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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 "image.h"
#include "filter/dwi_brain_mask.h"
#include "filter/mask_clean.h"
using namespace MR;
using namespace App;
#define DEFAULT_CLEAN_SCALE 2
void usage () {
AUTHOR = "David Raffelt (david.raffelt@florey.edu.au), Thijs Dhollander (thijs.dhollander@gmail.com) and Ben Jeurissen (ben.jeurissen@uantwerpen.be)";
SYNOPSIS = "Generates a whole brain mask from a DWI image";
DESCRIPTION
+ "All diffusion weighted and b=0 volumes are used to "
"obtain a mask that includes both brain tissue and CSF."
+ "In a second step peninsula-like extensions, where the "
"peninsula itself is wider than the bridge connecting it "
"to the mask, are removed. This may help removing "
"artefacts and non-brain parts, e.g. eyes, from "
"the mask.";
REFERENCES
+ "Dhollander T, Raffelt D, Connelly A. " // Internal
"Unsupervised 3-tissue response function estimation from single-shell or multi-shell diffusion MR data without a co-registered T1 image. "
"ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 2016, 5";
ARGUMENTS
+ Argument ("input",
"the input DWI image containing volumes that are both diffusion weighted and b=0")
.type_image_in ()
+ Argument ("output",
"the output whole-brain mask image")
.type_image_out ();
OPTIONS
+ Option ("clean_scale", "the maximum scale used to cut bridges. A certain maximum scale cuts "
"bridges up to a width (in voxels) of 2x the provided scale. Setting "
"this to 0 disables the mask cleaning step. (Default: " + str(DEFAULT_CLEAN_SCALE, 2) + ")")
+ Argument ("value").type_integer (0, 1e6)
+ DWI::GradImportOptions();
}
void run () {
auto header = Header::open(argument[0]);
if (header.ndim() != 4)
throw Exception ("input DWI image must be 4D");
auto grad = DWI::get_DW_scheme (header);
auto input = header.get_image<float>().with_direct_io (3);
Filter::DWIBrainMask dwi_brain_mask_filter (header, grad);
dwi_brain_mask_filter.set_message ("computing dwi brain mask");
auto temp_mask = Image<bool>::scratch (dwi_brain_mask_filter, "brain mask");
dwi_brain_mask_filter (input, temp_mask);
Header H_out (temp_mask);
auto output = Image<bool>::create (argument[1], H_out);
unsigned int scale = get_option_value<unsigned int> ("clean_scale", DEFAULT_CLEAN_SCALE);
if (scale > 0) {
try {
Filter::MaskClean clean_filter (temp_mask, std::string("applying mask cleaning filter"));
clean_filter.set_scale (scale);
clean_filter (temp_mask, temp_mask);
for (auto l = Loop (0,3) (input, temp_mask, output); l; ++l) {
if (temp_mask.value()) {
bool all_zero = true;
for (auto vl = Loop (3) (input); vl; ++vl) {
if (std::isfinite (float(input.value())) && input.value()) {
all_zero = false;
break;
}
}
output.value() = !all_zero;
} else {
output.value() = false;
}
}
} catch (...) {
WARN("Unable to run mask cleaning filter (image is not truly 3D); skipping");
for (auto l = Loop (0,3) (temp_mask, output); l; ++l)
output.value() = temp_mask.value();
}
}
else {
for (auto l = Loop (0,3) (temp_mask, output); l; ++l)
output.value() = temp_mask.value();
}
}
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