DOC - fixed missing links with merge from dipy docs

Author: matthew-brett

doc/source/dicom/dicom.rst

@@ -12,7 +12,6 @@ Contents:
    dicom_info
    dicom_orientation
    dicom_fields
-   bmatrix
    dicom_mosaic
    siemens_csa
    spm_dicom

doc/source/links_names.txt

@@ -8,9 +8,12 @@
    __not_case_sensitive__, so only one target definition is needed for
    nipy, NIPY, Nipy, etc...
 
-.. _nipy: http://neuroimaging.scipy.org
-.. _`NIPY developer resources`: http://nipy.sourceforge.net/devel
+.. _nipy: http://nipy.org
 .. _`Brain Imaging Center`: http://bic.berkeley.edu/
+.. _dipy: http://nipy.org/dipy
+.. _`dipy github`: http://github.com/Garyfallidis/dipy
+.. _nibabel: http://nipy.sourceforge.net/nibabel
+.. _nipy development guidelines: http://nipy.sourceforge.net/devel
 
 .. Documentation tools
 .. _graphviz: http://www.graphviz.org/
@@ -45,6 +48,7 @@
 .. _pyflakes: http://divmod.org/trac/wiki/DivmodPyflakes
 .. _virtualenv: http://pypi.python.org/pypi/virtualenv
 .. _git: http://git.or.cz/
+.. _github: http://github.com
 .. _flymake: http://flymake.sourceforge.net/
 .. _rope: http://rope.sourceforge.net/
 .. _pymacs: http://pymacs.progiciels-bpi.ca/pymacs.html
@@ -63,34 +67,54 @@
 .. _ipython: http://ipython.scipy.org
 .. _`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/
-.. _pythonxy: http://www.pythonxy.com/
-.. _EPD: http://www.enthought.com/products/epd.php
+.. _setuptools: http://pypi.python.org/pypi/setuptools
 
 .. 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 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
 
 .. Functional imaging labs
 .. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk
@@ -113,6 +137,21 @@
 .. _`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
+
 .. People
 .. _Matthew Brett: https://cirl.berkeley.edu/mb312/
 .. _Yaroslav O. Halchenko: http://www.onerussian.com