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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 "app.h"
#include "command.h"
#include "datatype.h"
#include "image.h"
#include "image_helpers.h"
#include "algo/copy.h"
#include "algo/loop.h"
#include "formats/list.h"
#include "dwi/tractography/ACT/act.h"
using namespace MR;
using namespace App;
#define MAX_ERROR 0.001
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Thoroughly check that one or more images conform to the expected ACT five-tissue-type (5TT) format";
ARGUMENTS
+ Argument ("input", "the 5TT image(s) to be tested").type_image_in().allow_multiple();
OPTIONS
+ Option ("voxels", "output mask images highlighting voxels where the input does not conform to 5TT requirements")
+ Argument ("prefix").type_text();
}
void run ()
{
const std::string voxels_prefix = get_option_value<std::string> ("voxels", "");
size_t major_error_count = 0, minor_error_count = 0;
for (size_t i = 0; i != argument.size(); ++i) {
auto in = Image<float>::open (argument[i]);
Image<bool> voxels;
Header H_out (in);
H_out.ndim() = 3;
H_out.datatype() = DataType::Bit;
if (voxels_prefix.size())
voxels = Image<bool>::scratch (H_out, "Scratch image for " + argument[i]);
try {
// This checks:
// - Floating-point image
// - 4-dimensional
// - 5 volumes
DWI::Tractography::ACT::verify_5TT_image (in);
// Manually loop through all voxels, make sure that for every voxel the
// sum of tissue partial volumes is either 0 or 1 (or close enough)
// Also make sure that individual partial volume fractions do not lie
// outside the range [0.0, 1.0]
size_t voxel_error_sum = 0, voxel_error_abs = 0;
for (auto outer = Loop(in, 0, 3) (in); outer; ++outer) {
default_type sum = 0.0;
bool abs_error = false;
for (auto inner = Loop(3) (in); inner; ++inner) {
sum += in.value();
if (in.value() < 0.0f || in.value() > 1.0f)
abs_error = true;
}
if (!sum) continue;
if (abs (sum-1.0) > MAX_ERROR) {
++voxel_error_sum;
if (voxels.valid()) {
assign_pos_of (in, 0, 3).to (voxels);
voxels.value() = true;
}
}
if (abs_error) {
++voxel_error_abs;
if (voxels.valid()) {
assign_pos_of (in, 0, 3).to (voxels);
voxels.value() = true;
}
}
}
if (voxel_error_sum == 1) {
INFO ("Image \"" + argument[i] + "\" contains just one isolated voxel with non-unity sum of partial volume fractions");
} else if (voxel_error_sum) {
WARN ("Image \"" + argument[i] + "\" contains " + str(voxel_error_sum) + " brain voxels with non-unity sum of partial volume fractions");
if (!voxel_error_abs)
++minor_error_count;
} else if (!voxel_error_abs) {
INFO ("Image \"" + argument[i] + "\" conforms to 5TT format");
}
if ((voxel_error_sum || voxel_error_abs) && voxels.valid()) {
std::string path = voxels_prefix;
if (argument.size() > 1) {
path += Path::basename (argument[i]);
} else {
bool has_extension = false;
for (auto p = MR::Formats::known_extensions; *p; ++p) {
if (Path::has_suffix (path, std::string (*p))) {
has_extension = true;
break;
}
}
if (!has_extension)
path += ".mif";
}
auto out = Image<bool>::create (path, H_out);
copy (voxels, out);
}
if (voxel_error_abs)
throw Exception ("Image \"" + argument[i] + "\" contains " + str(voxel_error_abs) + " brain voxels with a non-physical partial volume fraction");
} catch (Exception& e) {
e.display();
WARN ("Image \"" + argument[i] + "\" does not conform to fundamental 5TT format requirements");
++major_error_count;
}
}
const std::string vox_option_suggestion = get_options ("voxels").size() ? (" (suggest checking " + std::string(argument.size() > 1 ? "outputs from" : "output of") + " -voxels option)") : " (suggest re-running using the -voxels option to see voxels where tissue fractions do not sum to 1.0)";
if (major_error_count) {
if (argument.size() > 1)
throw Exception (str(major_error_count) + " input image" + (major_error_count > 1 ? "s do" : " does") + " not conform to 5TT format");
else
throw Exception ("Input image does not conform to 5TT format");
} else if (minor_error_count) {
if (argument.size() > 1) {
WARN (str(minor_error_count) + " input image" + (minor_error_count > 1 ? "s do" : " does") + " not perfectly conform to 5TT format, but may still be applicable" + vox_option_suggestion);
} else {
WARN ("Input image does not perfectly conform to 5TT format, but may still be applicable" + vox_option_suggestion);
}
} else {
CONSOLE(std::string(argument.size() > 1 ? "All images" : "Input image") + " checked OK");
}
}
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