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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 "header.h"
#include "image.h"
#include "image_helpers.h"
#include "progressbar.h"
#include "algo/loop.h"
#include "dwi/tractography/ACT/act.h"
#include "dwi/tractography/ACT/tissues.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Generate a mask image appropriate for seeding streamlines on the grey matter-white matter interface";
REFERENCES
+ "Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. " // Internal
"Anatomically-constrained tractography:"
"Improved diffusion MRI streamlines tractography through effective use of anatomical information. "
"NeuroImage, 2012, 62, 1924-1938";
ARGUMENTS
+ Argument ("5tt_in", "the input 5TT segmented anatomical image").type_image_in()
+ Argument ("mask_out", "the output mask image") .type_image_out();
OPTIONS
+ Option("mask_in", "Filter an input mask image according to those voxels that lie upon the grey matter - white matter boundary. "
"If no input mask is provided, the output will be a whole-brain mask image calculated using the anatomical image only.")
+ Argument ("image", "the input mask image").type_image_in();
}
class Processor
{ MEMALIGN(Processor)
public:
Processor (const Image<bool>& mask) : mask (mask) { }
Processor (const Processor&) = default;
bool operator() (Image<float>& input, Image<float>& output)
{
// If a mask is defined, but is false in this voxel, do not continue processing
bool process_voxel = true;
if (mask.valid()) {
assign_pos_of (input, 0, 3).to (mask);
process_voxel = mask.value();
}
if (process_voxel) {
// Generate a non-binary seeding mask.
// Image intensity should be proportional to the tissue gradient present across the voxel
// Remember: This seeding mask is generated in the same space as the 5TT image: exploit this
// (no interpolators should be necessary)
// Essentially looking for an absolute gradient in (GM - WM) - just do in three axes
// - well, not quite; needs to be the minimum of the two
default_type gradient = 0.0;
for (size_t axis = 0; axis != 3; ++axis) {
assign_pos_of (output, 0, 3).to (input);
default_type multiplier = 0.5;
if (!output.index(axis)) {
multiplier = 1.0;
} else {
input.move_index (axis, -1);
}
const DWI::Tractography::ACT::Tissues neg (input);
if (output.index(axis) == output.size(axis)-1) {
multiplier = 1.0;
input.index(axis) = output.index(axis);
} else {
input.index(axis) = output.index(axis) + 1;
}
const DWI::Tractography::ACT::Tissues pos (input);
gradient += Math::pow2 (multiplier * std::min (abs (pos.get_gm() - neg.get_gm()), abs (pos.get_wm() - neg.get_wm())));
}
output.value() = std::max (0.0, std::sqrt (gradient));
assign_pos_of (output, 0, 3).to (input);
} else {
output.value() = 0.0f;
}
return true;
}
private:
Image<bool> mask;
};
void run ()
{
auto input = Image<float>::open (argument[0]);
DWI::Tractography::ACT::verify_5TT_image (input);
check_3D_nonunity (input);
// TODO It would be nice to have the capability to define this mask based on another image
// This will however require the use of interpolators
Image<bool> mask;
auto opt = get_options ("mask_in");
if (opt.size()) {
mask = Image<bool>::open (opt[0][0]);
if (!dimensions_match (input, mask, 0, 3))
throw Exception ("Mask image provided using the -mask option must match the input 5TT image");
}
Header H;
if (mask.valid()) {
H = mask;
H.datatype() = DataType::Float32;
H.datatype().set_byte_order_native();
} else {
H = input;
H.ndim() = 3;
}
auto output = Image<float>::create (argument[1], H);
ThreadedLoop ("Generating GMWMI seed mask", input, 0, 3)
.run (Processor (mask), input, output);
}
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