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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/loop.h"
#include "fixel/types.h"
#include "dwi/tractography/mapping/mapper.h"
#include "dwi/tractography/mapping/loader.h"
#include "dwi/tractography/mapping/writer.h"
using namespace MR;
using namespace App;
using Fixel::index_type;
#define DEFAULT_ANGLE_THRESHOLD 45.0
class TrackProcessor { MEMALIGN (TrackProcessor)
public:
using SetVoxelDir = DWI::Tractography::Mapping::SetVoxelDir;
TrackProcessor (Image<index_type>& fixel_indexer,
const vector<Eigen::Vector3d>& fixel_directions,
vector<uint16_t>& fixel_TDI,
const float angular_threshold):
fixel_indexer (fixel_indexer) ,
fixel_directions (fixel_directions),
fixel_TDI (fixel_TDI),
angular_threshold_dp (std::cos (angular_threshold * (Math::pi/180.0))) { }
bool operator () (const SetVoxelDir& in) {
// For each voxel tract tangent, assign to a fixel
vector<int32_t> tract_fixel_indices;
for (SetVoxelDir::const_iterator i = in.begin(); i != in.end(); ++i) {
assign_pos_of (*i).to (fixel_indexer);
fixel_indexer.index(3) = 0;
index_type num_fibres = fixel_indexer.value();
if (num_fibres > 0) {
fixel_indexer.index(3) = 1;
index_type first_index = fixel_indexer.value();
index_type last_index = first_index + num_fibres;
index_type closest_fixel_index = 0;
float largest_dp = 0.0;
const Eigen::Vector3d dir (i->get_dir().normalized());
for (index_type j = first_index; j < last_index; ++j) {
const float dp = abs (dir.dot (fixel_directions[j]));
if (dp > largest_dp) {
largest_dp = dp;
closest_fixel_index = j;
}
}
if (largest_dp > angular_threshold_dp) {
tract_fixel_indices.push_back (closest_fixel_index);
fixel_TDI[closest_fixel_index]++;
}
}
}
return true;
}
private:
Image<index_type> fixel_indexer;
const vector<Eigen::Vector3d>& fixel_directions;
vector<uint16_t>& fixel_TDI;
const float angular_threshold_dp;
};
void usage ()
{
AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";
SYNOPSIS = "Compute a fixel TDI map from a tractogram";
ARGUMENTS
+ Argument ("tracks", "the input tracks.").type_tracks_in()
+ Argument ("fixel_folder_in", "the input fixel folder. Used to define the fixels and their directions").type_directory_in()
+ Argument ("fixel_folder_out", "the fixel folder to which the output will be written. This can be the same as the input folder if desired").type_text()
+ Argument ("fixel_data_out", "the name of the fixel data image.").type_text();
OPTIONS
+ Option ("angle", "the max angle threshold for assigning streamline tangents to fixels (Default: " + str(DEFAULT_ANGLE_THRESHOLD, 2) + " degrees)")
+ Argument ("value").type_float (0.0, 90.0);
}
template <class VectorType>
void write_fixel_output (const std::string& filename,
const VectorType& data,
const Header& header)
{
auto output = Image<float>::create (filename, header);
for (size_t i = 0; i < data.size(); ++i) {
output.index(0) = i;
output.value() = data[i];
}
}
void run ()
{
const std::string input_fixel_folder = argument[1];
Header index_header = Fixel::find_index_header (input_fixel_folder);
auto index_image = index_header.get_image<index_type>();
const index_type num_fixels = Fixel::get_number_of_fixels (index_header);
const float angular_threshold = get_option_value ("angle", DEFAULT_ANGLE_THRESHOLD);
vector<Eigen::Vector3d> positions (num_fixels);
vector<Eigen::Vector3d> directions (num_fixels);
const std::string output_fixel_folder = argument[2];
Fixel::copy_index_and_directions_file (input_fixel_folder, output_fixel_folder);
{
auto directions_data = Fixel::find_directions_header (input_fixel_folder).get_image<default_type>().with_direct_io();
// Load template fixel directions
Transform image_transform (index_image);
for (auto i = Loop ("loading template fixel directions and positions", index_image, 0, 3)(index_image); i; ++i) {
const Eigen::Vector3d vox ((default_type)index_image.index(0), (default_type)index_image.index(1), (default_type)index_image.index(2));
index_image.index(3) = 1;
index_type offset = index_image.value();
index_type fixel_index = 0;
for (auto f = Fixel::Loop (index_image) (directions_data); f; ++f, ++fixel_index) {
directions[offset + fixel_index] = directions_data.row(1);
positions[offset + fixel_index] = image_transform.voxel2scanner * vox;
}
}
}
vector<uint16_t> fixel_TDI (num_fixels, 0.0);
const std::string track_filename = argument[0];
DWI::Tractography::Properties properties;
DWI::Tractography::Reader<float> track_file (track_filename, properties);
// Read in tracts, and compute whole-brain fixel-fixel connectivity
const size_t num_tracks = properties["count"].empty() ? 0 : to<int> (properties["count"]);
if (!num_tracks)
throw Exception ("no tracks found in input file");
{
using SetVoxelDir = DWI::Tractography::Mapping::SetVoxelDir;
DWI::Tractography::Mapping::TrackLoader loader (track_file, num_tracks, "mapping tracks to fixels");
DWI::Tractography::Mapping::TrackMapperBase mapper (index_image);
mapper.set_upsample_ratio (DWI::Tractography::Mapping::determine_upsample_ratio (index_header, properties, 0.333f));
mapper.set_use_precise_mapping (true);
TrackProcessor tract_processor (index_image, directions, fixel_TDI, angular_threshold);
Thread::run_queue (
loader,
Thread::batch (DWI::Tractography::Streamline<float>()),
mapper,
Thread::batch (SetVoxelDir()),
tract_processor);
}
track_file.close();
Header output_header (Fixel::data_header_from_index (index_image));
write_fixel_output (Path::join (output_fixel_folder, argument[3]), fixel_TDI, output_header);
}
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