.. 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...

.. _nipy: http://neuroimaging.scipy.org
.. _nipype: http://nipy.sourceforge.net/nipype
.. _`Brain Imaging Center`: http://bic.berkeley.edu/
.. _dipy: http://nipy.sourceforge.net/dipy
.. _`dipy github`: http://github.com/Garyfallidis/dipy
.. _nibabel: http://nipy.sourceforge.net/nibabel
.. _dipy: http://nipy.sourceforge.net/dipy

.. _Neuron: http://www.neuron.yale.edu/neuron
.. _XPPAUT: http://www.math.pitt.edu/~bard/xpp/xpp.html
.. _Genesis: http://www.genesis-sim.org

.. 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

.. 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

.. Source control
.. _git: http://git-scm.com/
.. _github: http://github.com
.. _github help: http://help.github.com
.. _msysgit: http://code.google.com/p/msysgit/downloads/list
.. _git-osx-installer: http://code.google.com/p/git-osx-installer/downloads/list
.. _bazaar: http://bazaar-vcs.org/

.. Other working process
.. _pynifti: http://niftilib.sourceforge.net/pynifti/
.. _nifticlibs: http://nifti.nimh.nih.gov
.. _nifti: http://nifti.nimh.nih.gov
.. _`nipy launchpad`: https://launchpad.net/nipy
.. _launchpad: https://launchpad.net/
.. _`nipy trunk`: https://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
.. _pep8: http://www.python.org/dev/peps/pep-0008/
.. _`numpy coding style`: http://scipy.org/scipy/numpy/wiki/CodingStyleGuidelines

.. Code support stuff
.. _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
.. _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
.. _screen: http://www.gnu.org/software/screen/
.. _ccache: http://ccache.samba.org/

.. Other python projects
.. _numpy: http://www.numpy.org
.. _scipy: http://www.scipy.org
.. _ipython: http://ipython.scipy.org
.. _`ipython manual`: http://ipython.scipy.org/doc/manual/html
.. _matplotlib: http://matplotlib.sourceforge.net
.. _pythonxy: http://www.pythonxy.com
.. _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/

.. Python imaging projects
.. _PyMVPA: http://www.pymvpa.org
.. _BrainVISA: http://brainvisa.info
.. _anatomist: http://brainvisa.info
.. _pydicom: http://code.google.com/p/pydicom/
.. _PyMGH/PyFSIO: http://code.google.com/p/pyfsio
.. _OpenMEEG: http://openmeeg.gforge.inria.fr
.. _PROBID: http://www.brainmap.co.uk/probid.htm

.. Not so python imaging projects
.. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
.. _CoSMoMVPA: http://www.github.com/CoSMoMVPA
.. _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
.. _LIPSIA: http://www.cbs.mpg.de/institute/software/lipsia
.. _FreeSurfer: http://surfer.nmr.mgh.harvard.edu
.. _voxbo: http://www.voxbo.org
.. _mricron: http://www.cabiatl.com/mricro/mricron
.. _slicer: http://www.slicer.org/
.. _XNAT: http://xnat.org

.. ML projects not mentioned above
.. _3dsvm: http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dsvm.html
.. _Elefant: http://elefant.developer.nicta.com.au
.. _LIBSVM: http://www.csie.ntu.edu.tw/~cjlin/libsvm
.. _MDP: http://mdp-toolkit.sourceforge.net
.. _Shogun: http://www.shogun-toolbox.org
.. _Orange: http://magix.fri.uni-lj.si/orange
.. _PyML: http://pyml.sourceforge.net
.. _MVPA Toolbox: http://www.csbmb.princeton.edu/mvpa/
.. _scikit-learn: http://scikit-learn.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 specs`: ftp://medical.nema.org/medical/dicom/2009/
.. _`DICOM object definitions`: ftp://medical.nema.org/medical/dicom/2009/09_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
.. _NeuroDebian: http://neuro.debian.net
.. _Debian: http://www.debian.org
.. _`Debian project`: http://www.debian.org
.. _Ubuntu: http://www.ubuntu.com
.. _Xubuntu: http://www.xubuntu.org
.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy
.. _`Debian Med`: http://debian-med.alioth.debian.org
.. _`Debian Science`: http://wiki.debian.org/DebianScience
.. _Comedi: http://www.comedi.org
.. _RTAI: https://www.rtai.org
.. |RTAI| replace:: :abbr:`RTAI (Real Time Application Interface)`
.. _Lin4Neuro: http://www.nemotos.net/lin4neuro
.. _fail2ban: http://www.fail2ban.org

.. Debian releases
.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
.. _Debian 7.0 (wheezy): http://www.debian.org/releases/wheezy
.. _Debian 7.8 (wheezy): http://www.debian.org/releases/wheezy
.. _Debian 8.0 (jessie): http://www.debian.org/releases/jessie

.. Desktop environments
.. _GNOME: http://www.gnome.org/
.. _GNOME3: http://www.gnome.org/gnome-3/
.. _XFCE: http://www.xfce.org/
.. _XFCE4: http://www.xfce.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
.. _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

.. 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 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

.. Some common terms as links outside and abbreviations
.. _FOSS: http://en.wikipedia.org/wiki/Free_and_Open_Source_Software
.. |FOSS| replace:: :abbr:`FOSS (Free and Open Source Software)`
.. _DFSG: http://www.debian.org/social_contract#guidelines
.. |DFSG| replace:: :abbr:`DFSG (Debian Free Software Guidelines)`

.. Homepages
.. _yoh: http://www.onerussian.com
.. _mih: http://mih.voxindeserto.de

.. Debian specifics
.. _ITP: http://www.debian.org/devel/wnpp
.. _ITPs: http://www.debian.org/devel/wnpp
.. |ITP| replace:: :abbr:`ITP (Intent to Package)`
.. |RFP| replace:: :abbr:`RFP (Request for packaging)`
.. |DBTS| replace:: :abbr:`DBTS (Debian Bug Tracking System)`
.. _debian-installer: http://www.debian.org/devel/debian-installer/

.. mailing lists
.. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
.. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
.. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream

.. task pages
.. _neuroscience-electrophysiology: http://blends.alioth.debian.org/science/tasks/neuroscience-electrophysiology
.. _task_bci: http://blends.alioth.debian.org/science/tasks/bci
.. _task_dataacquisition: http://blends.alioth.debian.org/science/tasks/dataacquisition
.. _task_psychophysics: http://blends.alioth.debian.org/science/tasks/psychophysics>

.. more to sort out
.. _NeuralEnsemble: http://www.neuralensemble.org
.. _`repository mirror`: http://neuro.debian.net/mirrors-status.html
