Task: Cognitive Neuroscience
Install: false
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


Recommends: psignifit
Why: Psychometric function fitting.


Recommends: amide
Why: Flexible volume slicing and rendering.

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

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

Recommends: python3-nibabel, python3-pydicom
Why: Python IO libraries for the NIfTI format.

Recommends: fsl
Why: Comprehensive MRI analysis suite.

Recommends: fslview

Suggests: python-mvpa2
#Why: Framework for multivariate pattern analysis of neuroimaging datasets.
#     No Python3 version

Recommends: python3-nipy, python3-nipype, python3-nitime, python3-dipy
#Why: Python frameworks for analysis in neuroimaging

Recommends: nifti2dicom, qnifti2dicom
Why: Requested by Daniele E. Domenichelli <daniele.domenichelli@gmail.com>

Recommends: caret
Why: Cortical reconstruction and volume-to-surface mapping.

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

Recommends: 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

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

Recommends: voxbo

Recommends: bioimagesuite
Remark: How to work together with upstream
 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

Recommends: afni
WNPP: 409849
Pkg-URL: http://neuro.debian.net/pkgs/afni.html

Recommends: 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.


Recommends: 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.


Recommends: 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.

Recommends: lipsia

Recommends: openmeeg-tools

Recommends: mricron

Recommends: itksnap

Recommends: python3-statsmodels

Recommends: 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...


Recommends: 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


Recommends: mriconvert

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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.

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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-URL: http://neuro.debian.net
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

Recommends: python3-pyxnat

Suggests: debruijn
Pkg-URL: http://neuro.debian.net/pkgs/debruijn.html

Suggests: freesurfer
Pkg-URL: http://neuro.debian.net/pkgs/freesurfer.html
Remark: The 'tktools' (tkmedit, tksurfer and tkregister2)  under the
  CorTechs license are not readily redistributable thus excluded.

Suggests: xnat

Suggests: python3-bioxtasraw

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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.

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Suggests: connectomeviewer
Published-Authors: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P
Published-DOI: 10.3389/fninf.2011.00003
Published-In: Front. Neuroinform. 5:3
Published-Title: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes
Published-Year: 2011

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Suggests: hid
Homepage: http://www.nitrc.org/projects/hid
Language: java
License: BSD, BIRN
Pkg-Description: database management system for clinical imaging
 The Human Imaging Database (HID) is an extensible database management
 system developed to handle the increasingly large and diverse
 datasets collected as part of the MBIRN and FBIRN collaboratories and
 throughout clinical imaging communities at large.
Published-Authors: Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.;
 Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt,
 H.J.; Papadopoulos, P.
Published-In: IEEE Transactions on Information Technology in
 Biomedicine, 12 (2)
Published-Title: A National Human Neuroimaging Collaboratory Enabled
 By The Biomedical Informatics Research Network (BIRN)
Published-Year: 2008
Registration: http://www.nitrc.org/account/register.php