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
|
.. -*- rst -*-
.. vim: ft=rst
.. This rst format file contains commonly used link targets
and name substitutions. It may be included in many files,
therefore it should only contain link targets and name
substitutions. Try grepping for "^\.\. _" to find plausible
candidates for this list.
.. NOTE: reST targets are
__not_case_sensitive__, so only one target definition is needed for
nipy, NIPY, Nipy, etc...
.. Transforms3d code stuff
.. _transforms3d github: http://github.com/matthew-brett/transforms3d
.. _transforms3d pypi: http://pypi.python.org/pypi/transforms3d
.. _transforms3d issues: http://github.com/matthew-brett/transforms3d/issues
.. _transforms3d travis-ci: https://travis-ci.org/matthew-brett/transforms3d
.. _versioneer: https://github.com/warner/python-versioneer
.. _transformations.py:
http://www.lfd.uci.edu/~gohlke/code/transformations.py.html
.. _Christoph Gohlke: http://www.lfd.uci.edu/~gohlke
.. _Matthew Brett: http://matthew.dynevor.org
.. Transform concepts
.. _`wikipedia affine`: http://en.wikipedia.org/wiki/Affine_transformation
.. _`wikipedia linear transform`: http://en.wikipedia.org/wiki/Linear_transformation
.. _`wikipedia rotation matrix`: http://en.wikipedia.org/wiki/Rotation_matrix
.. _`wikipedia homogenous coordinates`: http://en.wikipedia.org/wiki/Homogeneous_coordinates
.. _`wikipedia axis angle`: http://en.wikipedia.org/wiki/Axis_angle
.. _`wikipedia Euler angles`: http://en.wikipedia.org/wiki/Euler_angles
.. _`Mathworld Euler angles`: http://mathworld.wolfram.com/EulerAngles.html
.. _`wikipedia quaternion`: http://en.wikipedia.org/wiki/Quaternion
.. _`wikipedia shear matrix`: http://en.wikipedia.org/wiki/Shear_matrix
.. _`wikipedia reflection`: http://en.wikipedia.org/wiki/Reflection_(mathematics)
.. nibabel
.. _nibabel: http://nipy.org/nibabel
.. _`nibabel github`: http://github.com/nipy/nibabel
.. _`nibabel mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
.. _nibabel pypi: http://pypi.python.org/pypi/nibabel
.. _nibabel issues: http://github.com/nipy/nibabel/issues
.. other related projects
.. _nipy community: http://nipy.org
.. _nipy: http://nipy.org/nipy
.. _`Brain Imaging Center`: http://bic.berkeley.edu/
.. _dipy: http://nipy.org/dipy
.. _`dipy github`: http://github.com/Garyfallidis/dipy
.. _nibabel: http://nipy.org/nibabel
.. _nipy development guidelines: http://nipy.org/devel
.. _`nipy github`: http://github.com/nipy/nipy
.. _nipy buildbot: http://nipy.bic.berkeley.edu
.. Documentation tools
.. _graphviz: http://www.graphviz.org/
.. _Sphinx: http://sphinx.pocoo.org/
.. _`Sphinx reST`: http://sphinx.pocoo.org/rest.html
.. _reST: http://docutils.sourceforge.net/rst.html
.. _docutils: http://docutils.sourceforge.net
.. _IPython notebook viewer: http://nbviewer.ipython.org
.. Licenses
.. _GPL: http://www.gnu.org/licenses/gpl.html
.. _BSD: http://www.opensource.org/licenses/bsd-license.php
.. _LGPL: http://www.gnu.org/copyleft/lesser.html
.. _MIT License: http://www.opensource.org/licenses/mit-license.php
.. Installation
.. _pypi: http://pypi.python.org/pypi
.. Working process
.. _pynifti: http://niftilib.sourceforge.net/pynifti/
.. _nifticlibs: http://nifti.nimh.nih.gov
.. _nifti: http://nifti.nimh.nih.gov
.. _`nipy sourceforge`: http://nipy.sourceforge.net/
.. _sourceforge: http://nipy.sourceforge.net/
.. _`nipy launchpad`: https://launchpad.net/nipy
.. _launchpad: https://launchpad.net/
.. _`nipy trunk`: http://code.launchpad.net/~nipy-developers/nipy/trunk
.. _`nipy mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel
.. _`nipy bugs`: https://bugs.launchpad.net/nipy
.. _sourceforge download page: http://sourceforge.net/projects/nipy/files
.. Code support stuff
.. _travis-ci: https://travis-ci.org
.. _pychecker: http://pychecker.sourceforge.net/
.. _pylint: http://www.logilab.org/project/pylint
.. _pyflakes: http://divmod.org/trac/wiki/DivmodPyflakes
.. _virtualenv: http://pypi.python.org/pypi/virtualenv
.. _github: http://github.com
.. _flymake: http://flymake.sourceforge.net/
.. _rope: http://rope.sourceforge.net/
.. _pymacs: http://pymacs.progiciels-bpi.ca/pymacs.html
.. _ropemacs: http://rope.sourceforge.net/ropemacs.html
.. _ECB: http://ecb.sourceforge.net/
.. _emacs_python_mode: http://www.emacswiki.org/cgi-bin/wiki/PythonMode
.. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/
.. _nose: http://somethingaboutorange.com/mrl/projects/nose
.. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html
.. Other python projects
.. _numpy: http://www.scipy.org/NumPy
.. _scipy: http://www.scipy.org
.. _ipython: http://ipython.scipy.org
.. _`ipython github`: http://github.com/ipython/ipython
.. _`ipython mailing list`: http://mail.scipy.org/mailman/listinfo/IPython-dev
.. _`ipython manual`: http://ipython.scipy.org/doc/manual/html
.. _matplotlib: http://matplotlib.sourceforge.net
.. _pythonxy: http://www.pythonxy.com
.. _EPD: http://www.enthought.com/products/epd.php
.. _ETS: http://code.enthought.com/projects/tool-suite.php
.. _`Enthought Tool Suite`: http://code.enthought.com/projects/tool-suite.php
.. _python: http://www.python.org
.. _mayavi: http://mayavi.sourceforge.net/
.. _sympy: http://code.google.com/p/sympy/
.. _networkx: http://networkx.lanl.gov/
.. _setuptools: http://pypi.python.org/pypi/setuptools
.. _distribute: http://packages.python.org/distribute
.. _pip: https://pip.readthedocs.org/en/latest
.. _pip install instructions:
https://pip.readthedocs.org/en/latest/installing.html
.. _twine: https://pypi.python.org/pypi/twine
.. _datapkg: http://okfn.org/projects/datapkg
.. _python imaging library: http://www.pythonware.com
.. Python imaging projects
.. _PyMVPA: http://www.pymvpa.org
.. _BrainVISA: http://brainvisa.info
.. _anatomist: http://brainvisa.info
.. _pydicom: http://code.google.com/p/pydicom/
.. Not so python imaging projects
.. _matlab: http://www.mathworks.com
.. _spm: http://www.fil.ion.ucl.ac.uk/spm
.. _spm8: http://www.fil.ion.ucl.ac.uk/spm/software/spm8
.. _eeglab: http://sccn.ucsd.edu/eeglab
.. _AFNI: http://afni.nimh.nih.gov/afni
.. _FSL: http://www.fmrib.ox.ac.uk/fsl
.. _FreeSurfer: http://surfer.nmr.mgh.harvard.edu
.. _voxbo: http://www.voxbo.org
.. _mricron: http://www.cabiatl.com/mricro/mricron
.. _slicer: http://www.slicer.org/
.. File formats
.. _DICOM: http://medical.nema.org/
.. _`wikipedia DICOM`: http://en.wikipedia.org/wiki/Digital_Imaging_and_Communications_in_Medicine
.. _GDCM: http://sourceforge.net/apps/mediawiki/gdcm
.. _DICOM standard : http://medical.nema.org/standard.html
.. _PS 3.1: http://medical.nema.org/Dicom/2011/11_01pu.pdf
.. _PS 3.2: http://medical.nema.org/Dicom/2011/11_02pu.pdf
.. _PS 3.3: http://medical.nema.org/Dicom/2011/11_03pu.pdf
.. _PS 3.4: http://medical.nema.org/Dicom/2011/11_04pu.pdf
.. _PS 3.5: http://medical.nema.org/Dicom/2011/11_05pu.pdf
.. _PS 3.6: http://medical.nema.org/Dicom/2011/11_06pu.pdf
.. _PS 3.7: http://medical.nema.org/Dicom/2011/11_07pu.pdf
.. _PS 3.8: http://medical.nema.org/Dicom/2011/11_08pu.pdf
.. _PS 3.10: http://medical.nema.org/Dicom/2011/11_10pu.pdf
.. _PS 3.11: http://medical.nema.org/Dicom/2011/11_11pu.pdf
.. _PS 3.12: http://medical.nema.org/Dicom/2011/11_12pu.pdf
.. _PS 3.14: http://medical.nema.org/Dicom/2011/11_14pu.pdf
.. _PS 3.15: http://medical.nema.org/Dicom/2011/11_15pu.pdf
.. _PS 3.16: http://medical.nema.org/Dicom/2011/11_16pu.pdf
.. _PS 3.17: http://medical.nema.org/Dicom/2011/11_17pu.pdf
.. _PS 3.18: http://medical.nema.org/Dicom/2011/11_18pu.pdf
.. _PS 3.19: http://medical.nema.org/Dicom/2011/11_19pu.pdf
.. _PS 3.20: http://medical.nema.org/Dicom/2011/11_20pu.pdf
.. _`DICOM specs`: ftp://medical.nema.org/medical/dicom/2011/
.. _DICOM data structures: http://medical.nema.org/dicom/2011/11_05pu.pdf
.. _DICOM data dictionary: http://medical.nema.org/dicom/2011/11_05pu.pdf
.. _`DICOM object definitions`: ftp://medical.nema.org/medical/dicom/2011/11_03pu3.pdf
.. _dcm2nii: http://www.cabiatl.com/mricro/mricron/dcm2nii.html
.. _`mricron install`: http://www.cabiatl.com/mricro/mricron/install.html
.. _dicom2nrrd: http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.4
.. _Nrrd: http://teem.sourceforge.net/nrrd/format.html
.. General software
.. _gcc: http://gcc.gnu.org
.. _xcode: http://developer.apple.com/TOOLS/xcode
.. _mingw: http://www.mingw.org
.. _cygwin: http://cygwin.com
.. _macports: http://www.macports.org/
.. _VTK: http://www.vtk.org/
.. _ITK: http://www.itk.org/
.. _swig: http://www.swig.org
.. version control
.. _git: http://git-scm.com
.. _mercurial: http://mercurial.selenic.com
.. _bzr: http://bazaar.canonical.com
.. _subversion: http://subversion.apache.org
.. Functional imaging labs
.. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk
.. _FMRIB: http://www.fmrib.ox.ac.uk
.. Other organizations
.. _enthought: <http://www.enthought.com>
.. _kitware: http://www.kitware.com
.. _NeuroDebian: http://neuro.debian.net
.. _nibabel NeuroDebian: http://neuro.debian.net/pkgs/python-nibabel.html
.. _nitrc: http://www.nitrc.org
.. General information links
.. _`wikipedia FMRI`: http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging
.. _`wikipedia PET`: http://en.wikipedia.org/wiki/Positron_emission_tomography
.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm
.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/
.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/
.. _MINC: http://wiki.bic.mni.mcgill.ca/index.php/MINC
.. _GIFTI: http://www.nitrc.org/projects/gifti
.. _MINC1:
https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference
.. _MINC2:
https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference
.. Mathematical methods
.. _`wikipedia ICA`: http://en.wikipedia.org/wiki/Independent_component_analysis
.. _`wikipedia PCA`: http://en.wikipedia.org/wiki/Principal_component_analysis
.. Mathematical ideas
.. _`wikipedia spherical coordinate system`: http://en.wikipedia.org/wiki/Spherical_coordinate_system
.. _`mathworld spherical coordinate system`: http://mathworld.wolfram.com/SphericalCoordinates.html
.. _`wikipedia affine`: http://en.wikipedia.org/wiki/Affine_transformation
.. _`wikipedia affine transform`: http://en.wikipedia.org/wiki/Affine_transformation
.. _`wikipedia linear transform`: http://en.wikipedia.org/wiki/Linear_transformation
.. _`wikipedia rotation matrix`: http://en.wikipedia.org/wiki/Rotation_matrix
.. _`wikipedia homogenous coordinates`: http://en.wikipedia.org/wiki/Homogeneous_coordinates
.. _`wikipedia axis angle`: http://en.wikipedia.org/wiki/Axis_angle
.. _`wikipedia Euler angles`: http://en.wikipedia.org/wiki/Euler_angles
.. _`Mathworld Euler angles`: http://mathworld.wolfram.com/EulerAngles.html
.. _`wikipedia quaternion`: http://en.wikipedia.org/wiki/Quaternion
.. _`wikipedia shear matrix`: http://en.wikipedia.org/wiki/Shear_matrix
.. _`wikipedia reflection`: http://en.wikipedia.org/wiki/Reflection_(mathematics)
.. _`wikipedia direction cosine`: http://en.wikipedia.org/wiki/Direction_cosine
.. philosophy
.. _0SAGA: http://nipyworld.blogspot.com/2010/11/0saga-software-model.html
.. People
.. _Matthew Brett: http://matthew.dynevor.org
.. _Yaroslav O. Halchenko: http://www.onerussian.com
.. _Michael Hanke: http://mih.voxindeserto.de
.. _Gaël Varoquaux: http://gael-varoquaux.info/
.. _Stephan Gerhard: http://www.unidesign.ch
.. Substitutions
.. |emdash| unicode:: U+02014
.. |--| unicode:: U+02014
|
