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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 "image_helpers.h"
#include "mrtrix.h"
#include "transform.h"
#include "algo/loop.h"
#include "file/path.h"
#include "file/utils.h"
#include "interp/nearest.h"
#include "connectome/connectome.h"
#include "connectome/lut.h"
#include <string>
#define SPINE_NODE_NAME std::string("Spinal_column")
using namespace MR;
using namespace App;
using namespace MR::Connectome;
using MR::Connectome::node_t;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Convert a connectome node image from one lookup table to another";
DESCRIPTION
+ "Typical usage is to convert a parcellation image provided by some other software, based on "
"the lookup table provided by that software, to conform to a new lookup table, particularly "
"one where the node indices increment from 1, in preparation for connectome construction; "
"examples of such target lookup table files are provided in share//mrtrix3//labelconvert//, "
"but can be created by the user to provide the desired node set // ordering // colours.";
EXAMPLES
+ Example ("Convert a Desikan-Killiany parcellation image as provided by FreeSurfer to have nodes incrementing from 1",
"labelconvert aparc+aseg.mgz FreeSurferColorLUT.txt mrtrix3//share//mrtrix3//labelconvert//fs_default.txt nodes.mif",
"Paths to the files in the example above would need to be revised according to their "
"locations on the user's system.");
ARGUMENTS
+ Argument ("path_in", "the input image").type_image_in()
+ Argument ("lut_in", "the connectome lookup table corresponding to the input image").type_file_in()
+ Argument ("lut_out", "the target connectome lookup table for the output image").type_file_in()
+ Argument ("image_out", "the output image").type_image_out();
OPTIONS
+ Option ("spine", "provide a manually-defined segmentation of the base of the spine where the streamlines terminate, so that "
"this can become a node in the connection matrix.")
+ Argument ("image").type_image_in();
}
void run ()
{
// Open the input file
auto H = Header::open (argument[0]);
Connectome::check (H);
auto in = H.get_image<node_t>();
// Load the lookup tables
LUT lut_in (argument[1]), lut_out (argument[2]);
// Build the mapping from input to output indices
const auto mapping = get_lut_mapping (lut_in, lut_out);
// Modify the header for the output file
H.datatype() = DataType::from<node_t>();
add_line (H.keyval()["comments"], "LUT: " + Path::basename (argument[2]));
// Create the output file
auto out = Image<node_t>::create (argument[3], H);
// Fill the output image with data
bool user_warn = false;
for (auto l = Loop (in) (in, out); l; ++l) {
const node_t orig = in.value();
if (orig < mapping.size())
out.value() = mapping[orig];
else
user_warn = true;
}
if (user_warn)
WARN ("Unexpected values detected in input image; suggest checking input image thoroughly");
// Need to manually search through the output LUT to see if the
// 'Spinal_column' node is in there, and appears only once
node_t spine_index = 0;
bool duplicates = false;
for (const auto& i : lut_out) {
if (i.second.get_name() == SPINE_NODE_NAME) {
if (!spine_index)
spine_index = i.first;
else
duplicates = true;
}
}
// If the spine segment option has been provided, add this retrospectively
auto opt = get_options ("spine");
if (opt.size()) {
if (duplicates)
throw Exception ("Cannot add spine node: \"" + SPINE_NODE_NAME + "\" appears multiple times in output LUT");
if (!spine_index)
throw Exception ("Cannot add spine node: \"" + SPINE_NODE_NAME + "\" not present in output LUT");
auto in_spine = Image<bool>::open (opt[0][0]);
if (dimensions_match (in_spine, out)) {
for (auto l = Loop (in_spine) (in_spine, out); l; ++l) {
if (in_spine.value())
out.value() = spine_index;
}
} else {
WARN ("Spine node is being created from the mask image provided using -spine option using nearest-neighbour interpolation;");
WARN ("recommend using the parcellation image as the basis for this mask so that interpolation is not required");
Transform transform (out);
Interp::Nearest<decltype(in_spine)> nearest (in_spine);
for (auto l = Loop (out) (out); l; ++l) {
Eigen::Vector3d p (out.index (0), out.index (1), out.index (2));
p = transform.voxel2scanner * p;
if (nearest.scanner (p) && nearest.value())
out.value() = spine_index;
}
}
} else if (spine_index) {
WARN ("Config file includes \"" + SPINE_NODE_NAME + "\" node, but user has not provided the segmentation using -spine option");
}
}
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