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
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
|
/*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 "BrainSet.h"
#include "BrainModelSurfaceMetricInterHemClusters.h"
#include "CommandMetricStatisticsInterhemisphericClusters.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandMetricStatisticsInterhemisphericClusters::CommandMetricStatisticsInterhemisphericClusters()
: CommandBase("-metric-statistics-interhemispheric-clusters",
"METRIC STATISTICS INTERHEMISPHERIC CLUSTERS")
{
}
/**
* destructor.
*/
CommandMetricStatisticsInterhemisphericClusters::~CommandMetricStatisticsInterhemisphericClusters()
{
}
/**
* get the script builder parameters.
*/
void
CommandMetricStatisticsInterhemisphericClusters::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Right Group A Metric File Name", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Right Group B Metric File Name", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Left Group A Metric File Name", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Left Group B Metric File Name", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Fiducial Coordinate File Name", FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Open Topology File Name", FileFilters::getTopologyOpenFileFilter());
paramsOut.addFile("Distoration Metric File Name", FileFilters::getMetricShapeFileFilter());
paramsOut.addInt("Distortion Column Number");
paramsOut.addString("Output File Names Prefix");
paramsOut.addInt("Iterations Shuffled T-Map");
paramsOut.addInt("Iterations Right/Left Shuffled T-Map");
paramsOut.addFloat("Positive Threshold");
paramsOut.addFloat("Negative Threshold");
paramsOut.addFloat("P-Value");
paramsOut.addInt("Variance Smoothing Iterations");
paramsOut.addFloat("Variance Smoothing Strength");
paramsOut.addBoolean("Do T-Map Degrees of Freedom");
paramsOut.addBoolean("Do T-Map P-Value");
paramsOut.addInt("Number of Threads", 1);
}
/**
* get full help information.
*/
QString
CommandMetricStatisticsInterhemisphericClusters::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<metric-file-name-right-A> \n"
+ indent9 + "<metric-file-name-right-B> \n"
+ indent9 + "<metric-file-name-left-A> \n"
+ indent9 + "<metric-file-name-left-B> \n"
+ indent9 + "<fiducial-coord-file> \n"
+ indent9 + "<open-topo-file> \n"
+ indent9 + "<distortion-metric-shape-file> \n"
+ indent9 + "<distortion-column-number> \n"
+ indent9 + "<output-file-names-prefix> \n"
+ indent9 + "<i-iterations-shuffled-tmap> \n"
+ indent9 + "<i-iterations-right-left-shuffled-tmap> \n"
+ indent9 + "<f-negative-threshold> \n"
+ indent9 + "<f-positive-threshold> \n"
+ indent9 + "<f-p-value> \n"
+ indent9 + "<i-variance-smoothing-iterations> \n"
+ indent9 + "<f-variance-smoothing-strength> \n"
+ indent9 + "<b-do-tmap-DOF> \n"
+ indent9 + "<b-do-tmap-pvalue> \n"
+ indent9 + "<number-of-threads> \n"
+ indent9 + " \n"
+ indent9 + "Search for interhemispheric clusters. \n"
+ indent9 + " \n"
+ indent9 + "The distortion column number starts at 1. \n"
+ indent9 + " \n"
+ indent9 + "Number of threads is the number of concurrent processes run \n"
+ indent9 + "during the cluster search of the shuffled metric file. \n"
+ indent9 + "Use \"1\" if you are running on a single processor system. \n"
+ indent9 + "Users on systems with multiple processors or multi-core systems \n"
+ indent9 + "should set the number of threads to the number of processors \n"
+ indent9 + "and/or cores to reduce execution time. \n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandMetricStatisticsInterhemisphericClusters::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString rightMetricShapeFileA =
parameters->getNextParameterAsString("Right Metric or Shape File A");
const QString rightMetricShapeFileB =
parameters->getNextParameterAsString("Right Metric or Shape File B");
const QString leftMetricShapeFileA =
parameters->getNextParameterAsString("Left Metric or Shape File A");
const QString leftMetricShapeFileB =
parameters->getNextParameterAsString("Left Metric or Shape File B");
const QString fiducialCoordFileName =
parameters->getNextParameterAsString("Fiducial Coordinate File Name");
const QString openTopoFileName =
parameters->getNextParameterAsString("Open Topology File Name");
const QString distortionMetricShapeFileName =
parameters->getNextParameterAsString("Distortion Metric/Shape File Name");
int distortionColumnNumber =
parameters->getNextParameterAsInt("Distortion Column Number");
const QString outputFileNamePrefix =
parameters->getNextParameterAsString("Output File Name Prefix");
const int iterations =
parameters->getNextParameterAsInt("Iterations");
const int rightLeftIterations =
parameters->getNextParameterAsInt("Right/Left Iterations");
const float negativeThreshold =
parameters->getNextParameterAsFloat("Negative Threshold");
const float positiveThreshold =
parameters->getNextParameterAsFloat("Positive Threshold");
const float pValue =
parameters->getNextParameterAsFloat("P-Value");
const int varianceSmoothingIterations =
parameters->getNextParameterAsInt("Variance Smoothing Iterations");
const float varianceSmoothingStrength =
parameters->getNextParameterAsFloat("Variance Smoothing Strength");
const bool doTMapDOF =
parameters->getNextParameterAsBoolean("Do T-Map DOF");
const bool doTMapPValue =
parameters->getNextParameterAsBoolean("Do T-Map P-Value");
const int numberOfThreads =
parameters->getNextParameterAsInt("Number of Threads");
if (distortionColumnNumber <= 0) {
throw CommandException("Distortion column number must be >= 1.");
}
distortionColumnNumber--; // algorithm starts at zero
const QString ext = rightMetricShapeFileA.endsWith(SpecFile::getMetricFileExtension())
? SpecFile::getMetricFileExtension()
: SpecFile::getSurfaceShapeFileExtension();
QString outputRightTMapFileName(outputFileNamePrefix + "_RIGHT_TMap" + ext);
QString outputLeftTMapFileName(outputFileNamePrefix + "_LEFT_TMap" + ext);
QString outputRightShuffledTMapFileName(outputFileNamePrefix + "_RIGHT_ShuffledTMap" + ext);
QString outputLeftShuffledTMapFileName(outputFileNamePrefix + "_LEFT_ShuffledTMap" + ext);
const QString outputTMapFileName(outputFileNamePrefix + "_TMap" + ext);
const QString outputShuffledTMapFileName(outputFileNamePrefix + "_ShuffledTMap" + ext);
const QString outputPaintFileName(outputFileNamePrefix + "_TMapClusters" + SpecFile::getPaintFileExtension());
const QString outputMetricFileName(outputFileNamePrefix + "_TMapClusters" + SpecFile::getMetricFileExtension());
const QString outputReportFileName(outputFileNamePrefix + "_TMap_Significant_Clusters" + SpecFile::getTextFileExtension());
BrainSet bs;
BrainModelSurfaceMetricInterHemClusters
interHem(&bs,
rightMetricShapeFileA,
rightMetricShapeFileB,
leftMetricShapeFileA,
leftMetricShapeFileB,
fiducialCoordFileName,
openTopoFileName,
distortionMetricShapeFileName,
outputRightTMapFileName,
outputLeftTMapFileName,
outputRightShuffledTMapFileName,
outputLeftShuffledTMapFileName,
outputTMapFileName,
outputShuffledTMapFileName,
outputPaintFileName,
outputMetricFileName,
outputReportFileName,
distortionColumnNumber,
iterations,
rightLeftIterations,
negativeThreshold,
positiveThreshold,
pValue,
varianceSmoothingIterations,
varianceSmoothingStrength,
doTMapDOF,
doTMapPValue,
numberOfThreads);
interHem.execute();
}
|
