Debian Science Project
Summary
Cognitive Neuroscience
Debian Science - pakker for kognitiv neurovidenskab

Denne metapakke installerer Debianpakker, som kan være nyttige for videnskabsfolk, der udfører kognitiv neurovidenskabelig forskning. Dette omhandler den fulde forskningsproces fra udførelse af psykofysiske eksperimenter, over dataindhentelse og analyse, til visualisering og opsætning af videnskabelige resultater.

Udvalget af pakker er målrettet anvendelsen af analyseteknikker. Metodeudviklere henvises til metapakkerne science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging og med-imaging-dev for en række yderligere programmer, som kan være nyttige i konteksten kognitiv neurovidenskab.

Description

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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
Program til medicinsk billedbehandling
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AMIDE: (Amide's a Medical Imaging Data Examiner, på dansk: Amides er et dataundersøgelsesværktøj til medicinsk billedbehandling) AMIDE er et værktøj til at fremvise og analysere medicinske billeder af datasæt. Dets egenskaber inkluderer simultan håndtering af adskillige datasæt, importeret fra en vifte af filformater, billedfusion, optegning og analyse for områder af interesse i 3D, optegnelse af volumen, og justering af stive legemer.

Amide importerer de fleste kliniske DICOM-filer (via DCMTK-biblioteket).

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/17673/simage/large-7640f62c8ac17498b7e825bdc3e3be71.png
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1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17674/simage/large-7756276dad8ba12ceeacc79f2df9fa3e.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
DICOM-medicinske billedfiler - manipulerings- og konverteringsværktøjer
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Redskaber til kommandolinjen for oprettelse, ændring, dumpning og validering af filer for DICOM-attributter. Understøtter konvertering af nogle proprietære medicinske billedformater til DICOM. Kan håndtere ældre ACR/NEMA-formatdata og nogle proprietære versioner såsom SPI.

dicomnifti
konverterer DICOM-filer til NIfTI-formatet
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dinifti-programmet konverterer MRI-billeder gemt i DICOM-formatet til NIfTI-formatet. NIfTI-formatet er tænkt som det nye standardbilledformat for medicinske billeder og kan bruges for eksempel med FSL, AFNI, SPM, Caret eller Freesurfer.

dinifti konverterer enkeltfiler, men understøter også fulde batchkonverteringer af fulde dicom-mapper. Derudover kan konverterede NIfTI- filer navngives korrekt, med brug af billedserieinformation fra DICOM- filerne.

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
semiautomatisk segmentering af strukturer i 3D-billeder
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SNAP tilbyder semiautomatisk segmentering af strukturer i medicinske billeder (f.eks. magnetisk ressonansbilleder af hjernen) med brug af aktiv konturmetoder, samt som manuel skitsetegning og billednavigering. Funktioner værd at nævne er:

  • Lænket markør for let 3D-navigering
  • Manuel segmentering i tre ortogonale planer på en gang
  • Understøttelse af mange forskellige 3D-billedformater, inklusiv NIfTI
  • Understøttelse af sammenfaldende, lænket visning og segmentering af flere billeder
  • Begrænset understøttelse af farvebilleder (f.eks. diffusion tensor-kort)
  • 3D-skæringsværktøj for hurtig efterbehandling af segmenteringsresultater
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
Medicinsk billedkonverteringsværktøj (DICOM, ECAT, ...)
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Dette projekt står for Medical Image Conversion, dvs. et medicinsk billedkonverteringsværktøj. Programmet er udgivet under (L)GPL. Den fulde C-kildekode fra biblioteket følger med. Det er et fleksibelt kommandolinjeredskab med en pæn grafisk grænseflade, som anvender GTK+- værktøjssættet. Formater som aktuelt understøttes er: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 og PNG.

Programmet giver også mulighed for at læse ej understøttede filer uden komprimering, at udskrive billedpunktsværdier eller at udtrække/ændre rækkefølge på specificerede billeder. Det er muligt at hente de rå binære/ascii-billedarray'er eller at skrive PNG for skrivebordsprogrammer.

Dette er kommandolinjeværktøjet for jobbehandling.

minc-tools
Medicinsk billedformatværktøjer for MNI
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Denne pakke indeholder værktøjer til at manipulere MINC-filer.

Minc-filformatet er et stærkt fleksibelt medicinsk billedfilformat bygget oven på det NetCDF-generaliserede dataformat. Formatet er simpelt, selvbeskrivende, kan udvides, flytbart og n-dimensionelt med programmeringsgrænseflader for dataadgang på lavt niveau og manipulering af diskenhed (volume) på højt niveau. Oven på bibliotekerne er en programpakke af generiske manipulationsværktøjer for billedfiler. Formatet, biblioteket og værktøjer er designet for brug i forskningsmiljøer for medicinsk billedfremstilling: De er simple og funktionsrige og gør intet for at vise en pæn brugerflade for brugerne.

mriconvert
Redskab til konvertering af medicinske billedfiler
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MRIConvert er et redskab til konvertering af medicinske billedfiler, der konverterer DICOM-filer til volumen-formaterne NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager og MetaImage volume.

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mricron
Magnetisk resonansbilledkonvertering, visning og analyse
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Dette er et visualiserings- og analyseværktøj baseret på en grafisk brugerflade for (funktionelle) magnetiske resonansbilleder. MRIcon kan bruges til at oprette 2D- eller 3D-optegninger af statistiske overlagskort på billeder med hjerneanatomi. Derudover tegner det anatomiske regioner-af-interesse (ROI), eller læsionskortlægning, samt grundlæggende analyse af funktionelle tidsserier (f.eks. oprettelse af plot af peristimulus signal-change).

Udover »mricorn« tilbyder denne pakke også »dcm2nii«, der understøtter konvertering af DICOM- og PAR/REC-billeder til NIfTI-formatet og »npm« for ikkeparametrisk dataanalyse.

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
Værktøjer leveret med NIfTI-biblioteket
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Niftilib er et sæt af i/o-biblioteker for læsning og skrivning af filer i NIfTI-1-dataformatet. NIfTI-l er et binært filformat for lagring af medicinske billeddata, f.eks. magnetisk resonansbillede (MRI) og funktionel MRI (fMRI) hjernebilleder.

Denne pakke tilbyder værktøjerne som leveres med biblioteket (nifti_tool, nifti_stats og nifti1_test).

nifti2dicom
Konverter 3D-medicinbilleder til DICOM 2D-serien
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Nifti2Dicom er et konverteringsværktøj, som konverterer 3D NIfTI-filer (og andre formater understøttet af ITK, inklusive Analyze, MetaImage Nrrd og VTK) til DICOM. Til forskel fra andre konverteringsværktøjer så kan det importere en DICOM- fil, som bruges til at importere patienten og studere DICOM-mærker, og giver dig mulighed for at redigere accessionsnummeret og andre DICOM-mærker, for at oprette en gyldig DICOM, som kan importeres i en PACS.

Denne pakke indeholder værktøjerne for kommandolinjen.

praat
program for taleanalyse og -syntese
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Ifølge programmets forfattere så udfører praat »fonetik via computeren«. Via sin grafiske grænseflade, flere funktioner for taleanalyse er tilgængelige: spektogrammer, cochleogrammer, og tonehøjde og formant- udtræk. Artikulær syntese samt syntese fra tonehøjde, formant og intensitet er også tilgængelig. Andre egenskaber indgår segmentering, brug af etiketter med brug af det fonetiske alfabet, samt beregning af statistikker. Praat er konfigurerbar og udvidelig gennem dets eget skriptsprog og har bestemmelser for kommunikation med andre programmer.

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
Tilpasser og tester hypoteser om psykometriske funktioner
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Psignifit tillader tilpasning af psykometriske funktioner til datasæt, mens der bevares fuld kontrol over et stort antal parametre. Data kan enten læses fra tekstfiler eller videresendes via en datakanal.

Psignifit udfører beregningen af konfidensintervaller samt goodness-of-fit test.

Dette er udgaven til kommandolinjen.

Bemærk: Dette er den forældede version 2.x af psignifit.

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python3-nibabel
Python 3-bindinger til diverse neuroimaging-dataformater
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NiBabel tilbyder læse- og skriveadgang til nogle almindelige filformater for medicinske og neuromæssige billeder inklusive: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC samt PAR/REC. De forskellige billedformatklasser giver fuld eller selektiv adgang til hovedinformation (meta) og adgang til billeddata gøres tilgængelig via NumPy-rammer. NiBabel er efterfølgeren til PyNIfTI.

python3-pydicom
DICOM-medicinsk fillæsning og -skrivning - Python 3
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Pydicom er et rent Pythonmodul til at fortolke DICOM-filer. DICOM er en standard (http://medical.nema.org) til at kommunikere medicinske billeder og relateret information såsom rapporter og radioterapiobjekter.

Pydicom gør det nemt at læse DICOM-filer i naturlige pythoniske strukturer for nem manipulering. Ændrede datasæt kan skrives igen til DICOM-formatfiler.

Denne pakke installerer modulet 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
Python 3-modul for estimering af statistiske modeller
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Statsmodels Python 3-modul tilbyder klasser og funktioner for estimering af flere kategorier af statistiske modeller. Disse inkluderer i øjeblikket lineære regressionsmodeller, OLS, GLS, WLS og GLS med AR(p)-fejl, generaliserede lineære modeller for flere distributionsfamilier og M-estimatorer for robuste lineære modeller. En omfattende liste over resultatstatistik er tilgængelig for hvert estimeringsproblem.

Please cite: Skipper Seabold and Josef Perktold: Statsmodels: Econometric and statistical modeling with python (eprint) (2010)
qnifti2dicom
Konverter 3D medicinske billeder til DICOM 2D-serier - grafisk brugerflade
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Nifti2Dicom er et konverteringsværktøj, som konverterer 3D NIfTI-filer (og andre formater understøttet af ITK, inklusive Analyze, MetaImage Nrrd og VTK) til DICOM. Til forskel fra andre konverteringsværktøjer så kan det importere en DICOM- fil, som bruges til at importere patienten og studere DICOM-mærker, og giver dig mulighed for at redigere accessionsnummeret og andre DICOM-mærker, for at oprette en gyldig DICOM, som kan importeres i en PACS.

Denne pakke indeholder den grafiske brugerflade for Qt5.

voxbo
Behandling, statistisk analyse og billedvisning af hjernedata
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Dette er et værktøjssæt til analyse af funktionelle eksperimenter for neurobilledoprettelse (hovedsagelig fMRI) og voxel-baserede læsion-adfærd kortlægning. VoxBo understøtter den modificerede GLM (for autokorrelerede data), samt standard-GLM for ikke automatiske korrelerede data. Værktøjskassen er designet til at være kompatibel med AFNI, FSL, SPM og andre.

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xmedcon
Medicinsk billedkonverteringsværktøj (DICOM, ECAT, ...) - grafisk brugerflade
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Dette projekt står for Medical Image Conversion, dvs. et medicinsk billedkonverteringsværktøj. Programmet er udgivet under (L)GPL. Den fulde C-kildekode fra biblioteket følger med. Det er et fleksibelt kommandolinjeredskab med en pæn grafisk grænseflade, som anvender GTK+- værktøjssættet. Formater som aktuelt understøttes er: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 og PNG.

Programmet giver også mulighed for at læse ej understøttede filer uden komprimering, at udskrive billedpunktsværdier eller at udtrække/ændre rækkefølge på specificerede billeder. Det er muligt at hente de rå binære/ascii-billedarray'er eller at skrive PNG for skrivebordsprogrammer.

Dette er programversionen til X baseret på GTK+. Behandler kun én fil ad gangen.

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Official Debian packages with lower relevance

connectomeviewer
Interaktiv analyse og visualisering for MR Connectomics
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Fremviseren, »The Connectome Viewer« er et udvideligt, skriptbart, pythonisk forskningsmiljø for visualisering og (netværks-)analyse i neurobilledbehandling og »connectomics«.

Med brug af formatet »Connectone File Format«, bliver forskellige datatyper såsom netværk, overflader, volume, spor og metadata håndteret og integreret. Fremviseren »The Connectome Viewer« er en del af værktøjssættet »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
Behandl biologiske plotdata med lille vinkel
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BioXTAS RAW er et Pythonprogram, baseret på en grafisk brugerflade, til reduktion og analyse af lille-vinkel røntgenplotdata (SAXS). Pakken er designet for biologiske SAXS-data.

BioXTAS RAW tilbyder et alternativ til lukkede kildeprogrammer såsom Primus og Scatter for primær dataanalyse. Da programmet kan kalibrere, maskere og integrere billeder, så er det også et alternativ til synchroton beamline-datakanaler, som videnskabsfolk kan installere på deres egen computer og bruge både hjemme og ved beamline.

science-psychophysics
Debian Science - pakker for psykofysik
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Denne metapakke vil installere Debianpakker, som kan være nyttige for udførsel af eksperimenter relateret til fysisk stimuli og deres fysiologiske effekter.

Udvalget af pakker er målrettet programmer for stimuli. For yderligere programmer relateret til analyse af de indhentede data se science-neuroscience-cognitive, med-imaging afhængig af domænanvendelsen. Kig derudover i science-bci da disse pakker ofte tilbyder en fuldstændig ramme inklusiv stimulilevering.

science-typesetting
Debian Science - opsætningspakker
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Denne metapakke vil installere Debian Science-pakker relateret til opsætning. Du er måske også interesseret i deb-mærket use::typesetting.

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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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 248069