Debian Science Project
Summary
Cognitive neuroscience
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.

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
software for Medical Imaging
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AMIDE: (Amide's a Medical Imaging Data Examiner) AMIDE is a tool for viewing and analyzing medical image data sets. It's capabilities include the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments.

Amide imports most clinical DICOM files (using the DCMTK library).

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)
Caret
CARET, ein rechnergestützter Werkzeugsatz für anatomische Rekonstruktion und Bearbeitung
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Diese Software ermöglicht die Erstellung, Anzeige und Bearbeitung von Oberflächenrekonstruktionen der Hirn- und Kleinhirnrinde, die Betrachtung von Volumina und die Darstellung von experimentellen Daten auf den Flächen und Volumina. Während Caret in erster Linie eine grafische Anwendung ist, liefert es auch das vielseitige Kommandozeilenwerkzeug »caret_command« mit, das einen erheblichen Teil von Carets Funktionalität unterstützt.

Caret kann stereotaktische Atlanten (Mensch, Affe, Maus und Ratte) aus einer offenen Onlinedatenbank laden und verwenden.

Einige Funktionen von Caret sind nur mit zusätzlichen Datendateien aus dem Paket caret-data verfügbar. Dazu gehören:

  • die Abbildung von Volumina auf Oberflächen mittels des PALS-Atlas
  • »Morphing« mit mehreren Auflösungen
  • Projektion von Brennpunkten mittels des PALS-Atlas
  • oberflächenbasierte Registrierung
  • Abflachen von Oberflächen

Derzeit ist das Paket caret-data nur im NeuroDebian-Depot verfügbar. Unter http://neuro.debian.net finden Sie weitere Informationen.

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
DICOM-Werkzeuge für Manipulation und Umwandlung medizinischer Bilddateien
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Befehlszeilenprogramme zum Erstellen, Modifizieren, Ausgeben und Validieren von Dateien von DICOM-Attributen. Unterstützt die Umwandlung einiger proprietärer medizinischer Bildformate zu DICOM. Kann Daten in den älteren Formaten ACR/NEMA und einige proprietäre Versionen dieser Formate wie beispielsweise SPI handhaben.

Dicomnifti
wandelt Dateien im DICOM-Format in das NIfTI-Format um
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dinifti wandelt im DICOM-Format gespeicherte MRI-Bilder in das NIfTI-Format um. Das NIfTI-Format ist angedacht, als das neue Standardformat für die medizinische Bildgebung. Es kann z.B. für FSL, AFNI, SPM, Caret und Freesurfer benutzt werden.

dinifti wandelt einzelne Dateien um. Es wird aber auch ein Batchmodus für die Umwandlung ganzer DICOM-Verzeichnisse unterstützt. Umgewandelte NIfTI-Dateien können entsprechend den Bildserien-Informationen aus den DICOM-Dateien benannt werden.

Fslview
Betrachter für (f)MRI und DTI-Daten
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Dieses Paket stellt einen Betrachter für 3d- und 4d-MRI-Daten und DTI-Bilder bereit. FSLView ist zudem in der Lage ANALYZE- und NIFTI-Dateien darzustellen. Der Betrachter unterstützt mehrere 2d-Betrachtungsmodi (orthogonal, lightbox oder einzelne Slices) ebenso wie das Rendern von 3d-Rauminhalten. Zusätzlich kann FSLView Zeitreihen darstellen und metrische und stereotaxische Atlas-Daten übereinander legen.

FSLView ist ein Teil von FSL.

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
Halbautomatische Segmentierung von Strukturen in 3D-Aufnahmen
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SNAP ermöglicht die halbautomatische Segmentierung von Strukturen in medizinischen Aufnahmen (z.B. von Magnetresonanztomographien des Gehirns) durch Aktiv-Kontur-Methoden, genauso wie eine manuelle Abgrenzung und die Navigation in der Aufnahme. Nennenswerte Fähigkeiten sind:

  • verlinkte Zeiger für eine nahtlose 3D-Navigation
  • gleichzeitige manuelle Aufteilung in drei orthogonalen Ebenen
  • Unterstützung für viele verschiedene 3D-Bildformate, einschließlich

    NIfTI * Unterstützung für eine gleichzeitige, verlinkte Ansicht und Aufteilung

    von mehreren Aufnahmen * eingeschränkte Unterstützung für farbige Aufnahmen ( z.B. diffusion

    tensor maps) * 3D-Ebenen-Schneidewerkzeug für schnelle Nachbearbeitung von

    Segmentierungsergebnissen

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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Lipsia
analysis suite for MRI and fMRI data
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Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)

This is a software package 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 efficient 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 of LIPSIA was the efficiency of the software implementation.

LIPSIA operates exclusively on data in the VISTA data format. However, the package contains converters for medical image data in iBruker, ANALYZE and NIfTI format -- converting VISTA images into NIfTI files is also supported.

Please cite: Gabriele Lohmann, Karsten Müller, Volker Bosch, Heiko Mentzel, Sven Hessler, Lin Chen, S. Zysset and D. Yves von Cramon: Lipsia—a new software system for the evaluation of functional magnetic resonance images of the human brain. Computerized Medical Imaging and Graphics 25:449-457 (2001)
Medcon
Werkzeug zur Konvertierung medizinischer Bilder (DICOM, ECAT, ...)
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Der Name dieses Projektes leitet sich von »Medical Image Conversion« (Umwandlung von Bildern in der Medizin) ab. Die Software wurde unter der (L)GPL veröffentlicht, stellt den kompletten C-Quellcode der Bibliothek zur Verfügung sowie ein flexibles Kommandozeilenwerkzeug und eine ansprechende grafische Benutzeroberfläche auf Grundlage von GTK+. Aktuell werden die folgenden Formate unterstützt: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 und PNG.

Das Programm ermöglicht außerdem, nicht unterstützte Dateien ohne Kompression zu lesen, die Pixelwerte auszugeben oder angegebene Bilder zu extrahieren/neu zu ordnen. Es ist möglich, rohe Binär-/ASCII-Bildfelder auszulesen oder PNG für Desktopanwendungen zu schreiben.

Dieses ist das Befehlszeilenwerkzeug für die Stapelverarbeitung.

Minc-tools
MNI - Werkzeuge für das medizinische Bildformat
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Dieses Paket enthält Programme zur Manipulation von MINC-Dateien.

Das Minc-Dateiformat ist ein sehr flexibles medizinisches Bild-Dateiformat, das auf dem generalisierten NetCDF-Datenformat aufbaut. Das Format ist einfach, selbstbeschreibend, erweiterbar, portabel und N-dimensional, mit Programmierschnittstellen sowohl für Datenzugriff auf niederer Ebene als auch zur Volume-Manipulation auf hoher Ebene. Auf diesen Bibliotheken aufbauend gibt es eine Sammlung von allgemeinen Bilddatei-Verarbeitungsprogrammen. Das Format, die Bibliotheken und Programme sind zur Verwendung in einer Forschungsumgebung für medizinische Bildverarbeitung gedacht; sie sind einfach und mächtig und versuchen nicht, gegenüber dem Benutzer eine nette Oberfläche zu bieten.

Mriconvert
medical image file conversion utility
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MRIConvert is a medical image file conversion utility that converts DICOM files to NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager, and MetaImage volume formats.

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Mricron
magnetic resonance image conversion, viewing and analysis
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This is a GUI-based visualization and analysis tool for (functional) magnetic resonance imaging. MRIcron can be used to create 2D or 3D renderings of statistical overlay maps on brain anatomy images. Moreover, it aids drawing anatomical regions-of-interest (ROI), or lesion mapping, as well as basic analysis of functional timeseries (e.g. creating plots of peristimulus signal-change).

In addition to 'mricron', this package also provides 'dcm2nii' that supports converting DICOM and PAR/REC images into the NIfTI format, and 'npm' for non-parametric data analysis.

Please cite: Chris Rorden, Hans-Otto Karnath, Leonardo Bonilha: Improving lesion-symptom mapping. (2007)
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Nifti-bin
Mit der NIfTI-Bibliothek gelieferte Hilfsprogramme
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Niftilib ist eine Sammlung von Ein- und Ausgabebibliotheken zum Lesen und Schreiben von Dateien im NIfTI-1-Datenformat. NIfTI-1 ist ein binäres Dateiformat zum Speichern von medizinischen Bilddaten wie Magnetresonanzbildern (MRI) und funktionalen Magnetresonanztomographiebildern (fMRI) des Gehirns.

Dieses Paket enthält die Hilfsprogramme, die mit der Bibliothek mitgeliefert werden (nifti_tool, nifti_stats und nifti1_test).

Nifti2dicom
convert 3D medical images to DICOM 2D series
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Nifti2Dicom is a convertion 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.

Openmeeg-tools
openmeeg library -- command line tools
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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)
Openwalnut-qt4
Multi-modal medical and brain data visualization tool.
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OpenWalnut is a tool for multi-modal medical and brain data visualization. Its universality allows it to be easily extended and used in a large variety of application cases. It is both, a tool for the scientific user and a powerful framework for the visualization researcher. Besides others, it is able to load NIfTI data, VTK line data and RIFF-format CNT/AVR-files. OpenWalnut provides many standard visualization tools like line integral convolution (LIC), isosurface-extraction, glyph-rendering or interactive fiber-data exploration. The powerful framework of OpenWalnut allows researchers and power-users to easily extend the functionality to their specific needs.

This package contains the QT4 GUI for OpenWalnut.

Praat
Programm zur Sprachanalyse und -synthese
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Laut den Autoren, macht praat Phonetik durch den Computer (frei übersetzt von »doing phonetics by computer«). Durch die grafische Oberfläche sind verschiedene Funktionalitäten zur Sprachanalyse vorhanden: Spektrogramme, Cochleogramme sowie Pitch- und Formant-Extraktion. Artikulationssythese als auch Synthesen von Pitch, Formant und Intensität sind ebenfalls verfügbar. Andere Fähigkeiten sind Segmentierung, Kennzeichnungen, die die Lautschrift benutzen und Berechnung von Statistiken. Praat ist konfigurier- und durch die eigene Skriptsprache erweiterbar und hat Vorkehrungen, um mit anderen Programmen zu kommunizieren.

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
Anpassung und Test von Hypothesen über psychometrische Funktionen
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Psignifit ermöglicht die Anpassung psychometrischer Funktionen an Datensätze und erhält dabei gleichzeitig die volle Kontrolle über eine große Anzahl von Parametern. Die Daten können entweder aus Textdateien gelesen oder durch eine Pipeline übergeben werden.

Psignifit berechnet Konfidenzintervalle und testet die Güte der Anpassung.

Dies ist die Kommandozeilenversion.

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Python3-nibabel
Python3 bindings to various neuroimaging data formats
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NiBabel provides read and write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, as well as PAR/REC. The various image format classes give full or selective access to header (meta) information and access to the image data is made available via NumPy arrays. NiBabel is the successor of 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-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 convertion 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 Qt4 GUI.

Slicer
software package for visualization and image analysis - main application
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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)
Voxbo
processing, statistical analysis, and display of brain imaging data
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This is a toolkit for analysis of functional neuroimaging (chiefly fMRI) experiments and voxel-based lesion-behavior mapping. VoxBo supports the modified GLM (for autocorrelated data), as well as the standard GLM for non-autocorrelated data. The toolkit is designed to be interoperable with AFNI, FSL, SPM and others.

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Xmedcon
Werkzeug zur Konvertierung medizinischer Bilder (DICOM, ECAT, …) - GUI
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Der Name dieses Projektes leitet sich von »Medical Image Conversion« (Umwandlung von Bildern in der Medizin) ab. Die Software wurde unter der (L)GPL veröffentlicht, stellt den kompletten C-Quellcode der Bibliothek zur Verfügung sowie ein flexibles Kommandozeilenwerkzeug und eine ansprechende grafische Benutzeroberfläche auf Grundlage von GTK+. Aktuell werden die folgenden Formate unterstützt: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 und PNG.

Das Programm ermöglicht außerdem, nicht unterstützte Dateien ohne Kompression zu lesen, die Pixelwerte auszugeben oder angegebene Bilder zu extrahieren/neu zu ordnen. Es ist möglich, rohe Binär-/ASCII-Bildfelder auszulesen oder PNG für Desktopanwendungen zu schreiben.

Dieses Paket enthält die GUI-Version für X, basierend auf GTK+. Hiermit kann stets nur eine Datei zur Zeit bearbeitet werden.

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Official Debian packages with lower relevance

Connectomeviewer
Interactive Analysis and Visualization for MR Connectomics
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The Connectome Viewer is a extensible, scriptable, pythonic research environment for visualization and (network) analysis in neuroimaging and connectomics.

Employing the Connectome File Format, diverse data types such as networks, surfaces, volumes, tracks and metadata are handled and integrated. The Connectome Viewer is part of the MR Connectome Toolkit.

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)
Science-psychophysics
Debian Science packages for Psychophysics
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This metapackage will install Debian packages which might be useful for carrying out any experiment relating physical stimuli and their psychological effects.

The selection of packages is targeting software for stimuli delivery. For additional software related to the analysis of the acquired data refer to science-neuroscience-cognitive, med-imaging depending on the domain of application. Additionally look into science-bci since those often provide a complete loop frameworks including stimuli delivery.

Science-typesetting
Debian Science: Pakete für den Schriftsatz
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Dieses Metapaket installiert Debian-Science-Pakete für den Schriftsatz. Vielleicht sind auch Pakete mit der Kennzeichnung use::typesetting interessant für Sie.

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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Version: 5.1.0+dev+cvs20120104-1

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.
Xnat
platform for data management and productivity tasks in neuroimaging
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Version: 1.7.5.1-1

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 203169