Debian Science Project
Summary
Cognitive Neuroscience
pacchetti Debian Science per neuroscienze cognitive

Questo metapacchetto installa i pacchetti Debian che potrebbero essere utili per gli scienziati che fanno ricerca nel campo delle neuroscienze cognitive. Ciò comprende il completo processo di ricerca dall'esecuzione di esperimenti psicofisici, passando per l'acquisizione e l'analisi dei dati, alla visualizzazione e impaginazione di risultati scientifici.

Questa selezione di pacchetti è mirata all'applicazione di tecniche d'analisi. Gli sviluppatori dei metodi si sono riferiti ai metapacchetti science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging e med-imaging-dev per una varietà di software aggiuntivi che possono essere utili nel contesto delle neuroscienze cognitive.

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 per immagini medicali
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AMIDE: (Amide's a Medical Imaging Data Examiner). AMIDE è uno strumento per visualizzare e analizzare insiemi di dati di immagini medicali. Tra le sue funzionalità sono incluse: la gestione simultanea di insiemi di dati multipli importati da diversi formati di file, la fusione di immagini, il disegno e l'analisi di regioni 3D di interesse, la resa dei volumi e l'allineamento di corpi rigidi.

Amide importa la maggior parte dei file DICOM clinici (usando la libreria 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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VersionURL
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17673/simage/large-7640f62c8ac17498b7e825bdc3e3be71.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/17678/simage/large-deeb0fc832965282d8e7bd9a43b6065e.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/17675/simage/large-d5d4f705acb3ff24758ea101b026c05b.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/16980/simage/large-bad825aa1bf433c09104699fb7be429c.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
strumenti di manipolazione e conversione di file di immagini medicali DICOM
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Utilità a riga di comando per creare, modificare, fare il dump e convalidare file di attributi DICOM. Supporta la conversione di alcuni formati per immagini medicali proprietari in DICOM. Può gestire dati nel vecchio formato ACR/NEMA e alcune versioni proprietarie di esso come SPI.

dicomnifti
converte file DICOM nel formato NIfTI
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Il programma dinifti converte immagini MRI memorizzate in formato DICOM nel formato NIfTI. Quest'ultimo è considerato il nuovo formato standard per le immagini medicali e può essere usato con, per esempio, FSL, AFNI, SPM, Caret o Freesurfer.

dinifti converte file singoli, ma supporta anche la conversione completamente automatica di complete directory dicom. In aggiunta, i file NIfTI convertiti possono essere rinominati in modo appropriato usando le informazioni sulle serie di immagini nei file 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
segmentazione semiautomatica di strutture in immagini 3D
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SNAP fornisce la segmentazione semiautomatica di strutture in immagini medicali (es. immagini di risonanza magnetica del cervello) usando metodi di contorno attivo e delineazione manuale e navigazione di immagini. Funzionalità notevoli sono:

  • cursore collegato per navigazione 3D senza interruzioni;
  • segmentazione manuale in 3 piani ortogonali contemporaneamente;
  • gestione di molti formati differenti di immagini 3D, incluso NIfTI;
  • gestione di visualizzazioni collegate concorrenti e segmentazione di immagini multiple;
  • gestione limitata di immagini a colori (es. mappe di tensori di diffusione);
  • strumento di taglio di piani 3D per post-elaborazione veloce dei risultati della segmentazione.
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
strumento di conversione di immagini medicali (DICOM, ECAT...)
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Questo progetto riguarda la conversione di immagini medicali. È rilasciato sotto licenza (L)GPL e viene fornito con il completo codice sorgente in C della libreria, una flessibile utilità a riga di comando e una bella interfaccia grafica che usa il toolkit GTK+. I formati attualmente gestiti sono: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 e PNG.

Può anche leggere file non supportati senza compressione, visualizzare i valori dei pixel o estrarre/riordinare le immagini specificate. È possibile recuperare i vettori grezzi delle immagini in formato binario o ASCII o produrre immagini PNG per le applicazioni desktop.

Questo è lo strumento a riga di comando per l'elaborazione di massa.

minc-tools
strumenti per immagini medicali in formato MNI
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Questo pacchetto contiene strumenti per manipolare file MINC.

Il formato di file Minc è un formato per immagini medicali altamente flessibile costruito sulla base del formato dati generalizzato NetCDF. Il formato è semplice, auto-descrittivo, estensibile, portabile e a N dimensioni, con interfacce di programmazione sia per accesso di basso livello ai dati, sia per manipolazione di volumi ad alto livello. Sopra alle librerie è costruita una suite di strumenti generici per la manipolazione di file immagine. Il formato, le librerie e gli strumenti sono pensati per l'uso in ambienti di ricerca sulle immagini medicali: sono semplici e potenti e non cercano in alcun modo di fornire una bella interfaccia per gli utenti.

mriconvert
utilità di conversione per file di immagini medicali
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MRIConvert è un'utilità di conversione per file di immagini medicali che converte i file DICOM nei formati di volumi NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager e MetaImage.

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mricron
conversione, visualizzazione e analisi di immagini di risonanza magnetica
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Questo è uno strumento di visualizzazione e analisi basato su GUI per immagini di risonanza magnetica (funzionale). MRIcron può essere usato per creare rendering 2D o 3D di mappe statistiche sovrapposte su immagini dell'anatomia del cervello. Inoltre aiuta a disegnare le ROI (regions-of-interest) anatomiche o la mappatura delle lesioni, e l'analisi di base delle serie temporali funzionali (es. creando grafici dei cambiamenti di segnali peristimolo).

Oltre a "mricron", questo pacchetto fornisce anche "dcm2nii", che gestisce la conversione di immagini DICOM e PAR/REC nel formato NIfTI, e "npm", per l'analisi di dati non parametrici.

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
strumenti forniti con la libreria NIfTI
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Niftilib è un insieme di librerie di I/O per la lettura e la scrittura di file dati nel formato NIfTI-1. NIfTI-1 è un formato binario per l'archiviazione di immagini mediche, tipo risonanza magnetica (RMN) o immagini cerebrali da RMN funzionale (fRMN).

Questo pacchetto comprende gli strumenti forniti con la libreria (nifti_tool, nifti_stats e nifti1_test).

nifti2dicom
converte immagini medicali 3D in serie di DICOM 2D
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Nifti2Dicom è uno strumento di conversione che converte file 3D NIfTI (e altri formati gestiti da ITK, inclusi Analyze, MetaImage Nrrd e VTK) in DICOM. A differenza di altri strumenti di conversione, può importare un file DICOM che viene usato per importare il paziente e studiare i tag DICOM, e permette di modificare il numero di accrescimento e altri tag DICOM per creare un DICOM valido che può essere importato in PACS.

Questo pacchetto include gli strumenti a riga di comando.

praat
programma per l'analisi e la sintesi del linguaggio
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Secondo i suoi autori, praat è "fonetica tramite il computer". Molteplici funzionalità di analisi del linguaggio sono disponibili tramite la sua interfaccia grafica: spettrogrammi, cocleogrammi, estrazione del tono e della formante. Sono altresì disponibili sintesi articolatorie, dal tono, dalla formante e dall'intensità. Fra le altre funzionalità si segnalano segmentazione, etichettatura con uso dell'alfabeto fonetico e computazione statistica. Praat è configurabile ed estensibile attraverso il suo linguaggio di script ed è inoltre predisposto per poter comunicare con altri programmi.

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
interpolazione e test delle ipotesi di funzioni psicometriche
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Psignifit permette l'adattamento di funzioni psicometriche a insiemi di dati mantenendo il controllo completo su un gran numero di parametri. I dati possono essere letti da file di testo o passati tramite una pipe.

Psignifit effettua il calcolo degli intervalli di fiducia ma anche dei test della bontà dell'adattamento.

Questa è la versione a riga di comando.

Notare che questa è la versione obsoleta 2.x di psignifit.

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python3-nibabel
collegamenti Python 3 a vari formati di dati per neuroimmagini
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NiBabel fornisce accesso in lettura e scrittura ad alcuni formati di file comuni per neuroimmagini e file medicali, inclusi: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, così come PAR/REC. Le varie classi per formato per immagini danno accesso pieno o selettivo alle informazioni delle intestazioni (metainformazioni) e l'accesso ai dati dell'immagine è reso disponibile attraverso matrici NumPy. NiBabel è il successore di PyNIfTI.

python3-pydicom
lettura e scrittura di file medicali DICOM (Python 3)
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pydicom è un modulo in Python puro per l'analisi di file DICOM. DICOM è uno standard (http://medical.nema.org) per comunicare le immagini medicali e le informazioni relative, come rapporti e oggetti di radioterapia.

pydicom rende facile la lettura di file DICOM in naturali strutture pythoniche per una facile manipolazione. Gli insiemi di dati modificati posso essere nuovamente scritti su file in formato DICOM.

Questo pacchetto installa il modulo per Python 3.

python3-pyxnat
interfaccia per accedere a dati di neuroimmagini su server XNAT
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pyxnat è una semplice libreria Python che si basa sull'API REST fornita dalla piattaforma XNAT a partire dalla sua versione 1.4. XNAT è un database estensibile per dati di neuroimmagini. L'obiettivo principale è di facilitare la comunicazione con un server XNAT per usare come plugin strumenti esterni o script Python per elaborare i dati. Ha:

  • funzionalità di navigazione delle risorse;
  • accesso in lettura e scrittura alle risorse;
  • ricerche complesse;
  • cache su disco dei file richiesti e delle risorse.
python3-statsmodels
modulo Python 3 per la stima di modelli statistici
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Il modulo Python 3 statsmodels fornisce classi e funzioni per la stima di diverse categorie di modelli statistici. Tra questi attualmente sono inclusi: modelli di regressione lineare, OLS, GLS, WLS e GLS con errori AR(p), modelli lineari generalizzati per diverse famiglie di distribuzione ed M stimatori per modelli lineari robusti. È disponibile un'ampia lista di statistiche dei risultati per ciascun problema di stima.

Please cite: Skipper Seabold and Josef Perktold: Statsmodels: Econometric and statistical modeling with python (eprint) (2010)
qnifti2dicom
converte immagini medicali 3D in serie di DICOM 2D (GUI)
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Nifti2Dicom è uno strumento di conversione che converte file 3D NIfTI (e altri formati gestiti da ITK, inclusi Analyze, MetaImage Nrrd e VTK) in DICOM. A differenza di altri strumenti di conversione, può importare un file DICOM che viene usato per importare il paziente e studiare i tag DICOM, e permette di modificare il numero di accrescimento e altri tag DICOM per creare un DICOM valido che può essere importato in PACS.

Questo pacchetto contiene l'interfaccia utente grafica Qt5.

voxbo
elaborazione, analisi statistica e visualizzazione di dati di immagini del cervello
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Questo è un toolkit per l'analisi di esperimenti di neuroimmagini funzionali (principalmente fMRI) e mappatura lesione-comportamento basata su voxel. VoxBo gestisce GLM modificato (per dati autocorrelati), oltre a GLM standard per dati non autocorrelati. Il toolkit è progettato per poter funzionare insieme a AFNI, FSL, SPM e altri.

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xmedcon
strumento di conversione di immagini medicali (DICOM, ECAT...) (GUI)
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Questo progetto riguarda la conversione di immagini medicali. È rilasciato sotto licenza (L)GPL e viene fornito con il completo codice sorgente in C della libreria, una flessibile utilità a riga di comando e una bella interfaccia grafica che usa il toolkit GTK+. I formati attualmente gestiti sono: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 e PNG.

Può anche leggere file non supportati senza compressione, visualizzare i valori dei pixel o estrarre/riordinare le immagini specificate. È possibile recuperare i vettori grezzi delle immagini in formato binario o ASCII o produrre immagini PNG per le applicazioni desktop.

Questa è la versione per X del programma, basata su GTK+. Elabora un solo file alla volta.

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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
pacchetti Debian Science per la psicofisica
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Questo metapacchetto installa i pacchetti Debian che possono essere utili per effettuare qualsiasi esperimento relativo a stimoli fisici e ai loro effetti psicologici.

La selezione dei pacchetti è focalizzata su software per la somministrazione di stimoli. Per software aggiuntivo relativo all'analisi dei dati acquisiti guardare science-neuroscience-cognitive e med-imaging, a seconda del campo di applicazione. In aggiunta guardare science-bci dato che quei pacchetti spesso forniscono infrastrutture per il ciclo completo di lavoro compresa la somministrazione degli stimoli.

science-typesetting
pacchetti Debian Science per la composizione tipografica
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Questo metapacchetto installa i pacchetti Debian Science relativi alla composizione tipografica. Chi installa questo pacchetto potrebbe essere interessato al debtag 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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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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License: XNAT_SLA
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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