Summary
Cognitive Neuroscience
Debian Science packages for Cognitive Neuroscience
This metapackage will install Debian packages which might be useful for
scientists doing cognitive neuroscience research. This comprises the full
research process from conducting psychophysical experiments, over data
acquisition and analysis, to visualization and typesetting of scientific
results.
The selection of packages is targeting the application of analysis
techniques. Methods developers are referred to the science-statistics,
science-imageanalysis, science-numericalcomputation, med-imaging, and
med-imaging-dev metapackages for a variety of additional software that
might be useful in the context of cognitive neuroscience.
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
software for Medical Imaging
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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 |
buster | 1.0.5-12 | amd64,arm64,armhf,i386 |
bookworm | 1.0.6-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.5-2 | amd64,armel,armhf,i386 |
stretch | 1.0.5-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.6-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.5-15 | amd64,arm64,armel,armhf,i386,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)
AMIDE is a tool for viewing and analyzing medical image data sets.
It's capabilities include the simultaneous handling of multiple data
sets imported from a variety of file formats, image fusion, 3D region
of interest drawing and analysis, volume rendering, and rigid body
alignments.
Amide imports most clinical DICOM files (using the DCMTK library).
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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 medical image files manipulation and conversion tools
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Versions of package dicom3tools |
Release | Version | Architectures |
sid | 1.00~20240118131615-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.00~20140902075059-1 | amd64,armel,armhf,i386 |
stretch | 1.00~20170109062447-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.00~20180803063840-1 | amd64,arm64,armhf,i386 |
bullseye | 1.00~20190724083540-1 | 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 |
bookworm | 1.00~20220618093127-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.00~20240118131615-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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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Command line utilities for creating, modifying, dumping and validating
files of DICOM attributes. Support conversion of some proprietary medical
image formats to DICOM. Can handle older ACR/NEMA format data, and some
proprietary versions of that such as SPI.
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dicomnifti
??? missing short description for package dicomnifti :-(
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Versions of package dicomnifti |
Release | Version | Architectures |
bookworm | 2.33.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.32.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.33.1-1 | amd64,arm64,armhf,i386 |
jessie | 2.32.1-1 | amd64,armel,armhf,i386 |
bullseye | 2.33.1-2 | 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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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
semi-automatic segmentation of structures in 3D images
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Versions of package itksnap |
Release | Version | Architectures |
stretch | 3.4.0-2 | amd64,i386 |
buster | 3.6.0-3 | amd64,i386 |
jessie | 2.2.0-1.1 | amd64,armel,armhf,i386 |
bullseye | 3.6.0-5 | amd64,i386 |
Debtags of package itksnap: |
field | medicine:imaging |
role | program |
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License: DFSG free
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SNAP provides semi-automatic segmentation of structures in medical
images (e.g. magnetic resonance images of the brain) using active
contour methods, as well as manual delineation and image navigation.
Noteworthy features are:
- Linked cursor for seamless 3D navigation
- Manual segmentation in three orthogonal planes at once
- Support for many different 3D image formats, including NIfTI
- Support for concurrent, linked viewing and segmentation of multiple images
- Limited support for color images (e.g., diffusion tensor maps)
- 3D cut-plane tool for fast post-processing of segmentation results
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medcon
Medical Image (DICOM, ECAT, ...) conversion tool
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Versions of package medcon |
Release | Version | Architectures |
bookworm | 0.23.0-gtk3+dfsg-1+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.13.0-2 | amd64,armel,armhf,i386 |
stretch | 0.14.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.16.1+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 0.16.3+dfsg-1+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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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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 command line tool for batch processing.
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minc-tools
MNI medical image format tools
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Versions of package minc-tools |
Release | Version | Architectures |
sid | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.2.00-6 | amd64,armel,armhf,i386 |
bookworm | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.3.00+dfsg-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.3.00+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.00+dfsg-3 | amd64,arm64,armhf,i386 |
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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This package contains tools to manipulate MINC files.
The Minc file format is a highly flexible medical image file format
built on top of the NetCDF generalized data format. The format is
simple, self-describing, extensible, portable and N-dimensional, with
programming interfaces for both low-level data access and high-level
volume manipulation. On top of the libraries is a suite of generic
image-file manipulation tools. The format, libraries and tools are
designed for use in a medical-imaging research environment: they are
simple and powerful and make no attempt to provide a pretty interface
to users.
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mriconvert
??? missing short description for package mriconvert :-(
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Versions of package mriconvert |
Release | Version | Architectures |
buster | 2.1.0-3 | amd64,arm64,armhf,i386 |
bookworm | 2.1.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,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 |
Debtags of package mriconvert: |
field | medicine:imaging |
role | program |
uitoolkit | wxwidgets |
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License: DFSG free
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mricron
magnetic resonance image conversion, viewing and analysis
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Versions of package mricron |
Release | Version | Architectures |
bookworm | 1.2.20211006+dfsg-4 | 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 |
bullseye | 1.0.20190902+dfsg-2 | amd64,arm64,armel,armhf,i386,ppc64el |
buster | 0.20140804.1~dfsg.1-3 | amd64,arm64,armhf,i386 |
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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This is a GUI-based visualization and analysis tool for (functional) magnetic
resonance imaging. MRIcron can be used to create 2D or 3D renderings of
statistical overlay maps on brain anatomy images. Moreover, it aids drawing
anatomical regions-of-interest (ROI), or lesion mapping, as well as basic
analysis of functional timeseries (e.g. creating plots of peristimulus
signal-change).
In addition to 'mricron', this package also provides 'dcm2nii' that supports
converting DICOM and PAR/REC images into the NIfTI format, and 'npm' for
non-parametric data analysis.
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nifti-bin
tools shipped with the NIfTI library
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Versions of package nifti-bin |
Release | Version | Architectures |
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 |
bullseye | 3.0.1-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.0.0-2 | amd64,arm64,armel,armhf,i386,mips,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 is a set of i/o libraries for reading and writing files in the
NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical
image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI)
brain images.
This package provides the tools that are shipped with the library
(nifti_tool, nifti_stats and 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 |
jessie | 0.4.9-1 | amd64,armel,armhf,i386 |
stretch | 0.4.11-1 | amd64,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 includes the command line tools.
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praat
program for speech analysis and synthesis
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Versions of package praat |
Release | Version | Architectures |
stretch | 6.0.23-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 6.4.22+dfsg-1 | armhf |
jessie | 5.4.0-1 | amd64,armel,armhf,i386 |
sid | 6.4.23+dfsg-1 | amd64,arm64,armel,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 6.3.07-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 6.1.38-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 6.0.48-1 | amd64,arm64,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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According to its authors, praat is "doing phonetics by computer". Through
its graphical interface, several speech analysis functionalities are
available: spectrograms, cochleograms, and pitch and formant
extraction. Articulatory synthesis, as well as synthesis from pitch,
formant, and intensity are also available. Other features are
segmentation, labelling using the phonetic alphabet, and computation of
statistics. Praat is configurable and extensible through its own scripting
language and has provisions for communicating with other programs.
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psignifit
Fitting and testing hypotheses about psychometric functions
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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 |
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 |
bookworm | 2.5.6-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.5.6-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.5.6-5 | amd64,arm64,armhf,i386 |
jessie | 2.5.6-3 | amd64,armel,armhf,i386 |
Debtags of package psignifit: |
field | statistics |
interface | commandline |
role | program |
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License: DFSG free
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Psignifit allows fitting of psychometric functions to datasets while
maintaining full control over a large number of parameters. Data
can either be read from text files or passed through a pipe.
Psignifit performs the calculation of confidence intervals as well as
goodness-of-fit tests.
This is the command line version.
Please note: This is the legacy version 2.x of psignifit.
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python3-nibabel
Python3 bindings to various neuroimaging data formats
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Versions of package python3-nibabel |
Release | Version | Architectures |
sid | 5.2.1-2 | all |
stretch | 2.1.0-1 | all |
bullseye | 3.2.1-2 | all |
bookworm | 5.0.0-2 | all |
buster | 2.3.2-1 | all |
trixie | 5.2.1-2 | all |
upstream | 5.3.2 |
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License: DFSG free
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NiBabel provides read and write access to some common medical and
neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
NIfTI1, MINC, as well as PAR/REC. The various image format classes give full
or selective access to header (meta) information and access to the image data
is made available via NumPy arrays. NiBabel is the successor of PyNIfTI.
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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 |
sid | 2.4.3-1 | all |
bullseye | 2.0.0-1 | all |
bookworm | 2.3.1-1 | all |
trixie | 2.4.3-1 | 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 |
sid | 1.6.2-2 | all |
bookworm | 1.5-2 | all |
bullseye | 1.4-1 | all |
trixie | 1.6.2-2 | 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 |
stretch-backports | 0.8.0-9~bpo9+1 | all |
buster | 0.8.0-9 | all |
bullseye | 0.12.2-1 | all |
bookworm | 0.13.5+dfsg-7 | 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 |
stretch | 0.4.11-1 | amd64,i386 |
jessie | 0.4.9-1 | amd64,armel,armhf,i386 |
bullseye | 0.4.11-3 | amd64,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
processing, statistical analysis, and display of brain imaging data
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Versions of package voxbo |
Release | Version | Architectures |
jessie | 1.8.5~svn1246-1.1 | amd64,armel,armhf,i386 |
buster | 1.8.5~svn1246-3 | amd64,arm64,armhf,i386 |
stretch | 1.8.5~svn1246-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package voxbo: |
field | medicine:imaging |
role | program |
uitoolkit | qt |
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License: DFSG free
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This is a toolkit for analysis of functional neuroimaging (chiefly
fMRI) experiments and voxel-based lesion-behavior mapping. VoxBo
supports the modified GLM (for autocorrelated data), as well as the
standard GLM for non-autocorrelated data. The toolkit is designed to be
interoperable with AFNI, FSL, SPM and others.
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xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)
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Versions of package xmedcon |
Release | Version | Architectures |
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 |
trixie | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 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 |
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
Interactive Analysis and Visualization for MR Connectomics
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Versions of package connectomeviewer |
Release | Version | Architectures |
buster | 2.1.0+dfsg-1 | all |
jessie | 2.1.0-1 | all |
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License: DFSG free
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The Connectome Viewer is a extensible, scriptable, pythonic research
environment for visualization and (network) analysis in neuroimaging
and connectomics.
Employing the Connectome File Format, diverse data types such as
networks, surfaces, volumes, tracks and metadata are handled and
integrated. The Connectome Viewer is part of the MR Connectome Toolkit.
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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
process biological small angle scattering data
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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 is a GUI based, Python program for reduction and
analysis of small-angle X-ray solution scattering (SAXS) data.
The package is designed for biological SAXS data.
BioXTAS RAW provides an alternative to closed source programs
such as Primus and Scatter for primary data analysis. Because
it can calibrate, mask, and integrate images it also provides
an alternative to synchrotron beamline pipelines that scientists
can install on their own computers and use both at home and at
the beamline.
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science-psychophysics
Debian Science packages for Psychophysics
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Versions of package science-psychophysics |
Release | Version | Architectures |
sid | 1.14.6 | all |
jessie | 1.4 | all |
stretch | 1.7 | all |
bullseye | 1.14.2 | all |
bookworm | 1.14.5 | all |
buster | 1.10 | all |
trixie | 1.14.6 | all |
Debtags of package science-psychophysics: |
role | metapackage |
suite | debian |
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License: DFSG free
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This metapackage will install Debian packages which might be useful for
carrying out any experiment relating physical stimuli and their
psychological effects.
The selection of packages is targeting software for stimuli delivery.
For additional software related to the analysis of the acquired data
refer to science-neuroscience-cognitive, med-imaging depending on the
domain of application. Additionally look into
science-bci since those often provide a complete loop
frameworks including stimuli delivery.
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science-typesetting
Debian Science typesetting packages
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Versions of package science-typesetting |
Release | Version | Architectures |
trixie | 1.14.6 | all |
bullseye | 1.14.2 | all |
buster | 1.10 | all |
stretch | 1.7 | all |
jessie | 1.4 | all |
sid | 1.14.6 | all |
bookworm | 1.14.5 | all |
Debtags of package science-typesetting: |
role | metapackage |
suite | debian |
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License: DFSG free
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This metapackage will install Debian Science packages related to
typesetting. You might also be interested in the use::typesetting
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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