> (argument[0]);
if (in_data_image.size(2) != 1)
throw Exception ("Only a single scalar value for each fixel can be output as a track scalar file, "
"therefore the input fixel data file must have dimension Nx1x1");
Header in_index_header = Fixel::find_index_header (Fixel::get_fixel_directory (argument[0]));
auto in_index_image = in_index_header.get_image<index_type>();
auto in_directions_image = Fixel::find_directions_header (Fixel::get_fixel_directory (argument[0])).get_image<float>().with_direct_io();
DWI::Tractography::Properties properties;
DWI::Tractography::Reader<float> reader (argument[1], properties);
properties.comments.push_back ("Created using fixel2tsf");
properties.comments.push_back ("Source fixel image: " + Path::basename (argument[0]));
properties.comments.push_back ("Source track file: " + Path::basename (argument[1]));
DWI::Tractography::ScalarWriter<float> tsf_writer (argument[2], properties);
float angular_threshold = get_option_value ("angle", DEFAULT_ANGULAR_THRESHOLD);
const float angular_threshold_dp = cos (angular_threshold * (Math::pi / 180.0));
const size_t num_tracks = properties["count"].empty() ? 0 : to<int> (properties["count"]);
DWI::Tractography::Mapping::TrackMapperBase mapper (in_index_image);
mapper.set_use_precise_mapping (true);
ProgressBar progress ("mapping fixel values to streamline points", num_tracks);
DWI::Tractography::Streamline<float> tck;
DWI::Tractography::TrackScalar<float> scalars;
const Transform transform (in_index_image);
Eigen::Vector3d voxel_pos;
while (reader (tck)) {
SetVoxelDir dixels;
mapper (tck, dixels);
scalars.clear();
scalars.set_index (tck.get_index());
scalars.resize (tck.size(), 0.0f);
for (size_t p = 0; p < tck.size(); ++p) {
voxel_pos = transform.scanner2voxel * tck[p].cast<default_type> ();
for (SetVoxelDir::const_iterator d = dixels.begin(); d != dixels.end(); ++d) {
if ((int)round(voxel_pos[0]) == (*d)[0] && (int)round(voxel_pos[1]) == (*d)[1] && (int)round(voxel_pos[2]) == (*d)[2]) {
assign_pos_of (*d).to (in_index_image);
Eigen::Vector3f dir = d->get_dir().cast<float>();
dir.normalize();
float largest_dp = 0.0f;
int32_t closest_fixel_index = -1;
in_index_image.index(3) = 0;
index_type num_fixels_in_voxel = in_index_image.value();
in_index_image.index(3) = 1;
index_type offset = in_index_image.value();
for (size_t fixel = 0; fixel < num_fixels_in_voxel; ++fixel) {
in_directions_image.index(0) = offset + fixel;
const float dp = abs (dir.dot (Eigen::Vector3f (in_directions_image.row(1))));
if (dp > largest_dp) {
largest_dp = dp;
closest_fixel_index = fixel;
}
}
if (largest_dp > angular_threshold_dp) {
in_data_image.index(0) = offset + closest_fixel_index;
const float value = in_data_image.value();
if (std::isfinite (value))
scalars[p] = in_data_image.value();
else
scalars[p] = 0.0f;
} else {
scalars[p] = 0.0f;
}
break;
}
}
}
tsf_writer (scalars);
progress++;
}
}
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