Debian Science Project
Summary
Cognitive Neuroscience
paquets pour les neurosciences cognitives de Debian Science

Ce métapaquet installe les paquets de Debian qui peuvent être utiles aux scientifiques intéressés dans la recherche en neurosciences cognitives. Cela comprend le processus de recherche complet, de la conduite d’expériences de psychophysique à la visualisation et composition typographique de résultats scientifiques.

La sélection de paquets vise les applications de technique d’analyse. Les développeurs de méthodes peuvent consulter les métapaquets science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging et med-imaging-dev pour divers logiciels supplémentaires qui pourraient être utiles dans la recherche en neurosciences cognitives.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Cognitive Neuroscience packages

Official Debian packages with high relevance

amide
programme pour l'imagerie médicale
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AMIDE (« AMIDE's a Medical Image Data Examiner ») est un outil pour la visualisation et l'analyse de jeux de données d'imagerie médicale. On peut noter parmi ses fonctionnalités la prise en charge simultanée de données importées de fichiers aux formats divers, la fusion d'images, la définition de régions d'intérêt tridimensionnelles, le rendu des volumes et l'alignement de structures solides.

Amide importe la plupart des fichiers cliniques DICOM (grâce à la bibliothèque DCMTK).

Please cite: Andreas Markus Loening and Sanjiv Sam Gambhir: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis. (PubMed) Molecular Imaging 2(3):131-7 (2003)
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caret
??? missing short description for package caret :-(
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Please cite: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon and Charles H. Anderson: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex. (PubMed,eprint) Journal of American Medical Informatics Association 8(5):443-459 (2001)
dicom3tools
outils de conversion et de manipulation de fichiers d'imagerie médicale DICOM
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Utilitaires en ligne de commande pour créer, modifier, vidanger et valider des fichiers d'attributs DICOM. Il gère la conversion de certains formats d'imagerie médicale propriétaires en DICOM. Il gère l'ancien format de données ACR/NEMA et certaines de ses versions propriétaires telle que SPI.

dicomnifti
Convertit les fichiers DICOM au format NIfTI
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Le programme dinifti convertit des images d'IRM du format DICOM au format NIfTI. Les fichiers au format NIfTI peuvent être lus par les programmes FSL, AFNI et SPM, Caret ou Freesurfer.

Dinifti convertit les fichiers un par un, ou à la chaîne au sein d'un répertoire, et peut donner des noms cohérents aux fichiers NIfTI en utilisant les informations présentes dans les fichiers DICOM.

fslview
??? missing short description for package fslview :-(
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Please cite: 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 and P.M. Matthews: Advances in functional and structural MR image analysis and implementation as FSL. (PubMed) NeuroImage 23:208-219 (2004)
itksnap
segmentation semi-automatique de structures pour les images en 3D
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SNAP fournit une segmentation semi-automatique de structures pour les images médicales (par exemple, des images de résonance magnétique du cerveau) en utilisant des méthodes de contour actif, ainsi que la délimitation manuelle et la navigation dans les images. Les caractéristiques notables sont :

  – curseur avec liens pour une navigation en 3D fluide ;
  – segmentation manuelle dans les trois plans orthogonaux en même temps ;
  – gestion de beaucoup de formats d’image 3D, y compris NIfTI ;
  – gestion concomitante, visualisations liées et segmentation de plusieurs
    images ;
  – gestion limitée des images en couleur (par exemple, cartes de tenseurs
    de diffusion) ;
  – outils de plan sécant en 3D pour un post-traitement rapide des
    résultats de segmentation.
Please cite: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee and Guido Gerig: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 31:1116-1128 (2006)
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medcon
Outil de conversion d'images médicales (DICOM, ECAT, etc.)
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Ce projet a pour but la conversion d’image médicale (Medical Image Conversion). Publié sous licence (L)GPL, il est livré avec le code source C complet de la bibliothèque, un outil flexible en ligne de commande et une interface graphique soignée utilisant la boîte à outils GTK+. Les formats pris en charge actuellement sont : Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 et PNG.

Le programme permet aussi de lire des fichiers non pris en charge et non compressés, pour afficher les valeurs de pixel ou pour extraire ou réorganiser les images indiquées. Il est possible de récupérer les tableaux d’image binaire ou ASCII RAW ou d’écrire des PNG pour des applications de bureau.

Ceci est l'outil en ligne de commande pour le traitement par lot.

minc-tools
Outils pour le format MNI d'imagerie médicale
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Ce paquet contient des outils permettant de manipuler des fichiers MINC.

Le format de fichiers MINC est un format de fichier très souple basé sur le format généralisé de données NetCDF. Il est simple, auto-décrit, extensible, portable et à N dimensions avec des interfaces de programmation que ce soit pour l'accès aux données de bas niveau ou à des manipulations de haut niveau en masse. Les bibliothèques ont permis l'écriture d'un ensemble d'outils de manipulation de fichiers génériques d'images. Le format, les bibliothèques et les outils sont prévus pour être utilisés dans un environnement de recherche en imagerie médicale : ils sont simples et efficaces sans chercher à fournir une belle interface aux utilisateurs.

mriconvert
utilitaire de conversion de fichier d’image médicale
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MRIConvert est un utilitaire de conversion de fichier d’image médicale pour des fichiers DICOM vers les formats NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager et MetaImage.

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mricron
conversion, visualisation et analyse d’images de résonance magnétique
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Il s’agit d’un outil de visualisation et d’analyse basé sur une interface graphique pour les images de résonance magnétique (fonctionnelle). MRIcron peut être utilisé pour créer des rendus en 2D ou 3D des cartes de superposition statistiques d’images d’anatomie de cerveau. De plus, il aide à dessiner des régions anatomiques d’intérêt (ROI), ou des cartes de lésion, ainsi qu’une analyse basique de séries temporelles (par exemple, création de tracés de péristimulus signal-modification).

En plus de « mricron », ce paquet fournit aussi « dcm2nii » qui prend en charge la conversion d’images DICOM et PAR/REC au format NIfTI, et « npm » pour l’analyse de données non paramétriques.

Please cite: Chris Rorden, Hans-Otto Karnath and Leonardo Bonilha: Improving lesion-symptom mapping. (PubMed) Journal of Cognitive Neuroscience 19(7):1081-1088 (2007)
nifti-bin
outils livrés avec la bibliothèque NIfTI
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Niftilib est un ensemble de bibliothèques d'entrées-sorties pour lire et écrire des fichiers au format NIfTI-1. NIfTI-1 est un format de fichier binaire pour stocker des images médicales, par exemple des images par résonance magnétique (IRM) et des images de cerveau par résonance magnétique fonctionnelle (IRMf).

Ce paquet fournit les outils livrés avec la bibliothèque (nifti_tool, nifti_stats et nifti1_test).

nifti2dicom
convert 3D medical images to DICOM 2D series
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Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS.

This package includes the command line tools.

praat
programme pour l'analyse et la synthèse de la parole
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Selon ses auteurs, Praat permet de « faire de la phonétique par ordinateur ». Au travers de son interface graphique, plusieurs fonctionnalités d'analyse de la parole sont disponibles : spectrogrammes, cochleogrammes, et l'extraction de l'accent de hauteur (accent musical) et des formants. La synthèse articulatoire, ainsi que la synthèse à partir de l'accent de hauteur, des formants, et de l'intensité sont également disponibles. Les autres caractéristiques sont la segmentation, l'étiquetage en utilisant l'alphabet phonétique, et le calcul des statistiques. Praat est configurable et extensible grâce à son propres langage de programmation et contient des interfaces pour communiquer avec d'autres programmes.

Please cite: Paul Boersma: Praat, a system for doing phonetics by computer. Glot International 5(9/10):341-345 (2001)
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psignifit
ajuster et essayer des hypothèses sur les fonctions psychométriques
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Psignifit permet d'ajuster des fonctions psychométriques à des jeux de données tout en gardant le contrôle d'un grand nombre de paramètres. Les données peuvent être lues depuis des fichiers texte ou à l’aide de l'entrée standard.

Le programme effectue le calcul des intervalles de confiance ainsi que de des tests de qualité de l'ajustement.

Ce paquet fournit la version en ligne de commande.

Remarque : il s’agit de l’ancienne version 2.x de psignifit.

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python3-nibabel
liaisons de Python 3 vers divers formats de données d’image cérébrale
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NiBabel permet de lire et écrire quelques formats médicaux communs et de neuro-imagerie, dont ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, ainsi que PAR/REC. Les diverses classes de format d’image procurent un accès total et sélectif aux (méta)informations d’en-tête et l’accès aux données d’image est rendu disponible à travers des tableaux de NumPy. NiBabel est le successeur de PyNIfTI.

python3-pydicom
DICOM medical file reading and writing (Python 3)
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pydicom is a pure Python module for parsing DICOM files. DICOM is a standard (http://medical.nema.org) for communicating medical images and related information such as reports and radiotherapy objects.

pydicom makes it easy to read DICOM files into natural pythonic structures for easy manipulation. Modified datasets can be written again to DICOM format files.

This package installs the module for Python 3.

python3-pyxnat
Interface to access neuroimaging data on XNAT servers
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pyxnat is a simple Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or Python scripts to process the data. It features:

  • resources browsing capabilities
  • read and write access to resources
  • complex searches
  • disk-caching of requested files and resources
python3-statsmodels
Python3 module for the estimation of statistical models
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statsmodels Python3 module 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 several distribution families and M-estimators for robust linear models. An extensive list of result statistics are available for each estimation problem.

Please cite: Skipper Seabold and Josef Perktold: Statsmodels: Econometric and statistical modeling with python (eprint) (2010)
qnifti2dicom
convert 3D medical images to DICOM 2D series (gui)
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Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS.

This package contains the Qt5 GUI.

voxbo
traitement, analyse statistique et affichage de données d’imagerie cérébrale
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Il s’agit d’une boîte à outils pour l’analyse des expériences d’imagerie par résonance magnétique fonctionnelle (principalement fMRI) et la cartographie basée sur les voxels de comportement de lésion. VoxBo prend en charge le GLM modifié (pour les données autocorrélées), ainsi que le GLM standard pour les données non autocorrélées. La boîte à outils est conçue pour être interopérable avec entre autres, AFNI, FSL et SPM.

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xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)
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This project stands for Medical Image Conversion. Released under the (L)GPL, it comes with the full C-source code of the library, a flexible command line utility and a neat graphical front-end using the GTK+ toolkit. The currently supported formats are: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.

The program also allows one to read unsupported files without compression, to print pixel values or to extract/reorder specified images. It is possible to retrieve the raw binary/ascii image arrays or to write PNG for desktop applications.

This is the program version for X based on GTK+. Processes only one file at a time.

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Official Debian packages with lower relevance

connectomeviewer
analyse interactive et visualisation pour la connectomique MR
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Connectome Viewer est un environnement extensible, scriptable et en python de visualisation et d'analyse (de réseau) en neuro-imagerie et connectomique.

Grâce au format de fichier Connectome, divers types de données tels que les réseaux, surfaces, volumes, traces et métadonnées sont gérés et intégrés. Connectome Viewer fait partie de la boîte à outils MR Connectome.

Please cite: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes. (2011)
python-mvpa2
??? missing short description for package python-mvpa2 :-(
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The package is enhanced by the following packages: python-mdp python-sklearn
python3-bioxtasraw
traitement de données biologiques de diffusion des rayons X aux petits angles
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BioXTAS RAW un programme graphique en Python pour la réduction et l’analyse de diffusion des rayons X aux petits angles (SAXS – Small Angle X-rays Scattering). Ce paquet est conçu pour des données biologiques SAXS.

BioXTAS RAW fournit un remplacement aux programmes source proches comme Primus et Scatter pour l’analyse basique de données. Parce qu’il calibre, masque et intègre des images, il fournit aussi une alternative aux pipelines de faisceau de synchrotron que les scientifiques installent sur leur propre ordinateur et utilisent à la maison et sur la ligne de faisceau.

science-psychophysics
paquets pour la psychophysique de Debian Science
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Ce métapaquet installe les paquets de Debian qui peuvent être utiles pour accomplir des expériences relatives aux stimuli physiques et leurs effets psychologiques.

Cette sélection de paquets concerne les logiciels d’exécution de stimulus. Pour d’autres logiciels concernant l’analyse des données obtenues, l’utilisateur recourra à science-neuroscience-cognitive, med-imaging en fonction du domaine concerné. De plus, il regardera dans les paquets de science-bci car ceux-ci fournissent souvent des structures de boucle incluant la fourniture de stimulus.

science-typesetting
paquets pour la composition typographique de Debian Science
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Ce métapaquet installe les paquets de Debian Science concernant la composition typographique. L’utilisateur peut aussi être intéressé par field::physics de debtag.

Debian packages in contrib or non-free

fsl
transitional dummy package
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The only purpose of this package is to enable upgrades to the new 'fsl-core' package which replaces 'fsl'. This package can safely be removed.

Users aiming to perform a complete FSL installation (including all data components) are advised to install the 'fsl-complete' package from NeuroDebian.

Please cite: Mark Jenkinson, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich and Stephen M. Smith: FSL. (PubMed) NeuroImage 62(2):782-790 (2012)

Packaging has started and developers might try the packaging code in VCS

bioimagesuite
integrated image analysis software suite
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Version: 2.0-1

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.

Please cite: X. Papademetris, M. Jackowski, N. Rajeevan, R. T. Constable and L. Staib: BioImage Suite: An integrated medical image analysis suite. (eprint) Insight Journal (2005)
Remark of Debian Science team: 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

debruijn
De Bruijn cycle generator
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Version: 1.6-2

Stimulus counter-balance is important for many experimental designs. This command-line software creates De Bruijn cycles, which are pseudo-random sequences with arbitrary levels of counterbalance. "Path-guided" de Bruijn cycles may also be created. These sequences encode a hypothesized neural modulation at specified temporal frequencies, and have enhanced detection power for BOLD fMRI experiments.

freesurfer
analysis and visualization of functional brain imaging data
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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.

This package depends upon the latest version of freesurfer.

Please cite: A. M. Dale, B. Fischl and M. I. Sereno: Cortical surface-based analysis. I. Segmentation and surface reconstruction. (PubMed) Neuroimage 9(2):179-94 (1999)
Remark of Debian Science team: The 'tktools' (tkmedit, tksurfer and tkregister2) under the
 CorTechs license are not readily redistributable thus excluded.
openmeeg-tools
openmeeg library -- command line tools
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Version: 2.4.2-1

OpenMEEG consists of state-of-the art solvers for forward problems in the field of MEG and EEG. Solvers are based on the symmetric Boundary Element method [Kybic et al, 2005], providing excellent accuracy, particularly for superficial cortical sources. OpenMEEG can compute four types of lead fields (EEG, MEG, Internal Potential and Electrical Impedence Tomography).

This package provides command line interface to openmeeg functionality.

Please cite: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi and Maureen Clerc: OpenMEEG: opensource software for quasistatic bioelectromagnetics. (PubMed,eprint) BioMedical Engineering OnLine 9:45 (2010)
slicer
software package for visualization and image analysis - main application
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Version: 4.10.2-1

Slicer is an application for computer scientists and clinical researchers. The platform provides functionality for segmentation, registration and three-dimensional visualization of multi-modal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software and image informatics frameworks.

3D Slicer main application.

Please cite: Steven Pieper, Michael Halle, Ron Kikinis: 3D SLICER. (2004)
xnat
platform for data management and productivity tasks in neuroimaging
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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.

Please cite: Daniel S. Marcus, Timothy R. Olsen, Mohana Ramaratnam and Randy L. Buckner: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data.. (PubMed,eprint) Neuroinformatics 5(1):11-34 (2007)

Unofficial packages built by somebody else

eeglab
toolbox for processing and visualization of electrophysiological data
Responsible: NeuroDebian Team
License: GPL-2+
Language: C, Matlab/Octave

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.

Please register by following this link if you are using eeglab.
Please cite: Delorme A and Makeig S: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics (2004)
mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
Responsible: Michael Hanke
License: no-free, but GPLed parts

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.

mni-n3
MNI Non-parametric Non-uniformity Normalization
Responsible: Michael Hanke
License: BSDish

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.

No known packages available but some record of interest (WNPP bug)

fieldtrip - wnpp
toolbox for MEG and EEG analysis
License: GPL-2+
Debian package not available
Language: Matlab/Octave

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 of Debian Science team: 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.

pysurfer - wnpp
visualize Freesurfer's data in Python
Responsible: NeuroDebian Team
License: BSD-3
Debian package not available
Language: 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.

spm8 - wnpp
analysis of brain imaging data sequences
Responsible: NeuroDebian team
License: GPL-2+
Debian package not available

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.

Please register by following this link if you are using spm8.
Please cite: Karl J. Friston, John T. Ashburner, Stephen Kiebel, Thomas E. Nichols and William D. Penny: Statistical Parametric Mapping: The Analysis of Functional Brain Images.. (2007)
Remark of Debian Science team: 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...

No known packages available

brainvisa
image processing factory for MR images
License: Free? (CeCill License)
Debian package not available

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.

hid
database management system for clinical imaging
License: BSD, BIRN
Debian package not available
Language: java

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.

Please register by following this link if you are using hid.
Please cite: 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.: A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN) (2008)
iqr
large-scale multi-level neuronal systems simulator
Responsible: NeuroDebian team
License: GPL-3+
Debian package not available

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.

Please cite: Ulysses Bernardet, Paul F.M.J. Verschure: iqr: A tool for the construction of multi-level simulations of brain and behaviour.. (2010)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 246355