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
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
|
/* 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 "image_helpers.h"
#include "algo/iterator.h"
#include "dwi/tractography/ACT/act.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Manually set the partial volume fractions in an ACT five-tissue-type (5TT) image using mask images";
ARGUMENTS
+ Argument ("input", "the 5TT image to be modified").type_image_in()
+ Argument ("output", "the output modified 5TT image").type_image_out();
OPTIONS
+ Option ("cgm", "provide a mask of voxels that should be set to cortical grey matter")
+ Argument ("image").type_image_in()
+ Option ("sgm", "provide a mask of voxels that should be set to sub-cortical grey matter")
+ Argument ("image").type_image_in()
+ Option ("wm", "provide a mask of voxels that should be set to white matter")
+ Argument ("image").type_image_in()
+ Option ("csf", "provide a mask of voxels that should be set to CSF")
+ Argument ("image").type_image_in()
+ Option ("path", "provide a mask of voxels that should be set to pathological tissue")
+ Argument ("image").type_image_in()
+ Option ("none", "provide a mask of voxels that should be cleared (i.e. are non-brain); note that this will supersede all other provided masks")
+ Argument ("image").type_image_in();
}
class Modifier
{ MEMALIGN(Modifier)
public:
Modifier (Image<float>& input_image, Image<float>& output_image) :
v_in (input_image),
v_out (output_image) { }
void set_cgm_mask (const std::string& path) { load (path, 0); }
void set_sgm_mask (const std::string& path) { load (path, 1); }
void set_wm_mask (const std::string& path) { load (path, 2); }
void set_csf_mask (const std::string& path) { load (path, 3); }
void set_path_mask (const std::string& path) { load (path, 4); }
void set_none_mask (const std::string& path) { load (path, 5); }
bool operator() (const Iterator& pos)
{
assign_pos_of (pos, 0, 3).to (v_out);
bool voxel_nulled = false;
if (buffers[5].valid()) {
assign_pos_of (pos, 0, 3).to (buffers[5]);
if (buffers[5].value()) {
for (auto i = Loop(3) (v_out); i; ++i)
v_out.value() = 0.0;
voxel_nulled = true;
}
}
if (!voxel_nulled) {
unsigned int count = 0;
float values[5] = { 0.0f, 0.0f, 0.0f, 0.0f, 0.0f };
for (size_t tissue = 0; tissue != 5; ++tissue) {
if (buffers[tissue].valid()) {
assign_pos_of (pos, 0, 3).to (buffers[tissue]);
if (buffers[tissue].value()) {
++count;
values[tissue] = 1.0;
}
}
}
if (count) {
if (count > 1) {
const float multiplier = 1.0 / float(count);
for (size_t tissue = 0; tissue != 5; ++tissue)
values[tissue] *= multiplier;
}
for (auto i = Loop(3) (v_out); i; ++i)
v_out.value() = values[v_out.index(3)];
} else {
assign_pos_of (pos, 0, 3).to (v_in);
for (auto i = Loop(3) (v_in, v_out); i; ++i)
v_out.value() = v_in.value();
}
}
return true;
}
private:
Image<float> v_in, v_out;
Image<bool> buffers[6];
void load (const std::string& path, const size_t index)
{
assert (index <= 5);
buffers[index] = Image<bool>::open (path);
if (!dimensions_match (v_in, buffers[index], 0, 3))
throw Exception ("Image " + str(path) + " does not match 5TT image dimensions");
}
};
void run ()
{
auto in = Image<float>::open (argument[0]);
DWI::Tractography::ACT::verify_5TT_image (in);
auto out = Image<float>::create (argument[1], in);
Modifier modifier (in, out);
auto
opt = get_options ("cgm"); if (opt.size()) modifier.set_cgm_mask (opt[0][0]);
opt = get_options ("sgm"); if (opt.size()) modifier.set_sgm_mask (opt[0][0]);
opt = get_options ("wm"); if (opt.size()) modifier.set_wm_mask (opt[0][0]);
opt = get_options ("csf"); if (opt.size()) modifier.set_csf_mask (opt[0][0]);
opt = get_options ("path"); if (opt.size()) modifier.set_path_mask (opt[0][0]);
opt = get_options ("none"); if (opt.size()) modifier.set_none_mask (opt[0][0]);
ThreadedLoop ("Modifying ACT 5TT image", in, 0, 3, 2).run (modifier);
}
|
