-
Notifications
You must be signed in to change notification settings - Fork 27
/
ElastixParameterSetDatabase.xml
295 lines (295 loc) · 13.2 KB
/
ElastixParameterSetDatabase.xml
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
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
<?xml version="1.0" encoding="UTF-8"?>
<ElastixParameterSetDatabase>
<ParameterSet id="default0"
modality="generic"
content="all"
description="'default' parameter files for starting elastix users"
publications="">
<ParameterFiles>
<File Name="Parameters_Rigid.txt" />
<File Name="Parameters_BSpline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="default-rigid"
modality="generic rigid"
content="all"
description="'default' parameter files for starting elastix users"
publications="">
<ParameterFiles>
<File Name="Parameters_Rigid.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0000"
modality="3D MR T1, monomodal"
content="brain"
description="interpatient; affine + B-spline transformation; mutual information"
publications="van der Lijn (2009) - Cerebellum Segmentation in MRI Using Atlas Registration and Local Multi-Scale Image Descriptors">
<ParameterFiles>
<File Name="Par0000affine.txt" />
<File Name="Par0000bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0001"
modality="3D MR BFFE, monomodal"
content="prostate"
description="interpatient; several transformation models; localised mutual information"
publications="Klein & Staring (2010) - elastix: a toolbox for intensity-based medical image registration">
<ParameterFiles>
<File Name="Par0001translation.txt" />
<File Name="Par0001bspline16.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0002"
modality="3D MR T1 & PET"
content="brain"
description="intrapatient; translation; mutual information"
publications="Klein & Staring (2010) - elastix: a toolbox for intensity-based medical image registration">
<ParameterFiles>
<File Name="Par0002.fs.MI.rigid.RandomCoordinate.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0003"
modality="3D CT, monomodal"
content="lung"
description="interpatient; affine + B-spline transformation; mutual information"
publications="Klein & Staring (2010) - elastix: a toolbox for intensity-based medical image registration">
<ParameterFiles>
<File Name="Par0003.affine.txt" />
<File Name="Par0003.bs-R4-fg.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0008"
modality="3D CT, monomodal"
content="lung"
description="intrapatient; B-spline transformation; mutual information"
publications="Murphy (2008) - Semi-Automatic Reference Standard Construction for Quantitative Evaluation of Lung CT Registration">
<ParameterFiles>
<File Name="Parameters.Par0008.affine.txt" />
<File Name="Parameters.Par0008.elastic.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0009"
modality="3D MRI, monomodal"
content="brain"
description="interpatient; B-spline transformation; mutual information"
publications="Artaechevarria (2009) - Combination strategies in multi-atlas image segmentation: application to brain MR data">
<ParameterFiles>
<File Name="Parameters.Par0009.affine.txt" />
<File Name="Parameters.Par0009.elastic.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0010"
modality="3D MR HASTE, monomodal"
content="brain"
description="interpatient; affine + B-spline transformation; mutual information"
publications="Klein (2010) - Early diagnosis of dementia based on intersubject whole-brain dissimilarities">
<ParameterFiles>
<File Name="Par0010affine.txt" />
<File Name="Par0010bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0011"
modality="3D CT, monomodal"
content="lung"
description="intrapatient (sometimes intra-sheep); B-spline transformation; normalized correlation"
publications="Staring (2010), Pulmonary Image Registration With <tt>elastix</tt> Using a Standard Intensity-Based Algorithm">
<ParameterFiles>
<File Name="Parameters.Par0011.affine.txt" />
<File Name="Parameters.Par0011.bspline1_s.txt" />
<File Name="Parameters.Par0011.bspline2_s.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0013"
modality="2D x-ray - 3D CT "
content="cerebral"
description="registration of interventional x-ray data to 3D CT for motion estimation, patient positioning or image guidance"
publications="van der Bom (2011), Evaluation of optimization methods for intensity-based 2D-3D registration in x-ray guided interventions">
<ParameterFiles>
<File Name="par0013Powel_NGC_singleImage.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0014"
modality="3D microCT"
content="whole-body mouse"
description="intra-mouse; B-spline transformation; combination of normalized correlation and the Euclidean distance metric"
publications="Baiker (2011), Automated Registration of Whole-Body Follow-Up MicroCT Data of Mice">
<ParameterFiles>
<File Name="Parameters.similarity.txt" />
<File Name="Parameters.NCC.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0015"
modality="3D CT, monomodal"
content="lung"
description="intrapatient; B-spline transformation; several similarity metrics"
publications="Staring (2013), Towards Local Progression Estimation of Pulmonary Emphysema using CT">
<ParameterFiles>
<File Name="Parameters.Par0015.expA.patient.NC.affine.txt" />
<File Name="Parameters.Par0015.expA.patient.NC.bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0017"
modality="3D MR, monomodal"
content="knee cartilage"
description="intrapatient; rigid; localized mutual information"
publications="Bron (2013) - Image registration improves human knee cartilage T1 mapping with delayed Gadolinium Enhanced MRI of Cartilage (dGEMRIC)">
<ParameterFiles>
<File Name="Par0017_cartilage_RigidLMI.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0018"
modality="3D MR, multi sequence"
content="carotid artery"
description="interpatient; several transformation models; mutual information based similarity metrics"
publications="van 't Klooster - Automated Registration of Multispectral MR Vessel Wall Images of the Carotid Artery">
<ParameterFiles>
<File Name="Par0018_3D_rigid_MI.txt" />
<File Name="Par0018_3D_affine_MI.txt" />
<File Name="Par0018_3D_bspline_MI_15.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0019"
modality="3D CT, monomodal"
content="head and neck"
description="inter patient; rigid and B-spline transformation, advanced mean square and normalized correlation metrics"
publications="Fortunati (2013) - Atlas based segmentation for hyperthermia treatment planning">
<ParameterFiles>
<File Name="Parameters_RigidAMS.txt" />
<File Name="Parameters_BSplineNCC.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0020"
modality="3D MR, multi-contrast"
content="rat brain"
description="intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty"
publications="Khmelinskii (2013) - [http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1674633 A visualization platform for high-throughput, follow-up, co-registered multi-contrast MRI rat brain data. Mengler (2014) - [http://www.sciencedirect.com/science/article/pii/S1053811913008963 Brain maturation of the adolescent rat cortex and striatum: changes in volume and myelination]">
<ParameterFiles>
<File Name="Par0020rigid.txt" />
<File Name="Par0020affine.txt" />
<File Name="Par0020bspline2.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0023"
modality="3D CT, 3D MR, multimodal"
content="head and neck"
description="intrapatient; rigid + B-spline transformation; localized mutual information combined with bending energy penalty"
publications="Leibfarth (2013), A strategy for multimodal deformable image registration to integrate PET/MR into radiotherapy treatment planning">
<ParameterFiles>
<File Name="Rigid.txt" />
<File Name="Deformable.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0025"
modality="3D MR, multi-contrast"
content="mouse brain"
description="intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty"
publications="Hammelrath (2015) - [http://www.sciencedirect.com/science/article/pii/S1053811915009039 Morphological maturation of the mouse brain: an ''in vivo'' MRI and histology investigation">
<ParameterFiles>
<File Name="Par0025rigid.txt" />
<File Name="Par0025affine.txt" />
<File Name="Par0025bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0026"
modality="3D MR, multi-contrast"
content="rat brain"
description="intra-subject, longitudinal data; rigid + affine + B-spline transformation"
publications=" Hammelrath (2016)">
<ParameterFiles>
<File Name="Par0026rigid.txt" />
<File Name="Par0026affine.txt" />
<File Name="Par0026bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0030"
modality="3D T1 fat-suppressed Ga-enhanced extremity MR"
content="wrist"
description="inter patient; Affine + B-spline transformation; normalized cross correlation. intra patient; Rigid transformation; mutual information"
publications="Roex - MSc thesis: Early Detection of Rheumatoid Arthritis using extremity MRI: Quantification of Bone Marrow Edema in the Carpal bones">
<ParameterFiles>
<File Name="Parameters0030_Euler.txt" />
<File Name="Parameters0030_Affine.txt" />
<File Name="Parameters0030_Bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0032"
modality="3D DCE-MRI"
content="breast"
description="intrapatient; rigid + B-spline transformation; mutual information"
publications="Gubern-Merida (2015), Automated localization of breast cancer in DCE-MRI">
<ParameterFiles>
<File Name="Par0032_rigid.txt" />
<File Name="Par0032_bsplines.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0033"
modality="3D MR"
content="mouse brain"
description="inter-subject; rigid + affine + B-spline transformation; mutual information metric with a transform bending energy penalty"
publications="Bink (2016), Kogelman (2016)">
<ParameterFiles>
<File Name="Par0033rigid.txt" />
<File Name="Par0033similarity.txt" />
<File Name="Par0033bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0034"
modality="2D CBF MR"
content="mouse brain"
description="inter-subject; rigid + affine + B-spline transformation; advanced normalized correlation + mutual information metric with a transform bending energy penalty"
publications="Bink (2016)">
<ParameterFiles>
<File Name="Par0034rigid.txt" />
<File Name="Par0034affine.txt" />
<File Name="Par0034bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0040"
modality="extremity MRI"
content="wrist"
description="intra-subject; affine transformation, mutual information metric"
publications="Aizenberg (2016)">
<ParameterFiles>
<File Name="Par0040affine.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0041"
modality="extremity MRI"
content="wrist"
description="inter-subject; similarity + B-spline transformation, advanced normalized correlation metric"
publications="Aizenberg (2016)">
<ParameterFiles>
<File Name="Par0041similarity.txt" />
<File Name="Par0041bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0042"
modality="MRI"
content="spine"
description="inter-subject; rigid + B-spline transformation, advanced normalized correlation metric"
publications="Aizenberg (2016)">
<ParameterFiles>
<File Name="Par0042rigid.txt" />
<File Name="Par0042bspline.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0043"
modality="CT/ MR-based pseudo-CT"
content="pelvis (prostate)"
description="intra-subject; multi-resolution (4), rigid + B-spline transformation, Mutual Information metric (Mattes) with Adaptive Stochastic Gradient Descent optimizer"
publications="Maspero M, et al. (2017), [http://iopscience.iop.org/article/10.1088/1361-6560/aa4fe7 Quantification of confounding factors in MRI-based dose calculations as applied to prostate IMRT.] Phys Med Biol. 62(3)">
<ParameterFiles>
<File Name="Par0043rigid.txt" />
</ParameterFiles>
</ParameterSet>
<ParameterSet id="par0044"
modality="3D CT, multi-contrast "
content="cardiac"
description="intra-subject; multi-image; affine (Mutual Information) + multi-image B-spline transformation (Mutual Information and mean square difference); "
publications="Giordano (2016)">
<ParameterFiles>
<File Name="Par0044Affine.txt" />
<File Name="Par0044NonRigid.txt" />
</ParameterFiles>
</ParameterSet>
</ElastixParameterSetDatabase>