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
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
Program til medicinsk billedbehandling
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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 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).
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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
DICOM-medicinske billedfiler - manipulerings- og konverteringsværktøjer
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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 | 1.00~20241114112559 |
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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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.
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dicomnifti
konverterer DICOM-filer til NIfTI-formatet
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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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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.
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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
semiautomatisk segmentering af strukturer i 3D-billeder
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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 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
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medcon
Medicinsk billedkonverteringsværktøj (DICOM, ECAT, ...)
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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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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.
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minc-tools
Medicinsk billedformatværktøjer for MNI
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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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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.
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mriconvert
Redskab til konvertering af medicinske billedfiler
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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 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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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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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.
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nifti-bin
Værktøjer leveret med NIfTI-biblioteket
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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 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).
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nifti2dicom
Konverter 3D-medicinbilleder til DICOM 2D-serien
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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 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.
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praat
program for taleanalyse og -syntese
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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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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.
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psignifit
Tilpasser og tester hypoteser om psykometriske funktioner
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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 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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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 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.
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python3-pydicom
DICOM-medicinsk fillæsning og -skrivning - 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 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.
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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
Python 3-modul for estimering af statistiske modeller
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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 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)
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qnifti2dicom
Konverter 3D medicinske billeder til DICOM 2D-serier - grafisk brugerflade
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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 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.
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voxbo
Behandling, statistisk analyse og billedvisning af hjernedata
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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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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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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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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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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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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«.
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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
Behandl biologiske plotdata med lille vinkel
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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 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.
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science-psychophysics
Debian Science - pakker for psykofysik
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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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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.
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science-typesetting
Debian Science - opsætningspakker
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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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Denne metapakke vil installere Debian Science-pakker relateret til
opsætning. Du er måske også interesseret i deb-mærket use::typesetting.
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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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