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 referred 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

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


Depends: psignifit
Why: Psychometric function fitting.


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.
Registration: http://www.fmrib.ox.ac.uk/fsldownloads/
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
Registration: http://www.fmrib.ox.ac.uk/fsldownloads/
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
Published-Title: 3D SLICER
Published-Authors: Steven Pieper, Michael Halle, Ron Kikinis
Published-In: Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 1:632-635
Published-Year: 2004
Published-URL: http://www.slicer.org/publications/item/view/91


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

Depends: voxbo
Registration: http://voxbo.org/usage.html


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 integrated 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://neuro.debian.net/pkgs/afni.html
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

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Depends: openmeeg-tools
Published-Authors: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi, Maureen Clerc
Published-In: BioMedical Engineering OnLine 45:9
Published-Title: OpenMEEG: opensource software for quasistatic bioelectromagnetics
Published-URL: http://www.biomedical-engineering-online.com/content/9/1/45
Published-Year: 2010


Depends: mricron
Published-Title: Improving lesion-symptom mapping
Published-Authors: Chris Rorden, Hans-Otto Karnath, Leonardo Bonilha
Published-In: Journal of Cognitive Neuroscience, 19: 1081-1088
Published-Year: 2007
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/17583985


Depends: itksnap
Published-Title: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability
Published-Authors: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig
Published-In: Neuroimage, 31: 1116-1128
Published-Year: 2006
Published-DOI: 10.1016/j.neuroimage.2006.01.015


Depends: python-pypsignifit
Homepage: http://psignifit.sourceforge.net/
License: MIT
Language: C++, Python
Responsible: Michael Hanke <michael.hanke@gmail.com>
WNPP: 580499
Pkg-Description: fitting and testing hypotheses about psychometric functions
 This package allows fitting of psychometric functions to datasets while
 maintaining full control over a large number of parameters. Psignifit performs
 the calculation of confidence intervals as well as goodness-of-fit tests.
 .
 This is the successor of 'psignifit' a commandline-based toolbox. The new
 version is primarily a python module, but other bindings will be added
 eventually.


Depends: python-scikits.statsmodels
Homepage: http://statsmodels.sourceforge.net/
Language: Python
License: BSD
Responsible: Yaroslav Halchenko <debian@onerussian.com>
Pkg-URL: http://neuro.debian.net/pkgs/python-scikits.statsmodels.html
WNPP: 570604
Why: Provides methodology used by 99.99% of cognitive neuroscientists
Pkg-Description: classes and functions for the estimation of statistical models
 scikits.statsmodels is a pure Python package that provides classes
 and functions for the estimation of several categories of statistical
 models. These currently include linear regression models, OLS, GLS,
 WLS and GLS with AR(p) errors, generalized linear models for six
 distribution families and M-estimators for robust linear models. An
 extensive list of result statistics are available for each estimation
 problem.


Depends: spm8
Registration: http://www.fil.ion.ucl.ac.uk/spm/software/download.html
Homepage: http://www.fil.ion.ucl.ac.uk/spm/software/spm8/
License: GPL-2+
Responsible: NeuroDebian team <team@neuro.debian.net>
WNPP: 592390
Pkg-Description: analysis of brain imaging data sequences
 Statistical Parametric Mapping (SPM) refers to the construction and assessment
 of spatially extended statistical processes used to test hypotheses about
 functional imaging data. These ideas have been instantiated in software that is
 called SPM. It is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.
Published-Authors: Karl J. Friston, John T. Ashburner, Stephen Kiebel, Thomas E. Nichols and William D. Penny
Published-Title: Statistical Parametric Mapping: The Analysis of Functional Brain Images.
Published-In: Elsevier/Academic Press: Amsterdam
Published-Year: 2007
Published-URL: http://www.elsevierdirect.com/product.jsp?isbn=9780123725608
Remark: This software is written for matlab, but initial tests indicate that
 some (significant) portion of it might also work with octave. More tests are
 pending...


Depends: iqr
Homepage: http://iqr.sourceforge.net
License: GPL-3+
Responsible: NeuroDebian team <team@neuro.debian.net>
Pkg-Description: large-scale multi-level neuronal systems simulator
 This graphical environment allows for designing large-scale multi-level
 neuronal systems that can control real-world devices, such as cameras and
 mobile robots, in real-time. iqr is an extensible framework with the ability
 to handle new, user-provided, neuron and synapse types, as well as custom
 interfaces to other hardware systems. iqr employes an XML-based format for
 system descriptions.
Published-Authors: Ulysses Bernardet, Paul F.M.J. Verschure
Published-Title: iqr: A tool for the construction of multi-level simulations of brain and behaviour.
Published-In: Neuroinformatics, 8: 113-134
Published-Year: 2010
Published-DOI: 10.1007/s12021-010-9069-7


Depends: mriconvert

 ; Added by blends-inject 0.0.5. [Please note here if modified manually]
Suggests: fieldtrip
Homepage: http://fieldtrip.fcdonders.nl
Language: Matlab/Octave
WNPP: 605492
License: GPL-2+
Pkg-Description: toolbox for MEG and EEG analysis
 The software includes algorithms for simple and advanced analysis of MEG and
 EEG data, such as time-frequency analysis, source reconstruction using dipoles,
 distributed sources and beamformers and non-parametric statistical testing. It
 supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of
 the most popular EEG systems, and new formats can be added easily. FieldTrip
 contains high-level functions that you can use to construct your own analysis
 protocols in Matlab. Furthermore, it easily allows developers to incorporate
 low-level algorithms for new EEG/MEG analysis methods.
Remark: The NIMH distributes a "port" of fieldtrip to Octave (at
 http://kurage.nimh.nih.gov/meglab/Meg/Software). It needs to be figured out
 whether this port can be incorporated into the official version, and to what
 degree it is complete. Packaging fieldtrip is required to complete the
 packaging of SPM8.

 ; Added by blends-inject 0.0.5. [Please note here if modified manually]
Suggests: eeglab
Homepage: http://sccn.ucsd.edu/eeglab
Language: C, Matlab/Octave
WNPP: 605739
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: GPL-2+
Pkg-Description: toolbox for processing and visualization of electrophysiological data
 EEGLAB is an interactive Matlab toolbox for processing continuous and
 event-related EEG, MEG and other electrophysiological data
 incorporating independent component analysis (ICA), time/frequency
 analysis, artifact rejection, event-related statistics, and several
 useful modes of visualization of the averaged and single-trial data.
Published-Authors: Delorme A and Makeig S
Published-In: Journal of Neuroscience Methods 134:9-21
Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics
Published-Year: 2004
Registration: http://sccn.ucsd.edu/eeglab/install.html

 ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Depends: pyxnat

 ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: debruijn
Homepage: http://www.cfn.upenn.edu/aguirre/wiki/public:de_bruijn_software
Language: C++
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: BSD (4-clause)
Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/debruijn.git
Vcs-Git: git://git.debian.org/git/pkg-exppsy/debruijn.git
Pkg-URL: http://neuro.debian.net/pkgs/debruijn.html
Pkg-Description: De Bruijn cycle generator
 Continuous carry-over, fMRI experiments present stimuli in a counter-balanced
 sequence, meaning every stimulus precedes and follows every other. Higher
 level counterbalancing is useful to guard against some modeling assumptions
 of the approach and to test for the effects of stimulus history and context.
 Sequences that efficiently provide this control of stimulus order are called
 de Bruijn cycles.
 .
 This package provides a commandline tool to generate de Bruijn cycles.
Published-Authors: GK Aguirre, MG Mattar, L Magis-Weinberg
Published-DOI: 10.1016/j.neuroimage.2011.02.005
Published-In: NeuroImage 56: 1293-1300
Published-Title: de Bruijn cycles for neural decoding
Published-Year: 2011

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Suggests: freesurfer
Homepage: http://surfer.nmr.mgh.harvard.edu/
Language: C/C++/Python/Perl/...
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: BSD-style FreeSurfer Software License Agreement v1.0
Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/freesurfer.git
Vcs-Git: git://git.debian.org/git/pkg-exppsy/freesurfer.git
Pkg-URL: http://neuro.debian.net/pkgs/freesurfer.html
Pkg-Description: analysis and visualization of functional brain imaging data
 FreeSurfer is a set of tools for analysis and visualization of
 structural and functional brain imaging data. It contains a fully
 automatic structural stream for processing cross sectional and
 longitudinal data.
 .
 FreeSurfer provides many anatomical analysis tools, including:
 representation of the cortical surface between white and gray matter,
 representation of the pial surface, segmentation of white matter from
 the rest of the brain, skull stripping, B1 bias field correction,
 nonlinear registration of the cortical surface of an individual with
 an sterotaxic atlas, labeling of regions of the cortical surface,
 statistical analysis of group morphometry differences, and labeling of
 subcortical brain structures, etc.
Published-In: see http://surfer.nmr.mgh.harvard.edu/fswiki/Articles
Registration: http://surfer.nmr.mgh.harvard.edu/fswiki/Registration
Remark: The 'tktools' (tkmedit, tksurfer and tkregister2)  under the
  CorTechs license are not readily redistributable thus excluded.

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Suggests: xnat
Homepage: http://www.xnat.org
Language: java
WNPP: 629143
License: XNAT SLA
Pkg-Description: platform for data management and productivity tasks in neuroimaging
 The primary functionality of XNAT is to provide a place to store and
 control access to neuroimaging data. This includes sophisticated user
 control, search and retrieval, and archiving capabilities. As
 open-source software, XNAT also supports a wide variety of
 research-based processing pipelines, and is able to link up with
 supercomputer processing power to dramatically shorten image
 processing time.
Published-Authors: Marcus, D.S., Olsen T., Ramaratnam M., and Buckner, R.L.
Published-In: Neuroinformatics 5(1): 11-34
Published-Title: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data.
Published-Year: 2007
Registration: http://www.xnat.org/download-xnat.html

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Suggests: pysurfer
Homepage: http://pysurfer.github.com/
Language: Python
WNPP: 641345
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: BSD-3
Pkg-Description: visualize Freesurfer's data in Python
 This is a Python package for visualization and interaction with cortical
 surface representations of neuroimaging data from Freesurfer. It
 extends Mayavi’s powerful visualization engine with a high-level interface for
 working with MRI and MEG data.
 .
 PySurfer offers both a command-line interface designed to broadly replicate
 Freesurfer’s Tksurfer program as well as a Python library for writing scripts
 to efficiently explore complex datasets.
