Task: Cognitive Neuroscience
Description: Debian Science packages for Cognitive Neuroscience
 This metapackage will install Debian packages which might be useful for
 scientists doing cognitive neuroscience research. This comprises the full
 research process from conducting psychophysical experiments, over data
 acquisition and analysis, to visualization and typesetting of scientific
 results.
 .
 The selection of packages is targeting the application of analysis
 techniques. Methods developers are refered to the science-statistics,
 science-imageanalysis, science-numericalcomputation, med-imaging, and
 med-imaging-dev metapackages for a variety of additional software that
 might be useful in the context of cognitive neuroscience.


Suggests: science-typesetting
Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/typesetting


Depends: amide
Why: Flexible volume slicing and rendering.
Published-Title: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis
Published-Authors: Andreas M. Loening, Sanjiv S. Gambhir
Published-In: Molecular Imaging, 2: 131-137
Published-Year: 2003
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/14649056
Published-DOI:


Depends: dicomnifti
Why: Fully automated DICOM-to-NIfTI converter.


Depends: minc-tools, medcon, xmedcon, nifti-bin
Why: Misc. image handling tools


Depends: python-nifti
Why: Python IO library for the NIfTI format.


Depends: fsl
Why: Comprehensive MRI analysis suite.
Published-Title: Advances in functional and structural MR image analysis and implementation as FSL
Published-Authors: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, P.M. Matthews
Published-In: NeuroImage, 23:208-219
Published-Year: 2004
Published-URL: http://dx.doi.org/10.1016/j.neuroimage.2004.07.051
Published-DOI: 10.1016/j.neuroimage.2004.07.051


Depends: fslview
Published-Title: Advances in functional and structural MR image analysis and implementation as FSL
Published-Authors: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, P.M. Matthews
Published-In: NeuroImage, 23:208-219
Published-Year: 2004
Published-URL: http://dx.doi.org/10.1016/j.neuroimage.2004.07.051
Published-DOI: 10.1016/j.neuroimage.2004.07.051


Depends: python-mvpa
Why: Framework for multivariate pattern analysis of neuroimaging datasets.
Published-Title: PyMVPA: a unifying approach to the analysis of neuroscientific data
Published-Authors: Michael Hanke, Yaroslav O. Halchenko, Per B. Sederberg, Emanuele Olivetti, Ingo Fründ, Jochem W. Rieger, Christoph S. Herrmann, James V. Haxby, Stephen José Hanson, Stefan Pollmann
Published-In: Frontiers in Neuroinformatics, 3:3
Published-Year: 2009
Published-URL: http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/003.2009/
Published-DOI: 10.3389/neuro.11.003.2009


Depends: caret
Why: Cortical reconstruction and volume-to-surface mapping.
Published-Title: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex
Published-Authors: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon, Charles H. Anderson
Published-In: Journal of American Medical Informatics Association, 8(5): 443-459
Published-Year: 2001
Published-URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?pubmedid=11522765


Depends: python-pyepl
Why: Library to write and run psychological experiments.
Published-Title: PyEPL: A cross-platform experiment-programming library
Published-Authors: Aaron S. Geller, Ian K. Schleifer, Per B. Sederberg, Joshua Jacobs, Michael J. Kahana
Published-In: Behavioral Research Methods, 39: 950-958
Published-Year: 2007
Published-URL: http://prdownloads.sourceforge.net/pyepl/pyepl_brmic.pdf?download


Depends: praat
Why: Speech synthesis and analysis -- standard tool for auditory stimulus
     generation.

Depends: slicer

Depends: dicom3tools
Why: Supports conversion from proprietary formats, such as GE into DICOM.

Depends: psychopy
Published-Title: PsychoPy - Psychophysics software in Python
Published-Authors: J. W. Peirce
Published-In: Journal of Neuroscience Methods, 162:8-13
Published-Year: 2007
Published-DOI: 10.1016/j.jneumeth.2006.11.017

Depends: bioimagesuite
Homepage: http://www.bioimagesuite.org/
License: GPL
Pkg-Description: integrated image analysis software suite
 BioImage Suite has extensive capabilities for both neuro/cardiac
 and abdominal image analysis and state of the art visualization.
 Many packages are available that are highly extensible, and provide
 functionality for image visualization and registration, surface
 editing, cardiac 4D multi-slice editing, diffusion tensor image
 processing, mouse segmentation and registration, and much more. It
 can be intergrated with other biomedical image processing software,
 such as FSL and SPM. This site provides information, downloads,
 documentation, and other resources for users of the software.
 .
 BioImage Suite was developed at Yale University and has been
 extensively used at different labs at Yale since 2004.
 .
 There is a forum at BioImage Suite site for discussion of
 compiling it from source and packaging issues at
 http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0

Depends: afni
Homepage: http://afni.nimh.nih.gov/
WNPP: 409849
Responsible: Michael Hanke <michael.hanke@gmail.com>
License: GPL
Pkg-URL: http://sourceforge.net/project/showfiles.php?group_id=61662&package_id=60298
Pkg-Description: environment for processing and displaying functional MRI data
 AFNI is an environment for processing and displaying functional
 MRI data. It provides a complete analysis toolchain, including
 3D cortical surface models, and mapping of volumetric data (SUMA).
 In addition to its own format AFNI understands the NIfTI format and is
 therefore easily usable in combination with FSL and Freesurfer.
Published-Title: AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages
Published-Authors: Robert W. Cox
Published-In: Computers and Biomedical Research, 29:162-173
Published-Year: 1996
Published-URL: http://afni.nimh.nih.gov/pub/dist/doc/papers/afni_paper1.pdf


Depends: mni-autoreg
Homepage: http://www.bic.mni.mcgill.ca/software/mni_autoreg/
License: no-free, but GPLed parts
Responsible: Michael Hanke <michael.hanke@gmail.com>
Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/pool/contrib/m/mni-autoreg-model/
Pkg-Description: MNI average brain (305 MRI) stereotaxic registration model
 This package provides a version of the MNI Average Brain (an average of 305
 T1-weighted MRI scans, linearly transformed to Talairach space) specially
 adapted for use with the MNI Linear Registration Package.
 .
  * average_305.mnc - a version of the average MRI that covers the whole brain
    (unlike the original Talairach atlas), sampled with 1mm cubic voxels
  * average_305_mask.mnc - a mask of the brain in average_305.mnc
  * average_305_headmask.mnc - another mask, required for nonlinear mode
 .
 Remark: Michael Hanke agreed to take over his stuff from mentors
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg
 and
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg-model
 to Debian Med svn and start group maintenance.


Depends: mni-n3
Homepage: http://www.bic.mni.mcgill.ca/software/N3/
License: BSDish
Responsible: Michael Hanke <michael.hanke@gmail.com>
Pkg-URL: http://mentors.debian.net/debian/pool/main/m/mni-n3/
Pkg-Description: MNI Non-parametric Non-uniformity Normalization
 MNI Non-parametric Non-uniformity Normalization (N3). This package provides
 the 'nu_correct' tool for unsupervised correction of radio frequency (RF)
 field inhomogenities in MR volumes. Two packages are provided:
  * mni-n3 - provides 'nu_correct'
  * libebtks-dev - MNI support library with numerical types and algorithms
 .
 Remark: Michael Hanke agreed to take over his stuff from mentors
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-n3
 to Debian Med svn and start group maintenance.


Depends: brainvisa
Homepage: http://brainvisa.info/
License: Free? (CeCill License)
Pkg-Description: image processing factory for MR images
 BrainVISA is a software, which embodies an image processing
 factory. A simple control panel allows the user to trigger some
 sequences of treatments on series of images. These treatments are
 performed by calls to command lines provided by different
 laboratories. These command lines, hence, are the building blocks on
 which are built the assembly lines of the factory. BrainVISA is
 distributed with a toolbox of building blocks dedicated to the
 segmentation of T1-weighted MR images. The product of the main
 assembly line made up from this toolbox is the following: grey/white
 classification for Voxel Based Morphometry, Meshes of each hemisphere
 surface for visualization purpose, Spherical meshes of each
 hemisphere white matter surface, a graph of the cortical folds, a
 labeling of the cortical folds according to a nomenclature of the
 main sulci.

Depends: lipsia
Published-Title: Lipsia—a new software system for the evaluation of functional magnetic resonance images of the human brain
Published-Authors: Gabriele Lohmann, Karsten Müller, Volker Bosch, Heiko Mentzel, Sven Hessler, Lin Chen, S. Zysset, D. Yves von Cramon
Published-In: Computerized Medical Imaging and Graphics, 25: 449-457
Published-Year: 2001
Published-URL: http://www.medicalimagingandgraphics.com/article/S0895-6111(01)00008-8
Published-DOI: 10.1016/S0895-6111(01)00008-8

Depends: openmeeg
Homepage: http://www-sop.inria.fr/odyssee/software/OpenMEEG
License: CeCILL-B
WNPP: 517346
Responsible: Yaroslav Halchenko <debian@onerussian.com>
Pkg-Description: library and tools for solving EEG and MEG forward and inverse problems
 Provides state-of-the art tools for processing EEG and MEG data.
 .
 The forward problem is implemented using the symmetric Boundary
 Element method [Kybic et al, 2005], providing excellent accuracy,
 particularly for superficial cortical sources.  The source
 localization procedures implemented in OpenMEEG are based on a
 distributed source model, with three different types of
 regularization: the Minimum Norm, and the L2 and L1
 norms of the surface gradient of the sources [Adde et al, 2005].

Depends: visionegg
Homepage: http://www.visionegg.org
License: LGPL
WNPP: 365856
Pkg-Description: Python library for 2D/3D visual stimulus generation
 The Vision Egg is a programming library that uses standard, inexpensive
 computer graphics cards to produce visual stimuli for vision research
 experiments.
Published-Title: Vision Egg: An Open-Source Library for Realtime Visual Stimulus Generation
Published-Authors: Andrew Straw
Published-In: Frontiers in Neuroinformatics
Published-Year: 2008
Published-URL: http://frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/004.2008/
Published-DOI: 10.3389/neuro.11.004.2008


Depends: openelectrophy
Homepage: http://neuralensemble.org/trac/OpenElectrophy
License: Cecill v2 (GPL-compatible)
Language: Python
Responsible: Michael Hanke <michael.hanke@gmail.com>
WNPP: 556552
Published-In: Frontiers in Neuroinformatics, 3:14
Published-Year: 2009
Published-DOI: 10.3389/neuro.11.014.2009
Pkg-Description: data analysis framework for intra- and extra-cellular recordings
 This package provide a library und GUI for analyzing electrophysiological
 data. The data handling and storage uses a MySQL-server. The package is written
 in pure Python.

