Debian Science Project
Summary
Cognitive Neuroscience
Pakiety naukowe Debiana do neurologii poznawczej

Ten metapakiet spowoduje zainstalowanie pakietów Debiana, które mogą być przydatne dla naukowców wykonujących badania związane z neurologią poznawczą. Obejmuje to cały proces badawczy od przeprowadzania eksperymentów psychofizycznych, poprzez pozyskiwanie i analizowanie danych do składania i wyświetlania wyników badań naukowych.

Niniejszy dobór pakietów ukierunkowany jest na zastosowanie technik analizy. Metody deweloperów zostały określone w metapakietach: science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging i med-imaging-dev dla wielu dodatkowych programów, które mogą być przydatne w kontekście poznawczej neurologii.

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
Oprogramowanie do obrazowania medycznego
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AMIDE: analizator zobrazowanych danych medycznych (ang. Amide's a Medical Imaging Data Examiner). AMIDE jest narzędziem do przeglądania i analizowania zestawów danych obrazów medycznych. Do jego możliwości można zaliczyć: jednoczesne przetwarzanie złożonych zbiorów danych importowanych z różnych formatów plików, łączenie obrazów, przedstawianie określonych analiz i rysunków w postaci trójwymiarowej, renderowanie objętości i wyrównywanie obrazów ciał stałych.

Amide importuje większość klinicznych plików DICOM (z wykorzystaniem biblioteki 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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1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17675/simage/large-d5d4f705acb3ff24758ea101b026c05b.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17676/simage/large-6cc9cfe18a76cd3b247214d8ae0339b6.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/16980/simage/large-bad825aa1bf433c09104699fb7be429c.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17677/simage/large-8f7aaa9529343865541ebc968e464c74.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17674/simage/large-7756276dad8ba12ceeacc79f2df9fa3e.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17678/simage/large-deeb0fc832965282d8e7bd9a43b6065e.png
0.9.1-2https://screenshots.debian.net/shrine/screenshot/356/simage/large-a3b9d7e99aafc8e159ad1288d6031445.png
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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
Narzędzia do zarządzania i konwersji plików obrazów medycznych DICOM
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Pakiet zawiera narzędzia wiersza poleceń do tworzenia, modyfikowania, przesyłania i sprawdzania poprawności plików z atrybutami DICOM. Obsługuje przekształcanie niektórych własnościowych formatów obrazów medycznych do DICOM. Umożliwia współpracę ze starszym formatem danych ACR/NEMA i niektórymi własnościowymi wersjami tego formatu, takimi jak SPI.

dicomnifti
Konwertowanie plików DICOM na format NIfTI
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Program dinifti przetwarza obrazy MRI przechowywane w formacie DICOM na format NIfTI. Format NIfTI uważany jest za nowy standard formatu obrazu do obrazowania medycznego i może być używany np. z FSL, AFNI, SPM, Carey lub Freesurfer.

Dinifti konwertuje pojedyncze pliki, ale także obsługuje w pełni zautomatyzowane konwersje wsadowe kompletnych katalogów DICOM. Ponadto, konwertowane pliki NIfTI mogą być odpowiednio nazywane, dzięki informacjom * obrazach z plików 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
Półautomatyczna segmentacja struktury obrazów 3D
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SNAP umożliwia półautomatyczną segmentację struktur w obrazach medycznych (np. obrazach rezonansu magnetycznego mózgu) przy użyciu metod aktywnych konturów, jak również ręcznego wytyczania i nawigacji w ramach obrazu. Godne uwagi cechy to:

  • połączony kursor do łatwej nawigacji 3D;
  • ręczna segmentacja w trzech prostopadłych płaszczyznach jednocześnie;
  • obsługa wielu różnych formatów obrazu 3D, w tym NIfTI;
  • obsługa równoczesnego podglądania i segmentacji wielu obrazów;
  • ograniczona obsługa kolorowych obrazów (np. map tensora dyfuzji);
  • narzędzie przycinania płaszczyzny 3D do przyspieszenia dalszego przetwarzania wyników segmentacji.
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
Narzędzie do konwersji formatów obrazów medycznych (DICOM, ECAT, ...)
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Program przeznaczony jest do konwertowania formatów obrazów medycznych i rozpowszechniany na podstawie licencji (L)GPL. Pakiet zawiera kompletny kod źródłowy w języku C, elastyczne narzędzie wiersza poleceń oraz przejrzysty interfejs graficzny, stworzony przy użyciu biblioteki GTK+. Aktualnie obsługuje następujące formaty: ACR/NEMA 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 i PNG.

Program umożliwia także odczytywanie nieskompresowanych, oficjalnie nieobsługiwanych plików, wyświetlanie wartości pikseli oraz wyodrębnianie/zmienianie kolejności poszczególnych obrazów. Możliwe jest również uzyskiwanie nieprzetworzonych obrazów w formatach binarnym lub ASCII oraz zapisywanie obrazów w formacie PNG, używanym w aplikacjach pulpitowych.

Jest to narzędzie wiersza poleceń do przetwarzania wsadowego.

minc-tools
Narzędzia do formatowania obrazów medycznych MNI
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Pakiet zawiera narzędzia do obsługi plików MINC.

Format pliku Minc to bardzo elastyczny format plików obrazów medycznych, zbudowany na bazie uogólnionego formatu danych NetCDF. Format ten jest prosty, samoopisujący się, rozszerzalny, przenośny i N-wymiarowy, z interfejsami programistycznymi zarówno do niskopoziomowego dostępu do danych, jak i do wysokopoziomowego zarządzania zawartością. Pakiet udostępnia zestaw narzędzi do obsługi plików graficznych, bazujący na bibliotekach. Format, biblioteki i narzędzia przeznaczone są do użytku w środowisku badawczym obrazowania medycznego: są proste i wydajne i nie starają się zapewnić użytkownikom ładnego interfejsu.

mriconvert
Narzędzie do konwersji medycznych plików graficznych
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MRIConvert jest narzędziem do konwersji medycznych plików graficznych, które przetwarza pliki DICOM do następujących formatów: NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager oraz MetaImage.

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mricron
Konwertowanie, przeglądanie i analizowanie obrazu rezonansu magnetycznego
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Jest to narzędzie z graficznym interfejsem użytkownika, służące do przeglądania i analizowania (funkcjonalnych) obrazów otrzymanych metodą rezonansu magnetycznego. MRIcron może być używany do tworzenia dwu- lub trójwymiarowych wizualizacji map statystycznych, nakładanych na zdjęcia anatomiczne mózgu. Ponadto, pomaga w rysowaniu anatomicznych obszarów zainteresowania (ROI), w odwzorowywaniu zmian oraz w podstawowej analizie funkcjonalnych szeregów czasowych (np. w tworzeniu wykresów przed i po stymulacyjnej zmiany sygnału).

Oprócz samego MRIcron, pakiet dostarcza również narzędzie dcm2nii, obsługujące konwersję obrazów DICOM i PAR/REC do formatu NIfTI oraz npm do nieparametrycznej analizy danych.

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
Narzędzia dostarczane z biblioteką NIfTI
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Niftilib jest zestawem bibliotek wejścia/wyjścia do odczytywania i zapisywania plików w formacie danych NIfTI-1. NIfTI-1 to binarny format pliku do przechowywania danych z obrazów medycznych, np. obrazów mózgu wykonanych metodą obrazowania rezonansu magnetycznego (MRI) oraz wyspecjalizowaną odmianą obrazowania rezonansu magnetycznego (fMRI).

Pakiet zawiera narzędzia, które dostarczane są z biblioteką NIfTI (nifti_tool, nifti_stats i 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
Program do analizy i syntezy mowy
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Według autorów, praat służy do obsługiwania komputerowej fonetyki. Za pośrednictwem interfejsu graficznego można uzyskać dostęp do różnych funkcji analizy mowy, dostępne są: spektrogramy, kochleogramy, wydobywanie intensywności i formatu dźwięku. Program umożliwia również syntezę artykulacji, intensywności, formatu oraz intonacji. Pozostałe funkcje to: segmentacja, znakowanie z wykorzystaniem alfabetu fonetycznego i obliczanie statystyk. Praat jest konfigurowalny i rozszerzalny poprzez własny język skryptowy, a ponadto potrafi komunikować się z innymi programami.

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
Fitting and testing hypotheses about psychometric functions
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Psignifit allows fitting of psychometric functions to datasets while maintaining full control over a large number of parameters. Data can either be read from text files or passed through a pipe.

Psignifit performs the calculation of confidence intervals as well as goodness-of-fit tests.

This is the command line version.

Please note: This is the legacy version 2.x of psignifit.

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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-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
Przetwarzanie, analiza statystyczna i wyświetlanie danych obrazowych mózgu
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Pakiet zawiera zestaw narzędzi do analiz eksperymentów z zakresu funkcjonalnego obrazowania rezonansu magnetycznego (głównie fMRI) oraz mapowania zmiennych zachowawczych baz vokselowych. VoxBo obsługuje zmodyfikowany GLM (dla danych skorelowanych automatycznie) oraz standardowe GLM dla danych nieskorelowanych automatycznie. Zestaw narzędziowy przeznaczony jest do współdziałania z AFNI, FSL, SPM i innymi.

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xmedcon
Graficzne narzędzie do konwersji obrazów medycznych (DICOM, ECAT, ...)
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Program przeznaczony jest do konwertowania formatów obrazów medycznych i rozpowszechniany na podstawie licencji (L)GPL. Pakiet zawiera kompletny kod źródłowy w języku C, elastyczne narzędzie wiersza poleceń oraz przejrzysty interfejs graficzny, stworzony przy użyciu biblioteki GTK+. Aktualnie obsługuje następujące formaty: ACR/NEMA 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 i PNG.

Program umożliwia także odczytywanie nieskompresowanych, oficjalnie nieobsługiwanych plików, wyświetlanie wartości pikseli oraz wyodrębnianie/zmienianie kolejności poszczególnych obrazów. Możliwe jest również uzyskiwanie nieprzetworzonych obrazów w formatach binarnym lub ASCII oraz zapisywanie obrazów w formacie PNG, używanym w aplikacjach pulpitowych.

Jest to graficzna wersja programu (działająca w środowisku X), z interfejsem opartym na bibliotece GTK+. Program przetwarza tylko jeden plik na raz.

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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)
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
process biological small angle scattering data
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BioXTAS RAW is a GUI based, Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The package is designed for biological SAXS data.

BioXTAS RAW provides an alternative to closed source programs such as Primus and Scatter for primary data analysis. Because it can calibrate, mask, and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.

science-psychophysics
Pakiety Naukowe Debiana do Psychofizyki
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Ten metapakiet instaluje pakiety Debiana, które mogą być przydatne do przeprowadzania dowolnego eksperymentu związanego z bodźcami fizycznymi i ich skutkami psychologicznymi.

Dobór pakietów został ukierunkowany na oprogramowanie do dostarczania bodźców. Dodatkowe oprogramowanie związane z analizą pozyskanych danych odnosi się do nauki-neurologii-poznawczej, obrazowania medycznego w zależności od dziedziny zastosowania. Dodatkowo warto zapoznać się z science-bci, ponieważ często zapewnia kompletne struktury pętli, łącznie z dostarczaniem bodźców.

science-typesetting
Pakiety naukowe Debiana do składania tekstu
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Niniejszy metapakiet służy do instalowania pakietów naukowych Debiana, mających związek ze składaniem tekstu. Osoby zainteresowane mogą skorzystać z odpowiedniego znacznika Debiana.

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.
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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License: free
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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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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 246113