.. 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://nipy.org
.. _`NIPY developer resources`: http://nipy.org/devel
.. _`Brain Imaging Center`: http://bic.berkeley.edu/
.. _nitime: http://nipy.org/nitime/
.. _nibabel: http://nipy.org/nibabel/
.. _nipype: http://nipy.org/nipype/
.. _ConnectomeViewer: http://www.connectomeviewer.org/viewer/
.. _NeuroDebian: http://neuro.debian.net/

.. 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

.. 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`: https://code.launchpad.net/~nipy-developers/nipy/trunk
.. _`nipy mailing list`: https://mail.python.org/mailman/listinfo/neuroimaging
.. _`nipy bugs`: https://bugs.launchpad.net/nipy

.. 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
.. _git: https://git-scm.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/
.. _bazaar: http://bazaar-vcs.org/
.. _subversion: http://subversion.tigris.org/
.. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html

.. Other python projects
.. _numpy: http://www.numpy.org/
.. _scipy: http://www.scipy.org
.. _ipython: https://ipython.org
.. _`ipython manual`: https://ipython.readthedocs.org/en/stable/
.. _matplotlib: http://matplotlib.org/
.. _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://www.sympy.org/
.. _networkx: https://networkx.github.io/
.. _pythonxy: https://python-xy.github.io/
.. _EPD: http://www.enthought.com/products/epd.php
.. _Traits: http://code.enthought.com/projects/traits/
.. _Miniconda: https://conda.io/miniconda.html
.. _neurodocker: https://github.com/kaczmarj/neurodocker

.. Python imaging projects
.. _PyMVPA: http://www.pymvpa.org
.. _BrainVISA: http://brainvisa.info
.. _anatomist: http://brainvisa.info

.. Not so python imaging projects
.. _matlab: http://www.mathworks.com
.. _spm: http://www.fil.ion.ucl.ac.uk/spm
.. _eeglab: http://sccn.ucsd.edu/eeglab
.. _ANTS: http://stnava.github.io/ANTs/
.. _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
.. _Slicer: http://slicer.org
.. _Camino: http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php
.. _Camino2Trackvis: http://camino-trackvis.sourceforge.net/
.. _MRtrix: http://www.brain.org.au/software/mrtrix/index.html
.. _MRtrix3: http://www.mrtrix.org/
.. _MNE: https://martinos.org/mne/index.html
.. _ANTS: http://stnava.github.io/ANTs/
.. _DIPY: http://dipy.org

.. General software
.. _gcc: http://gcc.gnu.org
.. _xcode: http://developer.apple.com/TOOLS/xcode
.. _mingw: http://www.mingw.org
.. _macports: http://www.macports.org/
.. _Vagrant: http://www.vagrantup.com/
.. _Docker: http://www.docker.com/
.. _Singularity: https://www.sylabs.io/singularity/
.. _Virtualbox: https://www.virtualbox.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

.. 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

.. Nipype Paper
.. _paper: http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00013/abstract
