File: README.md

package info (click to toggle)
ants 2.1.0-5
  • links: PTS, VCS
  • area: main
  • in suites: sid, stretch
  • size: 10,656 kB
  • sloc: cpp: 84,137; sh: 11,419; perl: 694; xml: 115; makefile: 74; python: 48
file content (313 lines) | stat: -rw-r--r-- 12,360 bytes parent folder | download
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
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
[![Build Status](https://travis-ci.org/stnava/ANTs.svg?branch=master)](https://travis-ci.org/stnava/ANTs)
============================
Advanced Normalization Tools
============================

Questions: [Discussion Site](http://sourceforge.net/p/advants/discussion/) or *new* [ANTsDoc](http://stnava.github.io/ANTsDoc/) or try [this version](http://issuu.com/brianavants/docs/ants2)

[ANTsTalk - subject to change at any moment](http://stnava.github.io/ANTsTalk/)

[ANTsRegistrationTalk - subject to change at any moment](http://stnava.github.io/ANTsRegistrationTalk/)

 Email: [antsr.me at gmail dot com](mailto:antsr.me@gmail.com)

 Install ANTs via pre-built:
[Packages](http://sourceforge.net/projects/advants/files/ANTS/)

 Build [ANTs](https://github.com/stnava/ANTs) from:
[Source-Code](http://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/)
(recommended)

[ANTs Dashboard](http://testing.psychiatry.uiowa.edu/CDash/index.php?project=ANTS) maintained by Hans J. Johnson

ANTs extracts information from complex datasets that include imaging
([Word Cloud](http://brianavants.files.wordpress.com/2013/05/avants_wordcloud.jpg)).
Paired with [ANTsR](http://stnava.github.io/software/2014/01/08/antsr/) (answer), ANTs is
useful for managing, interpreting and visualizing multidimensional data.
ANTs is
[popularly](https://sourceforge.net/projects/advants/files/ANTS/stats/timeline?dates=2010-07-19+to+2099-05-25)
considered a state-of-the-art medical image registration and
segmentation toolkit. ANTsR is an emerging tool supporting standardized
multimodality image analysis. ANTs depends on the Insight ToolKit
[(ITK)](http://www.itk.org), a widely used medical image processing
library to which ANTs developers contribute.

Authors
-------

### Brian B. Avants - UPENN

**Role:** Creator, Algorithm Design, Implementation,
[more](http://stnava.github.io/Resume/)

### Nicholas J. Tustison - UVA

**Role:** Compeller, Algorithm Design, Implementation Guru,
[more](http://ntustison.github.io/CV/)

### Hans J. Johnson - UIowa

**Role:** Large-Scale Application, Testing, Software design

### Team Members

**Core:** Gang Song (Originator), Philip A. Cook, Jeffrey T. Duda (DTI), Ben M. Kandel (Perfusion, multivariate analysis), Kent Williams (software engineer, UIowa)


Image Registration
------------------

Diffeomorphisms: [SyN](http://www.ncbi.nlm.nih.gov/pubmed/17659998),
Independent Evaluation:
[Klein](http://www.ncbi.nlm.nih.gov/pubmed/19195496),
[Murphy](http://www.ncbi.nlm.nih.gov/pubmed/21632295), Template
Construction
[(2004)](http://www.ncbi.nlm.nih.gov/pubmed/15501083)[(2010)](http://www.ncbi.nlm.nih.gov/pubmed/19818860),
[Similarity Metrics](http://www.ncbi.nlm.nih.gov/pubmed/20851191),
[Multivariate
registration](http://www.ncbi.nlm.nih.gov/pubmed/18995188), [Multiple
modality analysis and statistical
bias](http://www.ncbi.nlm.nih.gov/pubmed/23151955)

Image Segmentation
------------------

Atropos Multivar-EM Segmentation
[(link)](http://www.ncbi.nlm.nih.gov/pubmed/21373993), Multi-atlas
methods [(link)](http://www.ncbi.nlm.nih.gov/pubmed/21237273N4), Bias
Correction [(link)](http://www.ncbi.nlm.nih.gov/pubmed/20378467), DiReCT
cortical thickness
[(link)](http://www.ncbi.nlm.nih.gov/pubmed/19150502), DiReCT in
[chimpanzees](http://www.ncbi.nlm.nih.gov/pubmed/23516289)

Multivariate Analysis Eigenanatomy [(1)](http://www.ncbi.nlm.nih.gov/pubmed/23286132) [(2)](http://www.ncbi.nlm.nih.gov/pubmed/23475817)
----------------------------------------------------------------------------------------------------------------------------------------

Prior-Based Eigenanatomy [(in
prep)](http://www.ncbi.nlm.nih.gov/pubmed/?), Sparse CCA
[(1)](http://www.ncbi.nlm.nih.gov/pubmed/20083207),
[(2)](http://www.ncbi.nlm.nih.gov/pubmed/20879247), Sparse Regression
[(link)](http://link.springer.com/chapter/10.1007%2F978-3-642-38868-2_8)

ImageMath Useful!
-----------------

morphology, GetLargestComponent, CCA, FillHoles ... much more!

Application Domains
-------------------

### Frontotemporal degeneration [PENN FTD center](http://ftd.med.upenn.edu)

### Multimodality Neuroimaging

-   [Structural MRI](http://jeffduda.github.io/NeuroBattery/)
-   Functional MRI
-   Network Analysis

### Lung Imaging

-   Structure
-   Perfusion MRI
-   Branching

### Multiple sclerosis (lesion filling) [example](https://github.com/armaneshaghi/LesionFilling_example)

Background & Theory
----------------------------------------------------------

-   The
    [SyN](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22SyN%22+AND+%22Avants+B%22)
    and [N4 bias
    correction](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22N4%22+AND+%22Tustison+N4ITK%22)
    papers and other relevant references in
    [Pubmed](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Tustison+N%22+AND+%22Avants+B%22)

-   Visualization: e.g. [a gource of ANTs
    development](http://vimeo.com/66781467)

-   [DiReCT](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22DIRECT%22+AND+%22Avants%22+AND+DAS)
    cortical thickness
    [papers](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Cortical+Thickness%22+AND+%22Avants%22)

-   A
    [folder](https://sourceforge.net/projects/advants/files/Documentation/)
    of relevant docs:
    [segmentation](http://sourceforge.net/projects/advants/files/Documentation/atropos.pdf/download),
    [registration](http://sourceforge.net/projects/advants/files/Documentation/antstheory.pdf/download),
    [usage(old)](http://sourceforge.net/projects/advants/files/Documentation/ants.pdf/download),
    [for clinical
    apps](http://sourceforge.net/projects/advants/files/Documentation/ANTSMethodologySummary.docx/download)

-   ANTs redesigned for generality, automation, multi-core computation
    with ITKv4

-   Dev'd ITKv4 with Kitware, GE, Natl. Lib of Medicine & Academia


ANTs has won several unbiased & international competitions
----------------------------------------------------------

-   New *antsRegistration* [bash
    example](https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh)

-   New *Eigenanatomy* for [multivariate neuroimage
    analysis](http://www.ncbi</a>.nlm.nih.gov/pubmed/23269595) via
    [PCA](http://www.ncbi.nlm.nih.gov/pubmed/23286132) &
    [CCA](http://www.ncbi.nlm.nih.gov/pubmed/20083207)

-   ANTs finished in 1st rank in [Klein 2009 intl. brain mapping
    competition](http://www.ncbi.nlm.nih.gov/pubmed/19195496)

-   ANTs finished 1st overall in [EMPIRE10 intl. lung mapping
    competition](http://www.ncbi.nlm.nih.gov/pubmed/21632295)

-   ANTs is the standard registration for
    [MICCAI-2013](http://www.miccai2013.org/) segmentation competitions

-   Conducting ANTs-based R tutorial @ MICCAI-2013

-   ITK-focused Frontiers in Neuroinformatics research topic
    [here](http://www.frontiersin.org/neuroinformatics/researchtopics/neuroinformatics_with_the_insi/1580)

-   Won the [BRATS 2013 challenge](http://martinos.org/qtim/miccai2013/) with [ANTsR](http://stnava.github.io/ANTsR/)

-   Won the best paper award at the [STACOM 2014 challenge](http://www.cardiacatlas.org/web/stacom2014/home)

Learning about ANTs
----------------------------------------------------------

**ANTs and ITK** [paper](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009425/)

**Pre-built ANTs templates with spatial priors** [download](http://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436)

**The ANTs Cortical Thickness Pipeline** [example](https://github.com/ntustison/KapowskiChronicles/blob/master/paper2.pdf?raw=true)

**"Cooking" tissue priors for templates**
  [example](https://github.com/ntustison/antsCookTemplatePriorsExample)
  (after you build your template)

**Basic Brain Mapping** [example](http://stnava.github.io/BasicBrainMapping/)

**Large deformation** [example](http://stnava.github.io/C/)

**Template construction** [example](http://ntustison.github.io/TemplateBuildingExample/)

**Automobile** [example](http://stnava.github.io/cars/)

**Asymmetry** [example](http://stnava.github.io/asymmetry/)

**Point-set** [mapping](http://stnava.github.io/chicken/)

**Feature matching** [example](http://stnava.github.io/featureMatching/) ... not up to date ...

**Chimpanzee cortical thickness** [example](https://github.com/stnava/WHopkinsNHP/)

**Global optimization** [example](http://stnava.github.io/butterfly/)

**Morphing** [example](http://stnava.github.io/Morpheus/)

**fMRI or Motion Correction** [example](http://stnava.github.io/fMRIANTs/)

**fMRI reproducibility** [example](http://stnava.github.io/RfMRI/)

**fMRI prediction** [example](http://stnava.github.io/Haxby2001/) ... WIP ...

**Cardiac** [example](http://stnava.github.io/LabelMyHeart)

**Brain extraction** [example](https://github.com/ntustison/antsBrainExtractionExample)

**N4 bias correction <-> segmentation** [example](https://github.com/ntustison/antsAtroposN4Example)

**Cortical thickness** [example](https://github.com/ntustison/antsCorticalThicknessExample)

**MALF labeling example** [example](https://github.com/ntustison/MalfLabelingExample)

**Bibliography** [bibtex of ANTs-related papers](https://github.com/stnava/ANTsBibliography)

**ANTs** [google scholar page](http://scholar.google.com/citations?user=ox-mhOkAAAAJ&hl=en)

Presentations: e.g. [a Prezi about
ANTs](http://prezi.com/mwrmcm-h9-w4/ants/?kw=view-mwrmcm-h9-w4&rc=ref-40024395)
(WIP)

Reproducible science as a teaching tool: e.g. [compilable ANTs
tutorial](https://github.com/stnava/ANTS_MultiModality) (WIP)

Other examples [slideshow](http://brianavants.wordpress.com)

Landmark-based mapping for e.g. hippocampus [discussed
here](https://sourceforge.net/p/advants/discussion/840261/thread/1cb7b165/?limit=50)

Brief ANTs segmentation [video](http://vimeo.com/67814201)

References
----------------------------------------------------------

[Google
Scholar](http://scholar.google.com/scholar?q=Advanced+Normalization+Tools+%22ANTs%22+-ant&hl=en&as_sdt=1%2C39&as_ylo=2008&as_yhi=)

[Pubmed](http://www.ncbi.nlm.nih.gov/pubmed?term=%22Avants%20B%22%20OR%20%22Tustison%20N%22)

Boilerplate ANTs 
------------------

Here is some boilerplate regarding ants image processing:

We will analyze multiple modality neuroimaging data with Advanced
Normalization Tools (ANTs) version >= 2.1 [1]
(http://stnava.github.io/ANTs/).  ANTs has proven performance in
lifespan analyses of brain morphology [1] and function [2] in both
adult [1] and pediatric brain data [2,5,6] including infants [7].
ANTs employs both probabilistic tissue segmentation (via Atropos [3])
and machine learning methods based on expert labeled data (via joint
label fusion [4]) in order to maximize reliability and consistency of
multiple modality image segmentation.  These methods allow detailed
extraction of critical image-based biomarkers such as volumes
(e.g. hippocampus and amygdala), cortical thickness and area and
connectivity metrics derived from structural white matter [13] or
functional connectivity [12]. Critically, all ANTs components are
capable of leveraging multivariate image features as well as expert
knowledge in order to learn the best segmentation strategy available
for each individual image [3,4].  This flexibility in segmentation and
the underlying high-performance normalization methods have been
validated by winning several internationally recognized medical image
processing challenges conducted within the premier conferences within
the field and published in several accompanying articles
[8][9][10][11].

References

[1] http://www.ncbi.nlm.nih.gov/pubmed/24879923

[2] http://www.ncbi.nlm.nih.gov/pubmed/24817849

[3] http://www.ncbi.nlm.nih.gov/pubmed/21373993

[4] http://www.ncbi.nlm.nih.gov/pubmed/21237273

[5] http://www.ncbi.nlm.nih.gov/pubmed/22517961

[6] http://www.ncbi.nlm.nih.gov/pubmed/24033570

[7] http://www.ncbi.nlm.nih.gov/pubmed/24139564

[8]  http://www.ncbi.nlm.nih.gov/pubmed/21632295

[9] http://www.ncbi.nlm.nih.gov/pubmed/19195496

[10] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837555/

[11] http://nmr.mgh.harvard.edu/~koen/MenzeTMI2014.pdf

[12] http://www.ncbi.nlm.nih.gov/pubmed/23813017

[13] http://www.ncbi.nlm.nih.gov/pubmed/24830834



ANTs was supported by: R01-EB006266-01



[![githalytics.com alpha](https://cruel-carlota.pagodabox.com/a912f82c8178a07889f508871d94e77d "githalytics.com")](http://githalytics.com/stnava/ANTs)