Summary
Cognitive Neuroscience
paquets pour les neurosciences cognitives de Debian Science
Ce métapaquet installe les paquets de Debian qui peuvent être utiles aux
scientifiques intéressés dans la recherche en neurosciences cognitives.
Cela comprend le processus de recherche complet, de la conduite
d’expériences de psychophysique à la visualisation et composition
typographique de résultats scientifiques.
La sélection de paquets vise les applications de technique d’analyse. Les
développeurs de méthodes peuvent consulter les métapaquets
science-statistics, science-imageanalysis, science-numericalcomputation,
med-imaging et med-imaging-dev pour divers logiciels supplémentaires qui
pourraient être utiles dans la recherche en neurosciences cognitives.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for Debian Science
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Science mailing list
Links to other tasks
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Debian Science Cognitive Neuroscience packages
Official Debian packages with high relevance
amide
programme pour l'imagerie médicale
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Versions of package amide |
Release | Version | Architectures |
sid | 1.0.6-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.6-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.5-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.5-12 | amd64,arm64,armhf,i386 |
jessie | 1.0.5-2 | amd64,armel,armhf,i386 |
trixie | 1.0.6-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.0.5-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package amide: |
field | medicine, medicine:imaging |
role | program |
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License: DFSG free
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AMIDE (« AMIDE's a Medical Image Data Examiner ») est un outil pour la
visualisation et l'analyse de jeux de données d'imagerie médicale. On peut
noter parmi ses fonctionnalités la prise en charge simultanée de données
importées de fichiers aux formats divers, la fusion d'images, la
définition de régions d'intérêt tridimensionnelles, le rendu des volumes
et l'alignement de structures solides.
Amide importe la plupart des fichiers cliniques DICOM (grâce à la
bibliothèque DCMTK).
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caret
??? missing short description for package caret :-(
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Versions of package caret |
Release | Version | Architectures |
jessie | 5.6.4~dfsg.1-3 | amd64,armel,armhf,i386 |
Debtags of package caret: |
role | program |
uitoolkit | qt |
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License: DFSG free
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dicom3tools
outils de conversion et de manipulation de fichiers d'imagerie médicale DICOM
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Versions of package dicom3tools |
Release | Version | Architectures |
bullseye | 1.00~20190724083540-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.00~20180803063840-1 | amd64,arm64,armhf,i386 |
stretch | 1.00~20170109062447-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.00~20140902075059-1 | amd64,armel,armhf,i386 |
sid | 1.00~20240118131615-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.00~20240118131615-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.00~20220618093127-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye-backports | 1.00~20220120135102-1~bpo11+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.00~20241003103319 |
Debtags of package dicom3tools: |
field | medicine, medicine:imaging |
role | program |
use | converting |
works-with | image |
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License: DFSG free
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Utilitaires en ligne de commande pour créer, modifier, vidanger et valider
des fichiers d'attributs DICOM. Il gère la conversion de certains formats
d'imagerie médicale propriétaires en DICOM. Il gère l'ancien format de
données ACR/NEMA et certaines de ses versions propriétaires telle que SPI.
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dicomnifti
Convertit les fichiers DICOM au format NIfTI
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Versions of package dicomnifti |
Release | Version | Architectures |
bullseye | 2.33.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.33.1-1 | amd64,arm64,armhf,i386 |
stretch | 2.32.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.32.1-1 | amd64,armel,armhf,i386 |
bookworm | 2.33.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package dicomnifti: |
interface | commandline |
role | program |
scope | utility |
use | converting |
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License: DFSG free
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Le programme dinifti convertit des images d'IRM du format DICOM au format
NIfTI. Les fichiers au format NIfTI peuvent être lus par les programmes
FSL, AFNI et SPM, Caret ou Freesurfer.
Dinifti convertit les fichiers un par un, ou à la chaîne au sein d'un
répertoire, et peut donner des noms cohérents aux fichiers NIfTI en
utilisant les informations présentes dans les fichiers DICOM.
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fslview
??? missing short description for package fslview :-(
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Versions of package fslview |
Release | Version | Architectures |
jessie | 4.0.1-4 | amd64,armel,armhf,i386 |
Debtags of package fslview: |
interface | x11 |
made-of | html |
role | documentation, program |
scope | utility |
suite | debian |
uitoolkit | qt |
use | viewing |
x11 | application |
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License: DFSG free
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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)
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itksnap
segmentation semi-automatique de structures pour les images en 3D
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Versions of package itksnap |
Release | Version | Architectures |
jessie | 2.2.0-1.1 | amd64,armel,armhf,i386 |
bullseye | 3.6.0-5 | amd64,i386 |
buster | 3.6.0-3 | amd64,i386 |
stretch | 3.4.0-2 | amd64,i386 |
Debtags of package itksnap: |
field | medicine:imaging |
role | program |
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License: DFSG free
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SNAP fournit une segmentation semi-automatique de structures pour les
images médicales (par exemple, des images de résonance magnétique du
cerveau) en utilisant des méthodes de contour actif, ainsi que la
délimitation manuelle et la navigation dans les images.
Les caractéristiques notables sont :
– curseur avec liens pour une navigation en 3D fluide ;
– segmentation manuelle dans les trois plans orthogonaux en même temps ;
– gestion de beaucoup de formats d’image 3D, y compris NIfTI ;
– gestion concomitante, visualisations liées et segmentation de plusieurs
images ;
– gestion limitée des images en couleur (par exemple, cartes de tenseurs
de diffusion) ;
– outils de plan sécant en 3D pour un post-traitement rapide des
résultats de segmentation.
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medcon
Outil de conversion d'images médicales (DICOM, ECAT, etc.)
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Versions of package medcon |
Release | Version | Architectures |
sid | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.23.0-gtk3+dfsg-1+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.16.3+dfsg-1+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.16.1+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 0.14.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.13.0-2 | amd64,armel,armhf,i386 |
Debtags of package medcon: |
field | biology |
interface | commandline |
role | program |
uitoolkit | gtk |
use | converting |
works-with | image, image:raster |
x11 | application |
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License: DFSG free
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Ce projet a pour but la conversion d’image médicale (Medical Image Conversion).
Publié sous licence (L)GPL, il est livré avec le code source C complet de la
bibliothèque, un outil flexible en ligne de commande et une interface graphique
soignée utilisant la boîte à outils GTK+. Les formats pris en charge
actuellement sont : Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 et
PNG.
Le programme permet aussi de lire des fichiers non pris en charge et non
compressés, pour afficher les valeurs de pixel ou pour extraire ou réorganiser
les images indiquées. Il est possible de récupérer les tableaux d’image
binaire ou ASCII RAW ou d’écrire des PNG pour des applications de bureau.
Ceci est l'outil en ligne de commande pour le traitement par lot.
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minc-tools
Outils pour le format MNI d'imagerie médicale
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Versions of package minc-tools |
Release | Version | Architectures |
buster | 2.3.00+dfsg-3 | amd64,arm64,armhf,i386 |
bullseye | 2.3.00+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.2.00-6 | amd64,armel,armhf,i386 |
stretch | 2.3.00+dfsg-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package minc-tools: |
field | medicine, medicine:imaging |
interface | commandline |
role | program |
scope | utility |
use | analysing, converting |
works-with | image, image:raster |
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License: DFSG free
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Ce paquet contient des outils permettant de manipuler des fichiers MINC.
Le format de fichiers MINC est un format de fichier très souple basé sur
le format généralisé de données NetCDF. Il est simple, auto-décrit,
extensible, portable et à N dimensions avec des interfaces de
programmation que ce soit pour l'accès aux données de bas niveau ou à des
manipulations de haut niveau en masse. Les bibliothèques ont permis
l'écriture d'un ensemble d'outils de manipulation de fichiers génériques
d'images. Le format, les bibliothèques et les outils sont prévus pour être
utilisés dans un environnement de recherche en imagerie médicale : ils
sont simples et efficaces sans chercher à fournir une belle interface aux
utilisateurs.
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mriconvert
utilitaire de conversion de fichier d’image médicale
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Versions of package mriconvert |
Release | Version | Architectures |
stretch | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.1.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0.7-2 | amd64,armel,armhf,i386 |
bullseye | 2.1.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.0-3 | amd64,arm64,armhf,i386 |
Debtags of package mriconvert: |
field | medicine:imaging |
role | program |
uitoolkit | wxwidgets |
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License: DFSG free
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MRIConvert est un utilitaire de conversion de fichier d’image médicale pour
des fichiers DICOM vers les formats NIfTI 1.1, Analyze 7.5, SPM99/Analyze,
BrainVoyager et MetaImage.
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mricron
conversion, visualisation et analyse d’images de résonance magnétique
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Versions of package mricron |
Release | Version | Architectures |
bullseye | 1.0.20190902+dfsg-2 | amd64,arm64,armel,armhf,i386,ppc64el |
stretch | 0.20140804.1~dfsg.1-2 | amd64,arm64,armel,armhf,i386 |
jessie | 0.20140804.1~dfsg.1-1 | amd64,armel,armhf,i386 |
buster | 0.20140804.1~dfsg.1-3 | amd64,arm64,armhf,i386 |
bookworm | 1.2.20211006+dfsg-4 | amd64,arm64,armel,armhf,i386,ppc64el |
trixie | 1.2.20211006+dfsg-6 | amd64,arm64,armel,armhf,i386,ppc64el |
sid | 1.2.20211006+dfsg-6 | amd64,arm64,armel,armhf,i386,ppc64el |
Debtags of package mricron: |
uitoolkit | gtk |
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License: DFSG free
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Il s’agit d’un outil de visualisation et d’analyse basé sur une interface
graphique pour les images de résonance magnétique (fonctionnelle). MRIcron
peut être utilisé pour créer des rendus en 2D ou 3D des cartes de
superposition statistiques d’images d’anatomie de cerveau. De plus, il
aide à dessiner des régions anatomiques d’intérêt (ROI), ou des cartes de
lésion, ainsi qu’une analyse basique de séries temporelles (par exemple,
création de tracés de péristimulus signal-modification).
En plus de « mricron », ce paquet fournit aussi « dcm2nii » qui prend en
charge la conversion d’images DICOM et PAR/REC au format NIfTI, et « npm »
pour l’analyse de données non paramétriques.
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nifti-bin
outils livrés avec la bibliothèque NIfTI
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Versions of package nifti-bin |
Release | Version | Architectures |
stretch | 2.0.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.1-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0.0-2 | amd64,armel,armhf,i386 |
sid | 3.0.1-9.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.1-9.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.0.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.0.0-3 | amd64,arm64,armhf,i386 |
Debtags of package nifti-bin: |
field | medicine, medicine:imaging |
interface | commandline |
role | program, shared-lib |
scope | utility |
use | checking, converting |
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License: DFSG free
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Niftilib est un ensemble de bibliothèques d'entrées-sorties pour lire et
écrire des fichiers au format NIfTI-1. NIfTI-1 est un format de fichier
binaire pour stocker des images médicales, par exemple des images par
résonance magnétique (IRM) et des images de cerveau par résonance
magnétique fonctionnelle (IRMf).
Ce paquet fournit les outils livrés avec la bibliothèque (nifti_tool,
nifti_stats et nifti1_test).
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nifti2dicom
convert 3D medical images to DICOM 2D series
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Versions of package nifti2dicom |
Release | Version | Architectures |
bullseye | 0.4.11-3 | amd64,i386 |
stretch | 0.4.11-1 | amd64,i386 |
buster | 0.4.11-1 | amd64,i386 |
jessie | 0.4.9-1 | amd64,armel,armhf,i386 |
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License: DFSG free
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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.
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praat
programme pour l'analyse et la synthèse de la parole
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Versions of package praat |
Release | Version | Architectures |
bullseye | 6.1.38-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 6.0.48-1 | amd64,arm64,i386 |
bookworm | 6.3.07-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 6.4.23+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 6.0.23-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.4.0-1 | amd64,armel,armhf,i386 |
Debtags of package praat: |
field | linguistics |
interface | x11 |
role | program |
scope | application |
uitoolkit | motif |
works-with | audio |
x11 | application |
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License: DFSG free
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Selon ses auteurs, Praat permet de « faire de la phonétique par
ordinateur ». Au travers de son interface graphique, plusieurs
fonctionnalités d'analyse de la parole sont disponibles : spectrogrammes,
cochleogrammes, et l'extraction de l'accent de hauteur (accent musical) et
des formants. La synthèse articulatoire, ainsi que la synthèse à partir de
l'accent de hauteur, des formants, et de l'intensité sont également
disponibles. Les autres caractéristiques sont la segmentation, l'étiquetage
en utilisant l'alphabet phonétique, et le calcul des statistiques. Praat est
configurable et extensible grâce à son propres langage de programmation et
contient des interfaces pour communiquer avec d'autres programmes.
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psignifit
ajuster et essayer des hypothèses sur les fonctions psychométriques
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Versions of package psignifit |
Release | Version | Architectures |
stretch | 2.5.6-3.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.5.6-3 | amd64,armel,armhf,i386 |
buster | 2.5.6-5 | amd64,arm64,armhf,i386 |
bullseye | 2.5.6-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.5.6-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.5.6-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.5.6-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package psignifit: |
field | statistics |
interface | commandline |
role | program |
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License: DFSG free
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Psignifit permet d'ajuster des fonctions psychométriques à des jeux de données tout en gardant le contrôle d'un grand nombre de paramètres. Les données peuvent être lues depuis des fichiers texte ou à l’aide de l'entrée standard.
Le programme effectue le calcul des intervalles de confiance ainsi que de des tests de qualité de l'ajustement.
Ce paquet fournit la version en ligne de commande.
Remarque : il s’agit de l’ancienne version 2.x de psignifit.
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python3-nibabel
liaisons de Python 3 vers divers formats de données d’image cérébrale
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Versions of package python3-nibabel |
Release | Version | Architectures |
buster | 2.3.2-1 | all |
bullseye | 3.2.1-2 | all |
bookworm | 5.0.0-2 | all |
trixie | 5.2.1-2 | all |
stretch | 2.1.0-1 | all |
sid | 5.2.1-2 | all |
upstream | 5.3.2 |
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License: DFSG free
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NiBabel permet de lire et écrire quelques formats médicaux communs et de
neuro-imagerie, dont ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC,
ainsi que PAR/REC. Les diverses classes de format d’image procurent un
accès total et sélectif aux (méta)informations d’en-tête et l’accès aux
données d’image est rendu disponible à travers des tableaux de NumPy.
NiBabel est le successeur de PyNIfTI.
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python3-pydicom
DICOM medical file reading and writing (Python 3)
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Versions of package python3-pydicom |
Release | Version | Architectures |
buster | 1.2.1-1 | all |
bookworm | 2.3.1-1 | all |
sid | 2.4.3-1 | all |
trixie | 2.4.3-1 | all |
bullseye | 2.0.0-1 | all |
upstream | 3.0.1 |
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License: DFSG free
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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.
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python3-pyxnat
Interface to access neuroimaging data on XNAT servers
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Versions of package python3-pyxnat |
Release | Version | Architectures |
bookworm | 1.5-2 | all |
trixie | 1.6.2-2 | all |
sid | 1.6.2-2 | all |
bullseye | 1.4-1 | all |
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License: DFSG free
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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
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python3-statsmodels
Python3 module for the estimation of statistical models
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Versions of package python3-statsmodels |
Release | Version | Architectures |
trixie | 0.14.4+dfsg-1 | all |
bookworm | 0.13.5+dfsg-7 | all |
bullseye | 0.12.2-1 | all |
stretch-backports | 0.8.0-9~bpo9+1 | all |
buster | 0.8.0-9 | all |
sid | 0.14.4+dfsg-1 | all |
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License: DFSG free
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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)
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qnifti2dicom
convert 3D medical images to DICOM 2D series (gui)
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Versions of package qnifti2dicom |
Release | Version | Architectures |
bullseye | 0.4.11-3 | amd64,i386 |
stretch | 0.4.11-1 | amd64,i386 |
jessie | 0.4.9-1 | amd64,armel,armhf,i386 |
buster | 0.4.11-1 | amd64,i386 |
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License: DFSG free
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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.
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voxbo
traitement, analyse statistique et affichage de données d’imagerie cérébrale
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Versions of package voxbo |
Release | Version | Architectures |
stretch | 1.8.5~svn1246-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.8.5~svn1246-3 | amd64,arm64,armhf,i386 |
jessie | 1.8.5~svn1246-1.1 | amd64,armel,armhf,i386 |
Debtags of package voxbo: |
field | medicine:imaging |
role | program |
uitoolkit | qt |
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License: DFSG free
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Il s’agit d’une boîte à outils pour l’analyse des expériences d’imagerie par
résonance magnétique fonctionnelle (principalement fMRI) et la cartographie
basée sur les voxels de comportement de lésion. VoxBo prend en charge le GLM
modifié (pour les données autocorrélées), ainsi que le GLM standard pour les
données non autocorrélées. La boîte à outils est conçue pour être
interopérable avec entre autres, AFNI, FSL et SPM.
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xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)
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Versions of package xmedcon |
Release | Version | Architectures |
jessie | 0.13.0-2 | amd64,armel,armhf,i386 |
trixie | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.23.0-gtk3+dfsg-1+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.16.1+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 0.14.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.16.3+dfsg-1+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package xmedcon: |
field | biology |
interface | commandline, x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | converting |
works-with | image, image:raster |
x11 | application |
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License: DFSG free
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This project stands for Medical Image Conversion. Released under the
(L)GPL, it comes with the full C-source code of the library, a
flexible command line utility and a neat graphical front-end using
the GTK+ toolkit. The currently supported formats are: Acr/Nema 2.0,
Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.
The program also allows one to read unsupported files without
compression, to print pixel values or to extract/reorder specified
images. It is possible to retrieve the raw binary/ascii image arrays
or to write PNG for desktop applications.
This is the program version for X based on GTK+. Processes only one
file at a time.
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Official Debian packages with lower relevance
connectomeviewer
analyse interactive et visualisation pour la connectomique MR
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Versions of package connectomeviewer |
Release | Version | Architectures |
jessie | 2.1.0-1 | all |
buster | 2.1.0+dfsg-1 | all |
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License: DFSG free
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Connectome Viewer est un environnement extensible, scriptable et en python
de visualisation et d'analyse (de réseau) en neuro-imagerie et connectomique.
Grâce au format de fichier Connectome, divers types de données tels que les
réseaux, surfaces, volumes, traces et métadonnées sont gérés et intégrés.
Connectome Viewer fait partie de la boîte à outils MR Connectome.
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python-mvpa2
??? missing short description for package python-mvpa2 :-(
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Versions of package python-mvpa2 |
Release | Version | Architectures |
stretch | 2.6.0-1 | all |
jessie | 2.3.1-2 | all |
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License: DFSG free
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python3-bioxtasraw
traitement de données biologiques de diffusion des rayons X aux petits angles
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Versions of package python3-bioxtasraw |
Release | Version | Architectures |
sid | 2.3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 2.1.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
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BioXTAS RAW un programme graphique en Python pour la réduction et
l’analyse de diffusion des rayons X aux petits angles (SAXS – Small Angle
X-rays Scattering). Ce paquet est conçu pour des données biologiques SAXS.
BioXTAS RAW fournit un remplacement aux programmes source proches comme
Primus et Scatter pour l’analyse basique de données. Parce qu’il calibre,
masque et intègre des images, il fournit aussi une alternative aux
pipelines de faisceau de synchrotron que les scientifiques installent sur
leur propre ordinateur et utilisent à la maison et sur la ligne de
faisceau.
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science-psychophysics
paquets pour la psychophysique de Debian Science
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Versions of package science-psychophysics |
Release | Version | Architectures |
bookworm | 1.14.5 | all |
stretch | 1.7 | all |
trixie | 1.14.6 | all |
sid | 1.14.6 | all |
bullseye | 1.14.2 | all |
buster | 1.10 | all |
jessie | 1.4 | all |
Debtags of package science-psychophysics: |
role | metapackage |
suite | debian |
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License: DFSG free
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Ce métapaquet installe les paquets de Debian qui peuvent être utiles pour
accomplir des expériences relatives aux stimuli physiques et leurs effets
psychologiques.
Cette sélection de paquets concerne les logiciels d’exécution de stimulus.
Pour d’autres logiciels concernant l’analyse des données obtenues,
l’utilisateur recourra à science-neuroscience-cognitive, med-imaging en
fonction du domaine concerné. De plus, il regardera dans les paquets de
science-bci car ceux-ci fournissent souvent des structures de boucle
incluant la fourniture de stimulus.
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science-typesetting
paquets pour la composition typographique de Debian Science
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Versions of package science-typesetting |
Release | Version | Architectures |
bookworm | 1.14.5 | all |
jessie | 1.4 | all |
stretch | 1.7 | all |
buster | 1.10 | all |
bullseye | 1.14.2 | all |
sid | 1.14.6 | all |
trixie | 1.14.6 | all |
Debtags of package science-typesetting: |
role | metapackage |
suite | debian |
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License: DFSG free
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Ce métapaquet installe les paquets de Debian Science concernant la
composition typographique. L’utilisateur peut aussi être intéressé par
field::physics de debtag.
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Debian packages in contrib or non-free
fsl
transitional dummy package
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Versions of package fsl |
Release | Version | Architectures |
buster | 5.0.8-6 (non-free) | all |
jessie | 5.0.7-4 (non-free) | all |
Debtags of package fsl: |
field | medicine:imaging |
interface | commandline, x11 |
role | program |
uitoolkit | tk |
use | analysing |
x11 | application |
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License: non-free
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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)
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Packaging has started and developers might try the packaging code in VCS
bioimagesuite
integrated image analysis software suite
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Versions of package bioimagesuite |
Release | Version | Architectures |
VCS | 2.0-1 | all |
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License: GPL-2+
Debian package not available
Version: 2.0-1
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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.
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debruijn
De Bruijn cycle generator
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Versions of package debruijn |
Release | Version | Architectures |
VCS | 1.6-2 | all |
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License: BSD-4-clause
Version: 1.6-2
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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.
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freesurfer
analysis and visualization of functional brain imaging data
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Versions of package freesurfer |
Release | Version | Architectures |
VCS | 5.1.0+dev+cvs20120104-1 | all |
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License: FreeSurfer-Software-License-Agreement
Version: 5.1.0+dev+cvs20120104-1
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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.
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openmeeg-tools
openmeeg library -- command line tools
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Versions of package openmeeg-tools |
Release | Version | Architectures |
VCS | 2.4.2-1 | all |
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License: CeCILL-B
Debian package not available
Version: 2.4.2-1
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OpenMEEG consists of state-of-the art solvers for forward problems in
the field of MEG and EEG. Solvers are based on the symmetric
Boundary Element method [Kybic et al, 2005], providing excellent
accuracy, particularly for superficial cortical sources. OpenMEEG can
compute four types of lead fields (EEG, MEG, Internal Potential and
Electrical Impedence Tomography).
This package provides command line interface to openmeeg functionality.
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slicer
software package for visualization and image analysis - main application
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Versions of package slicer |
Release | Version | Architectures |
VCS | 4.10.2-1 | all |
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License: free
Debian package not available
Version: 4.10.2-1
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Slicer is an application for computer scientists and clinical researchers. The
platform provides functionality for segmentation, registration and
three-dimensional visualization of multi-modal image data, as well as advanced
image analysis algorithms for diffusion tensor imaging, functional magnetic
resonance imaging and image-guided therapy. Standard image file formats are
supported, and the application integrates interface capabilities to biomedical
research software and image informatics frameworks.
3D Slicer main application.
Please cite:
Steven Pieper, Michael Halle, Ron Kikinis:
3D SLICER.
(2004)
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xnat
platform for data management and productivity tasks in neuroimaging
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Versions of package xnat |
Release | Version | Architectures |
VCS | 1.7.5.1-1 | all |
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License: XNAT_SLA
Debian package not available
Version: 1.7.5.1-1
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The primary functionality of XNAT is to provide a place to store and
control access to neuroimaging data. This includes sophisticated user
control, search and retrieval, and archiving capabilities. As
open-source software, XNAT also supports a wide variety of
research-based processing pipelines, and is able to link up with
supercomputer processing power to dramatically shorten image
processing time.
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Unofficial packages built by somebody else
eeglab
toolbox for processing and visualization of electrophysiological data
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License: GPL-2+
Language: C, Matlab/Octave
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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)
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mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
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License: no-free, but GPLed parts
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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.
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mni-n3
MNI Non-parametric Non-uniformity Normalization
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License: BSDish
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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.
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No known packages available but some record of interest (WNPP bug)
toolbox for MEG and EEG analysis
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License: GPL-2+
Debian package not available
Language: Matlab/Octave
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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.
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visualize Freesurfer's data in Python
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License: BSD-3
Debian package not available
Language: Python
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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.
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analysis of brain imaging data sequences
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License: GPL-2+
Debian package not available
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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.
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No known packages available
brainvisa
image processing factory for MR images
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License: Free? (CeCill License)
Debian package not available
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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.
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hid
database management system for clinical imaging
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License: BSD, BIRN
Debian package not available
Language: java
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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)
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iqr
large-scale multi-level neuronal systems simulator
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License: GPL-3+
Debian package not available
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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.
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