# package names
select names = libnifti2 odin mitools afni-atlases python-pyssdh python-networkx
r-cran-glmnet python-rpy2 python-nibabel-snapshot
- python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev
+ python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab
# Information about prospective packages to be imported from taskfiles
prospective =
openmeeg-tools = openmeeg-tools libopenmeeg-dev python-openmeeg libopenmeeg1
libbiosig-dev = libbiosig-dev python-biosig octave-biosig biosig-tools libbiosig0
libgdf-dev = libgdf-dev libgdf0 libgdf0-dbg libgdf-dev gdf-tools octave-gdf matlab-gdf
+spm8 = matlab-spm8 spm8-common spm8-data spm8-doc
[mirrors]
de = http://apsy.gse.uni-magdeburg.de/debian
gifti-bin = 75
imagej = 256
itksnap = 110
+jist = 228
libminc-dev = 129
-minc-tools = 129
libgiftiio-dev = 75
libnifti2 = 26
libnifti-dev = 26
-nifti-bin = 26
-odin = 153
+matlab-spm8 = 24
+minc-tools = 129
+mipav = 70
mitools = 153
mricron = 152
mrtrix = 128
+nifti-bin = 26
+odin = 153
python-mvpa = 162
python-nipype = 325
slicer = 50
+spm8 = 24
voxbo = 73
-mipav = 70
-jist = 228
--- /dev/null
+Package development in progress
+===============================
+
+The current SPM8 package is work-in-progress. It might undergo significant
+changes and package content and functionality between package updates. In
+particular, only fMRI-related functionality is supposed to work at this time.
+All MEG/EEG tools require the fieldtrip toolbox that will be packaged
+separately in the future.
+
+However, testing, bug reports and suggestions for improvements are most welcome!
+Please post them to 592390@bugs.debian.org
as root or use sudo).
-.. include:: links_names.rst
-.. include:: substitutions.rst
+.. include:: link_names.txt
+.. include:: substitutions.txt
+++ /dev/null
-.. _gpg_signatures:
-
-
-Package authentication
-======================
-
-
-When you start using this repository, you might get warning messages like this::
-
- The following signatures couldn't be verified because
- the public key is not available.`
-
-Or you will be asked questions like this over and over::
-
- WARNING: The following packages cannot be authenticated!
- ...
- Install these packages without verification [y/N]?
-
-This is because your APT installation does not know the GPG key that is used to
-sign the release files of this repository. Making APT happy again is easy:
-
-1. Get the key. Either download the `repository key from here
- <http://apsy.gse.uni-magdeburg.de/debian/apsy.gse.uni-magdeburg.de.asc>`_
- or fetch it from *subkeys.pgp.net*.
-
-2. Now feed the key into APT by invoking::
-
- apt-key add #file#
-
- Where `#file#` has to be replaced with the location of the key file you just
- downloaded. You need to have superuser-privileges to do this (either do it
- as root or use sudo).
-
.. toctree::
:hidden:
+ datasets
livecd
- gpg
- setup
- links_names
- substitutions
+ vm_welcome
quotes-nihr01
quotes-nitrc
-.. include:: links_names.rst
-.. include:: substitutions.rst
+
+.. include:: link_names.txt
+.. include:: substitutions.txt
--- /dev/null
+.. 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
+
+.. 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
+
+.. Other python projects
+.. _numpy: http://www.scipy.org/NumPy
+.. _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/
+
+.. 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
+.. _NeuroDebian: http://neuro.debian.net
+.. _Debian: http://www.debian.org
+.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy
+.. _`Debian Med`: http://debian-med.alioth.debian.org
+.. _`Debian Science`: http://wiki.debian.org/DebianScience
+
+.. 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
+
+.. 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
+++ /dev/null
-.. 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
-
-.. 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
-
-.. Other python projects
-.. _numpy: http://www.scipy.org/NumPy
-.. _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/
-
-.. 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
-.. _NeuroDebian: http://neuro.debian.net
-.. _Debian: http://www.debian.org
-.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy
-.. _`Debian Med`: http://debian-med.alioth.debian.org
-.. _`Debian Science`: http://wiki.debian.org/DebianScience
-
-.. 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
-
-.. 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
+++ /dev/null
-The packages are available through an APT repository You can either browse the
-archive or add this line to your `/etc/apt/sources.list`::
-
- deb http://apsy.gse.uni-magdeburg.de/debian #distro# #section#
-
-Replace `#distro#` with ..., depending on which distribution you are using.
-Note that not every package is available for all distributions. You need to
-replace #section# with the value(s) corresponding to the package(s) you are
-interested in (get it from the table below). Multiple sections are allowed.
-Please, do not forget to update your package index, e.g. by running apt-get
-update. If no binary packages are available for your distribution, you can
-still download the source packages. Simply add this to your
-`/etc/apt/sources.list` (you have to replace #distro# and #section# as
-described above)::
-
- deb-src http://apsy.gse.uni-magdeburg.de/debian #distro# #section#
-
-After the usual apt-get update you can get and build the packages with e.g.
-apt-src or whatever you like. To build e.g. dicomnifti you can do this: apt-src
-install dicomnifti
-
-This downloads the sources and installs all build-dependencies if necessary.
-You need root-privileges to install the build-dependencies, so apt-src might
-ask for a password. Now invoke: apt-src build dicomnifti
-
-This will build all binary packages which should appear in the current
-directory (if everything worked well). You can now install the packages with
-dpkg.
-
-
-
-.. include:: links_names.rst
-.. include:: substitutions.rst
+.. include:: link_names.txt
+.. include:: substitutions.txt
+++ /dev/null
-.. Substitutions for the whole doc tree
-
-.. |team| replace:: :ref:`NeuroDebian team <chap_team>`
-.. |we| replace:: :ref:`we <chap_team>`
-.. |spread| replace:: :ref:`spread the word about NeuroDebian <chap_spread>`
-.. |repos| replace:: :ref:`NeuroDebian repositories <repository_howto>`
-.. |exppsy| replace:: Experimental Psychology
--- /dev/null
+.. Substitutions for the whole doc tree
+
+.. |team| replace:: :ref:`NeuroDebian team <chap_team>`
+.. |we| replace:: :ref:`we <chap_team>`
+.. |spread| replace:: :ref:`spread the word about NeuroDebian <chap_spread>`
+.. |repos| replace:: :ref:`NeuroDebian repositories <repository_howto>`
+.. |exppsy| replace:: Experimental Psychology
projects / neurodebian.git / commitdiff