1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
|
/* 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 "progressbar.h"
#include "algo/threaded_copy.h"
#include "dwi/gradient.h"
#include "math/least_squares.h"
#include "metadata/phase_encoding.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Convert mean dwi (trace-weighted) images to mean ADC maps";
ARGUMENTS
+ Argument ("input", "the input image.").type_image_in ()
+ Argument ("output", "the output image.").type_image_out ();
OPTIONS
+ DWI::GradImportOptions();
}
using value_type = float;
class DWI2ADC { MEMALIGN(DWI2ADC)
public:
DWI2ADC (const Eigen::MatrixXd& binv, size_t dwi_axis) :
dwi (binv.cols()),
adc (2),
binv (binv),
dwi_axis (dwi_axis) { }
template <class DWIType, class ADCType>
void operator() (DWIType& dwi_image, ADCType& adc_image) {
for (auto l = Loop (dwi_axis) (dwi_image); l; ++l) {
value_type val = dwi_image.value();
dwi[dwi_image.index (dwi_axis)] = val ? std::log (val) : 1.0e-12;
}
adc = binv * dwi;
adc_image.index(3) = 0;
adc_image.value() = std::exp (adc[0]);
adc_image.index(3) = 1;
adc_image.value() = adc[1];
}
protected:
Eigen::VectorXd dwi, adc;
const Eigen::MatrixXd& binv;
const size_t dwi_axis;
};
void run () {
auto header_in = Header::open (argument[0]);
auto grad = DWI::get_DW_scheme (header_in);
size_t dwi_axis = 3;
while (header_in.size (dwi_axis) < 2)
++dwi_axis;
INFO ("assuming DW images are stored along axis " + str (dwi_axis));
Eigen::MatrixXd b (grad.rows(), 2);
for (ssize_t i = 0; i < b.rows(); ++i) {
b(i,0) = 1.0;
b(i,1) = -grad (i,3);
}
auto binv = Math::pinv (b);
Header header_out (header_in);
header_out.datatype() = DataType::Float32;
DWI::stash_DW_scheme (header_out, grad);
Metadata::PhaseEncoding::clear_scheme (header_out.keyval());
header_out.ndim() = 4;
header_out.size(3) = 2;
auto dwi = header_in.get_image<value_type>();
auto adc = Image<value_type>::create (argument[1], header_out);
ThreadedLoop ("computing ADC values", dwi, 0, 3)
.run (DWI2ADC (binv, dwi_axis), dwi, adc);
}
|
