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
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
|
/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* CARET is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "BrainModelVolume.h"
#include "BrainModelVolumeProbAtlasToFunctional.h"
#include "BrainSet.h"
#include "CommandVolumeProbAtlasToFunctional.h"
#include "DisplaySettingsProbabilisticAtlas.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeProbAtlasToFunctional::CommandVolumeProbAtlasToFunctional()
: CommandBase("-volume-prob-atlas-to-functional",
"VOLUME PROB ATLAS TO FUNCTIONAL VOLUMES")
{
}
/**
* destructor.
*/
CommandVolumeProbAtlasToFunctional::~CommandVolumeProbAtlasToFunctional()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeProbAtlasToFunctional::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Prob Atlas Volume",
FileFilters::getVolumeProbAtlasFileFilter());
paramsOut.addString("Functional Volume Name Prefix");
paramsOut.addString("Functional Volume Name Suffix");
}
/**
* get full help information.
*/
QString
CommandVolumeProbAtlasToFunctional::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-prob-atlas-volume-file-name>\n"
+ indent9 + "<output-functional-volume-prefix-name>\n"
+ indent9 + "<output-functional-volume-suffix-name>\n"
+ indent9 + "\n"
+ indent9 + "For each region name that is not ???, GYRAL, or GYRUS,\n"
+ indent9 + "create a functional volume where each voxel is the\n"
+ indent9 + "number volumes that have the region identified for\n"
+ indent9 + "the voxel.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeProbAtlasToFunctional::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get inputs
//
const QString inputProbAtlasVolumeFileName =
parameters->getNextParameterAsString("Input Prob Atlas Volume File Name");
const QString functionalVolumePrefixName =
parameters->getNextParameterAsString("Output Functional Volume File Name Prefix");
const QString functionalVolumeSuffixName =
parameters->getNextParameterAsString("Output Functional Volume File Name Suffix");
//
// Create and read the prob atlas volume
//
BrainSet bs;
bs.readVolumeFile(inputProbAtlasVolumeFileName,
VolumeFile::VOLUME_TYPE_PROB_ATLAS,
false,
false);
BrainModelVolume* bmv = bs.getBrainModelVolume();
if (bmv == NULL) {
throw CommandException("Unable to find volumes after reading files.");
}
if (bs.getNumberOfVolumeProbAtlasFiles() <= 0) {
throw CommandException("No prob atlas volume files were read.");
}
VolumeFile* firstProbAtlasVolumeFile = NULL;
if (bs.getNumberOfVolumeProbAtlasFiles() > 0) {
firstProbAtlasVolumeFile = bs.getVolumeProbAtlasFile(0);
}
//
// Create the functional volume
//
VolumeFile functionalVolume(*bs.getVolumeProbAtlasFile(0));
functionalVolume.setVolumeType(VolumeFile::VOLUME_TYPE_FUNCTIONAL);
//
// Process each prob atlas name
//
DisplaySettingsProbabilisticAtlas* dspa = bs.getDisplaySettingsProbabilisticAtlasVolume();
const int numNames = firstProbAtlasVolumeFile->getNumberOfRegionNames();
for (int i = 0; i < numNames; i++) {
//
// Get the name
//
const QString areaName = firstProbAtlasVolumeFile->getRegionNameFromIndex(i);
if ((areaName != "???") &&
(areaName != "GYRAL") &&
(areaName != "GYRUS")) {
//
// Turn on only this name
//
for (int j = 0; j < numNames; j++) {
if (i == j) {
dspa->setAreaSelected(j, true);
}
else {
dspa->setAreaSelected(j, false);
}
}
//
// Name for functional volume
//
const QString funcVolumeName =
functionalVolumePrefixName
+ areaName
+ functionalVolumeSuffixName;
//
// Convert to functional volume
//
BrainModelVolumeProbAtlasToFunctional paf(&bs,
&functionalVolume,
funcVolumeName,
areaName);
paf.execute();
//
// Write the functional volume
//
functionalVolume.writeFile(funcVolumeName);
}
}
}
|
