-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
256 lines (220 loc) · 10.6 KB
/
index.html
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
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="A Computational Environment for Radiological Research CERR">
<meta name="author" content="Joseph O. Deasy">
<meta name="author" content="Aditya P. Apte">
<link rel="stylesheet" href="CERR_core/WebPage/css/cerrstyle.css">
<title>A Computational Environment for Radiological Research</title>
<!-- Bootstrap core CSS -->
<link href="CERR_core/WebPage/vendor/bootstrap/css/bootstrap.min.css" rel="stylesheet">
<!-- Custom styles for this template -->
<link href="CERR_core/WebPage/css/2-col-portfolio.css" rel="stylesheet">
</head>
<body>
<!-- Navigation -->
<nav class="navbar navbar-expand-lg navbar-light bg-light fixed-top">
<div class="container" id="navbar">
<a class="navbar-brand" href="">CERR</a>
<button class="navbar-toggler" type="button" data-toggle="tab" data-target="#navbarResponsive" aria-controls="navbarResponsive" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarResponsive">
<ul class="nav navbar-nav nav-tabs ml-auto">
<li class="nav-item">
<a class="nav-link active" data-toggle="tab" href="#features">Features
<span class="sr-only">(current)</span>
</a>
</li>
<li class="nav-item">
<a class="nav-link" data-toggle="tab" href="#news">News
</a>
</li>
<li class="nav-item">
<a class="nav-link" href="https://github.com/cerr/CERR/wiki">Wiki</a>
</li>
<li class="nav-item">
<a class="nav-link" href="https://groups.google.com/forum/#!forum/cerr-forum">User Group</a>
</li>
<li class="nav-item">
<a class="nav-link" data-toggle="tab" href="#team">Team</a>
</li>
</ul>
</div>
</div>
</nav>
<!-- Page Content -->
<div class="tab-content">
<div class="tab-pane container fade" id="team">
<ul>
<li> Aditya P. Apte, Ph.D. </li>
<li> Aditi Iyer, M.S. </li>
<li> Eve LoCastro, M.S. </li>
<li> Joseph O. Deasy, Ph.D. </li>
</ul>
</div>
<div class="tab-pane container fade" id="news">
<table class="news-table">
<tr>
<th> Date </th>
<th> Type </th>
<th> Description </th>
<th> GitHub hash </th>
</tr>
<tr>
<td> 09/30/2020 </td>
<td> Bug </td>
<td> Based SUV calculation on type of Decay correction. Used Series time for decay correction = "START". Note that Acquisition time was used irrespective of decay correction type. </td>
<td> a9cb4fd </td>
</tr>
<tr>
<td> 10/12/2020 </td>
<td> Bug </td>
<td> Fixed bug where structure segments on 1st and last row of image were not rasterized. </td>
<td> 95c4647 </td>
</tr>
</table>
</div>
<div class="tab-pane container active" id="features">
<!-- Page Heading -->
<h1 class="my-4">A Computational Environment for Radiological Research
<small>Features</small>
</h1>
<div class="row">
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/Auto-Segmentation-models">Deep Learning segmentation models</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/Auto-Segmentation-models"><img class="card-img-top" src="CERR_core/WebPage/images/dl_seg_container.png" alt=""></a>
<div class="card-body">
<p class="card-text">CERR provides a platform to deploy deep learning segmentation models.
Models can be deployed on Windows/Max/Linux operating systems via Singularity containers or Anaconda environments.
CERR provides a large number of pre and post processing options to pass datasets to segmentation models.
A library of models for segmenting structures useful for Radiotherapy outcomes modeling of Prostate, H&N and Lung is included. </p>
</div>
</div>
</div>
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/Radiomics">Radiomics and Texture calculation</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/Radiomics"><img class="card-img-top" src="CERR_core/WebPage/images/texture_gui.png" alt=""></a>
<div class="card-body">
<p class="card-text">CERR's Radiomics capabilities are built keeping in mind Speed, Quality Assurance and Interfacing with Clinical Software.</p>
</div>
</div>
</div>
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/Importing-to-CERR">Data Import</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/Importing-to-CERR"><img class="card-img-top" src="CERR_core/WebPage/images/data_import.png" alt=""></a>
<div class="card-body">
<p class="card-text">CERR can import data from a wide variety of formats such as RTOG, DICOM, MHA, NRRD. Various DICOM modalities like CT, PET, MR, US, MG, RTSTRUCT, PR, RTDOSE, RTPLAN are supported.</p>
</div>
</div>
</div>
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/Contouring-tools">Contouring</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/Contouring-tools"><img class="card-img-top" src="CERR_core/WebPage/images/contouring_tools_brush_eraser.png" alt=""></a>
<div class="card-body">
<p class="card-text">CERR provides Pencil, Brush and Active-contour based thresholding tools for manual segmentations. </p>
</div>
</div>
</div>
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/dose-volume-histograms">Outcomes Modeling</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/dose-volume-histograms"><img class="card-img-top" src="CERR_core/WebPage/images/dvh_outcomes.png" alt=""></a>
<div class="card-body">
<p class="card-text">CERR provides utility functions to batch extract dose volume histogram (DVH) based features. These features can be used for modeling toxicity and tumor control. </p>
</div>
</div>
</div>
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/IMRT-optimization-interfacing-with-an-external-solver">IMRTP</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/IMRT-optimization-interfacing-with-an-external-solver"><img class="card-img-top" src="CERR_core/WebPage/images/imrtp_gui.jpg" alt=""></a>
<div class="card-body">
<p class="card-text">CERR provides access to the underlying RTPLAN meta-data. The dose calculation options are QIB and Monte Carlo algorithms. The influence matrix and the beamlets are accessible for IMRTP research.</p>
</div>
</div>
</div>
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/ROE">ROE</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/ROE"><img class="card-img-top" src="CERR_core/WebPage/images/roe.png" alt=""></a>
<div class="card-body">
<p class="card-text">Radiotherapy Outcomes Explorer (ROE) is useful in exploring the clinical impact of scaling dose on Tumor Control Probability (TCP) and Normal Tissue Complication Probability (NTCP) in radiotherapy.</p>
</div>
</div>
</div>
<div class="col-lg-6 portfolio-item">
<div class="card h-100">
<h4 class="card-title">
<a href="https://github.com/cerr/CERR/wiki/Data-Structure-(The-planC-object)">User-friendly access to RT and Radiology meta-data</a>
</h4>
<a href="https://github.com/cerr/CERR/wiki/Data-Structure-(The-planC-object)"><img class="card-img-top" src="CERR_core/WebPage/images/planC_structure.png" alt="" width="80" height="280"></a>
<div class="card-body">
<p class="card-text">CERR provides an extensible data structure for radiotherapy and radiology objects. This makes it convenient to extract and transform the underlying data for prototyping algorithms.</p>
</div>
</div>
</div>
</div>
</div> <!-- end class="tab-content" -->
<!-- /.row -->
<!-- Pagination -->
<!--
<ul class="pagination justify-content-center">
<li class="page-item">
<a class="page-link" href="#" aria-label="Previous">
<span aria-hidden="true">«</span>
<span class="sr-only">Previous</span>
</a>
</li>
<li class="page-item">
<a class="page-link" href="#">1</a>
</li>
<li class="page-item">
<a class="page-link" href="#">2</a>
</li>
<li class="page-item">
<a class="page-link" href="#">3</a>
</li>
<li class="page-item">
<a class="page-link" href="#" aria-label="Next">
<span aria-hidden="true">»</span>
<span class="sr-only">Next</span>
</a>
</li>
</ul>
-->
</div>
<!-- /.container -->
<!-- Footer -->
<footer class="py-1 bg-light fixed-bottom">
<div class="container">
<p class="m-0 text-center text-black">Copyright © CERR 2020</p>
</div>
<!-- /.container -->
</footer>
<!-- Bootstrap core JavaScript -->
<script src="CERR_core/WebPage/vendor/jquery/jquery.min.js"></script>
<script src="CERR_core/WebPage/vendor/popper/popper.min.js"></script>
<script src="CERR_core/WebPage/vendor/bootstrap/js/bootstrap.min.js"></script>
</body>
</html>