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.


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: fslview, fsl
Why: Comprehensive MRI analysis suite.


Depends: python-mvpa
Why: Framework for multivariate pattern analysis of neuroimaging datasets.


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


Depends: python-pyepl
Why: Library to write and run psychological experiments.


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


Depends: dicom3tools
Why: Supports conversion from proprietary formats, such as GE into DICOM.
Homepage: http://www.dclunie.com/dicom3tools/workinprogress/
License: BSD
WNPP: 508901
Responsible: Mathieu Malaterre <mathieu.malaterre@gmail.com>
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dicom3tools/trunk
Pkg-Description: DICOM medical image files manipulation and conversion tools
 Command line utilities for creating, modifying, dumping and validating
 files of DICOM attributes. Support conversion of some proprietary medical
 image formats to DICOM. Can handle older ACR/NEMA format data, and some
 proprietary versions of that such as SPI.


Depends: python-psychopy
Homepage: http://www.psychopy.org
License: BSD
Pkg-Description: generate psychophysical stimuli
 Pygame/pyglet-based Python library to conduct psychophysical experiments.
 PsychoPy is primarily focusing on the visual domain, but additionally
 supports handling pre-generated stimuli, such as movies.


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: slicer
Homepage: http://www.slicer.org/
License: BSD like
WNPP: 500841
Responsible: Dominique Belhachemi <domibel@cs.tu-berlin.de>
Pkg-Description: visualization, registration, segmentation, and quantification of medical data
 The 3D Slicer is freely available, open-source software for visualization,
 registration, segmentation, and quantification of medical data. The slicer
 source seems to be available via CVS only.
 .
 The license statement can be seen at
 http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl


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.


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
Homepage: http://www.cbs.mpg.de/institute/software/lipsia
License: GPL
Responsible: Felix Botner <botner@cbs.mpg.de>
Pkg-URL: ftp://lipsia.cbs.mpg.de/lipsia
Pkg-Description: Analysis of MRI and fMRI data - binary
 Leipzig Image Processing and Statistical Inference Algorithms
 (LIPSIA)
 .
 The software package LIPSIA was developed by the Max Planck Institute
 of Cognitive Neuroscience, Leipzig, for the data processing and
 evaluation of functional magnetic resonance images. The analysis of
 fMRI data comprises various aspects including filtering, spatial
 transformation, statistical evaluation as well as segmentation and
 visualization. All these aspects are covered by LIPSIA. For the
 statistical evaluation, a number of well established and
 peer-reviewed algorithms were implemented in LIPSIA that allow an
 effcient and user-friendly processing of fMRI data sets. As the
 amount of data that must be handled is enormous, an important aspect
 in the development LIPSIA was the efficiency of the software
 implementation. In LIPSIA, particular emphasis was placed on the
 development of new visualization and segmentation techniques that
 support visualizations of individual brain anatomy so that experts
 can assess the exact location of activation patterns in individual
 brains. LIPSIA is non- commercial. LIPSIA is freely available upon
 request. However, as we don't have suffcient manpower, we can't
 support an unlimited number of LIPSIA users.  Therefore, we plan to
 offer LIPSIA initially on lytoa limited number of cooperation
 partners. Please contact us, if you are interested in becoming a
 LIPSIA cooperation partner.


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].
