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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 "dwi/tractography/ACT/act.h"
#include "dwi/tractography/ACT/tissues.h"
using namespace MR;
using namespace App;
#define VALUE_DEFAULT_BG 0.0
#define VALUE_DEFAULT_CGM 0.5
#define VALUE_DEFAULT_SGM 0.75
#define VALUE_DEFAULT_WM 1.0
#define VALUE_DEFAULT_CSF 0.15
#define VALUE_DEFAULT_PATH 2.0
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Generate an image for visualisation purposes from an ACT 5TT segmented anatomical image";
ARGUMENTS
+ Argument ("input", "the input 4D tissue-segmented image").type_image_in()
+ Argument ("output", "the output 3D image for visualisation").type_image_out();
OPTIONS
+ Option ("bg", "image intensity of background (default: " + str(VALUE_DEFAULT_BG, 2) + ")")
+ Argument ("value").type_float (0.0, 1.0)
+ Option ("cgm", "image intensity of cortical grey matter (default: " + str(VALUE_DEFAULT_CGM, 2) + ")")
+ Argument ("value").type_float (0.0, 1.0)
+ Option ("sgm", "image intensity of sub-cortical grey matter (default: " + str(VALUE_DEFAULT_SGM, 2) + ")")
+ Argument ("value").type_float (0.0, 1.0)
+ Option ("wm", "image intensity of white matter (default: " + str(VALUE_DEFAULT_WM, 2) + ")")
+ Argument ("value").type_float (0.0, 1.0)
+ Option ("csf", "image intensity of CSF (default: " + str(VALUE_DEFAULT_CSF, 2) + ")")
+ Argument ("value").type_float (0.0, 1.0)
+ Option ("path", "image intensity of pathological tissue (default: " + str(VALUE_DEFAULT_PATH, 2) + ")")
+ Argument ("value").type_float (0.0, 10.0);
}
void run ()
{
auto input = Image<float>::open (argument[0]);
DWI::Tractography::ACT::verify_5TT_image (input);
Header H (input);
H.ndim() = 3;
const float bg_multiplier = get_option_value ("bg", VALUE_DEFAULT_BG);
const float cgm_multiplier = get_option_value ("cgm", VALUE_DEFAULT_CGM);
const float sgm_multiplier = get_option_value ("sgm", VALUE_DEFAULT_SGM);
const float wm_multiplier = get_option_value ("wm", VALUE_DEFAULT_WM);
const float csf_multiplier = get_option_value ("csf", VALUE_DEFAULT_CSF);
const float path_multiplier = get_option_value ("path", VALUE_DEFAULT_PATH);
auto output = Image<float>::create (argument[1], H);
auto f = [&] (decltype(input)& in, decltype(output)& out) {
const DWI::Tractography::ACT::Tissues t (in);
const float bg = 1.0 - (t.get_cgm() + t.get_sgm() + t.get_wm() + t.get_csf() + t.get_path());
out.value() = (bg_multiplier * bg) + (cgm_multiplier * t.get_cgm()) + (sgm_multiplier * t.get_sgm())
+ (wm_multiplier * t.get_wm()) + (csf_multiplier * t.get_csf()) + (path_multiplier * t.get_path());
};
ThreadedLoop (output).run (f, input, output);
}
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