Debian Science Project
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

Debian Science Cognitive Neuroscience packages

Official Debian packages with high relevance

amide
software for Medical Imaging
Versions of package amide
ReleaseVersionArchitectures
sid1.0.6-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster1.0.5-12amd64,arm64,armhf,i386
bookworm1.0.6-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie1.0.5-2amd64,armel,armhf,i386
stretch1.0.5-7amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
trixie1.0.6-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.0.5-15amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package amide:
fieldmedicine, medicine:imaging
roleprogram
Popcon: 31 users (15 upd.)*
Versions and Archs
License: DFSG free
Git

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).

Please cite: Andreas Markus Loening and Sanjiv Sam Gambhir: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis. (PubMed) Molecular Imaging 2(3):131-7 (2003)
Other screenshots of package amide
VersionURL
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17678/simage/large-deeb0fc832965282d8e7bd9a43b6065e.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17677/simage/large-8f7aaa9529343865541ebc968e464c74.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17676/simage/large-6cc9cfe18a76cd3b247214d8ae0339b6.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17675/simage/large-d5d4f705acb3ff24758ea101b026c05b.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17674/simage/large-7756276dad8ba12ceeacc79f2df9fa3e.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17673/simage/large-7640f62c8ac17498b7e825bdc3e3be71.png
0.9.1-2https://screenshots.debian.net/shrine/screenshot/356/simage/large-a3b9d7e99aafc8e159ad1288d6031445.png
Screenshots of package amide
caret
??? missing short description for package caret :-(
Versions of package caret
ReleaseVersionArchitectures
jessie5.6.4~dfsg.1-3amd64,armel,armhf,i386
Debtags of package caret:
roleprogram
uitoolkitqt
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git
Please cite: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon and Charles H. Anderson: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex. (PubMed,eprint) Journal of American Medical Informatics Association 8(5):443-459 (2001)
dicom3tools
DICOM medical image files manipulation and conversion tools
Versions of package dicom3tools
ReleaseVersionArchitectures
sid1.00~20240118131615-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie1.00~20140902075059-1amd64,armel,armhf,i386
stretch1.00~20170109062447-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.00~20180803063840-1amd64,arm64,armhf,i386
bullseye1.00~20190724083540-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye-backports1.00~20220120135102-1~bpo11+1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.00~20220618093127-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.00~20240118131615-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
upstream1.00~20241003103319
Debtags of package dicom3tools:
fieldmedicine, medicine:imaging
roleprogram
useconverting
works-withimage
Popcon: 24 users (12 upd.)*
Newer upstream!
License: DFSG free
Git

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.

dicomnifti
??? missing short description for package dicomnifti :-(
Versions of package dicomnifti
ReleaseVersionArchitectures
bookworm2.33.1-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.32.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.33.1-1amd64,arm64,armhf,i386
jessie2.32.1-1amd64,armel,armhf,i386
bullseye2.33.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package dicomnifti:
interfacecommandline
roleprogram
scopeutility
useconverting
Popcon: 9 users (8 upd.)*
Versions and Archs
License: DFSG free
Git
fslview
??? missing short description for package fslview :-(
Versions of package fslview
ReleaseVersionArchitectures
jessie4.0.1-4amd64,armel,armhf,i386
Debtags of package fslview:
interfacex11
made-ofhtml
roledocumentation, program
scopeutility
suitedebian
uitoolkitqt
useviewing
x11application
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git
Please cite: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady and P.M. Matthews: Advances in functional and structural MR image analysis and implementation as FSL. (PubMed) NeuroImage 23:208-219 (2004)
itksnap
semi-automatic segmentation of structures in 3D images
Versions of package itksnap
ReleaseVersionArchitectures
stretch3.4.0-2amd64,i386
buster3.6.0-3amd64,i386
jessie2.2.0-1.1amd64,armel,armhf,i386
bullseye3.6.0-5amd64,i386
Debtags of package itksnap:
fieldmedicine:imaging
roleprogram
Popcon: 2 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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
Please cite: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee and Guido Gerig: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 31:1116-1128 (2006)
Screenshots of package itksnap
medcon
Medical Image (DICOM, ECAT, ...) conversion tool
Versions of package medcon
ReleaseVersionArchitectures
bookworm0.23.0-gtk3+dfsg-1+deb12u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie0.13.0-2amd64,armel,armhf,i386
stretch0.14.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.16.1+dfsg-1amd64,arm64,armhf,i386
bullseye0.16.3+dfsg-1+deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie0.24.0-gtk3+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid0.24.0-gtk3+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package medcon:
fieldbiology
interfacecommandline
roleprogram
uitoolkitgtk
useconverting
works-withimage, image:raster
x11application
Popcon: 16 users (19 upd.)*
Versions and Archs
License: DFSG free
Git

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.

minc-tools
MNI medical image format tools
Versions of package minc-tools
ReleaseVersionArchitectures
sid2.3.00+dfsg-10amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie2.3.00+dfsg-10amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie2.2.00-6amd64,armel,armhf,i386
bookworm2.3.00+dfsg-10amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.3.00+dfsg-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.3.00+dfsg-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.3.00+dfsg-3amd64,arm64,armhf,i386
Debtags of package minc-tools:
fieldmedicine, medicine:imaging
interfacecommandline
roleprogram
scopeutility
useanalysing, converting
works-withimage, image:raster
Popcon: 8 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

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.

mriconvert
??? missing short description for package mriconvert :-(
Versions of package mriconvert
ReleaseVersionArchitectures
buster2.1.0-3amd64,arm64,armhf,i386
bookworm2.1.0-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.1.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.0.7-2amd64,armel,armhf,i386
bullseye2.1.0-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package mriconvert:
fieldmedicine:imaging
roleprogram
uitoolkitwxwidgets
Popcon: 8 users (6 upd.)*
Versions and Archs
License: DFSG free
Git
Screenshots of package mriconvert
mricron
magnetic resonance image conversion, viewing and analysis
Versions of package mricron
ReleaseVersionArchitectures
bookworm1.2.20211006+dfsg-4amd64,arm64,armel,armhf,i386,ppc64el
stretch0.20140804.1~dfsg.1-2amd64,arm64,armel,armhf,i386
jessie0.20140804.1~dfsg.1-1amd64,armel,armhf,i386
bullseye1.0.20190902+dfsg-2amd64,arm64,armel,armhf,i386,ppc64el
buster0.20140804.1~dfsg.1-3amd64,arm64,armhf,i386
trixie1.2.20211006+dfsg-6amd64,arm64,armel,armhf,i386,ppc64el
sid1.2.20211006+dfsg-6amd64,arm64,armel,armhf,i386,ppc64el
Debtags of package mricron:
uitoolkitgtk
Popcon: 25 users (31 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Please cite: Chris Rorden, Hans-Otto Karnath and Leonardo Bonilha: Improving lesion-symptom mapping. (PubMed) Journal of Cognitive Neuroscience 19(7):1081-1088 (2007)
nifti-bin
tools shipped with the NIfTI library
Versions of package nifti-bin
ReleaseVersionArchitectures
jessie2.0.0-2amd64,armel,armhf,i386
sid3.0.1-9.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie3.0.1-9.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm3.0.1-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.0.1-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.0.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.0.0-3amd64,arm64,armhf,i386
Debtags of package nifti-bin:
fieldmedicine, medicine:imaging
interfacecommandline
roleprogram, shared-lib
scopeutility
usechecking, converting
Popcon: 8 users (20 upd.)*
Versions and Archs
License: DFSG free
Git

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).

nifti2dicom
convert 3D medical images to DICOM 2D series
Versions of package nifti2dicom
ReleaseVersionArchitectures
bullseye0.4.11-3amd64,i386
jessie0.4.9-1amd64,armel,armhf,i386
stretch0.4.11-1amd64,i386
buster0.4.11-1amd64,i386
Popcon: 0 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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.

praat
program for speech analysis and synthesis
Versions of package praat
ReleaseVersionArchitectures
stretch6.0.23-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid6.4.22+dfsg-1armhf
jessie5.4.0-1amd64,armel,armhf,i386
sid6.4.23+dfsg-1amd64,arm64,armel,i386,mips64el,ppc64el,riscv64,s390x
bookworm6.3.07-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye6.1.38-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster6.0.48-1amd64,arm64,i386
Debtags of package praat:
fieldlinguistics
interfacex11
roleprogram
scopeapplication
uitoolkitmotif
works-withaudio
x11application
Popcon: 20 users (21 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Please cite: Paul Boersma: Praat, a system for doing phonetics by computer. Glot International 5(9/10):341-345 (2001)
Screenshots of package praat
psignifit
Fitting and testing hypotheses about psychometric functions
Versions of package psignifit
ReleaseVersionArchitectures
stretch2.5.6-3.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
trixie2.5.6-8amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid2.5.6-8amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm2.5.6-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.5.6-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.5.6-5amd64,arm64,armhf,i386
jessie2.5.6-3amd64,armel,armhf,i386
Debtags of package psignifit:
fieldstatistics
interfacecommandline
roleprogram
Popcon: 3 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package psignifit
python3-nibabel
Python3 bindings to various neuroimaging data formats
Versions of package python3-nibabel
ReleaseVersionArchitectures
sid5.2.1-2all
stretch2.1.0-1all
bullseye3.2.1-2all
bookworm5.0.0-2all
buster2.3.2-1all
trixie5.2.1-2all
upstream5.3.2
Popcon: 31 users (23 upd.)*
Newer upstream!
License: DFSG free
Git

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.

python3-pydicom
DICOM medical file reading and writing (Python 3)
Versions of package python3-pydicom
ReleaseVersionArchitectures
buster1.2.1-1all
sid2.4.3-1all
bullseye2.0.0-1all
bookworm2.3.1-1all
trixie2.4.3-1all
upstream3.0.1
Popcon: 38 users (17 upd.)*
Newer upstream!
License: DFSG free
Git

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.

python3-pyxnat
Interface to access neuroimaging data on XNAT servers
Versions of package python3-pyxnat
ReleaseVersionArchitectures
sid1.6.2-2all
bookworm1.5-2all
bullseye1.4-1all
trixie1.6.2-2all
Popcon: 1 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

pyxnat is a simple Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or Python scripts to process the data. It features:

  • resources browsing capabilities
  • read and write access to resources
  • complex searches
  • disk-caching of requested files and resources
python3-statsmodels
Python3 module for the estimation of statistical models
Versions of package python3-statsmodels
ReleaseVersionArchitectures
trixie0.14.4+dfsg-1all
stretch-backports0.8.0-9~bpo9+1all
buster0.8.0-9all
bullseye0.12.2-1all
bookworm0.13.5+dfsg-7all
sid0.14.4+dfsg-1all
Popcon: 45 users (74 upd.)*
Versions and Archs
License: DFSG free
Git

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)
qnifti2dicom
convert 3D medical images to DICOM 2D series (gui)
Versions of package qnifti2dicom
ReleaseVersionArchitectures
stretch0.4.11-1amd64,i386
jessie0.4.9-1amd64,armel,armhf,i386
bullseye0.4.11-3amd64,i386
buster0.4.11-1amd64,i386
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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.

voxbo
processing, statistical analysis, and display of brain imaging data
Versions of package voxbo
ReleaseVersionArchitectures
jessie1.8.5~svn1246-1.1amd64,armel,armhf,i386
buster1.8.5~svn1246-3amd64,arm64,armhf,i386
stretch1.8.5~svn1246-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package voxbo:
fieldmedicine:imaging
roleprogram
uitoolkitqt
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package voxbo
xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)
Versions of package xmedcon
ReleaseVersionArchitectures
buster0.16.1+dfsg-1amd64,arm64,armhf,i386
stretch0.14.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.13.0-2amd64,armel,armhf,i386
trixie0.24.0-gtk3+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid0.24.0-gtk3+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm0.23.0-gtk3+dfsg-1+deb12u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.16.3+dfsg-1+deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package xmedcon:
fieldbiology
interfacecommandline, x11
roleprogram
scopeutility
uitoolkitgtk
useconverting
works-withimage, image:raster
x11application
Popcon: 15 users (19 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package xmedcon

Official Debian packages with lower relevance

connectomeviewer
Interactive Analysis and Visualization for MR Connectomics
Versions of package connectomeviewer
ReleaseVersionArchitectures
buster2.1.0+dfsg-1all
jessie2.1.0-1all
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

The Connectome Viewer is a extensible, scriptable, pythonic research environment for visualization and (network) analysis in neuroimaging and connectomics.

Employing the Connectome File Format, diverse data types such as networks, surfaces, volumes, tracks and metadata are handled and integrated. The Connectome Viewer is part of the MR Connectome Toolkit.

Please cite: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes. (2011)
python-mvpa2
??? missing short description for package python-mvpa2 :-(
Versions of package python-mvpa2
ReleaseVersionArchitectures
stretch2.6.0-1all
jessie2.3.1-2all
Popcon: 7 users (0 upd.)*
Versions and Archs
License: DFSG free
Git
The package is enhanced by the following packages: python-mdp python-sklearn
python3-bioxtasraw
process biological small angle scattering data
Versions of package python3-bioxtasraw
ReleaseVersionArchitectures
sid2.3.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64
bookworm2.1.1-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
Popcon: 2 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

BioXTAS RAW is a GUI based, Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The package is designed for biological SAXS data.

BioXTAS RAW provides an alternative to closed source programs such as Primus and Scatter for primary data analysis. Because it can calibrate, mask, and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.

science-psychophysics
Debian Science packages for Psychophysics
Versions of package science-psychophysics
ReleaseVersionArchitectures
sid1.14.6all
jessie1.4all
stretch1.7all
bullseye1.14.2all
bookworm1.14.5all
buster1.10all
trixie1.14.6all
Debtags of package science-psychophysics:
rolemetapackage
suitedebian
Popcon: 1 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

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.

science-typesetting
Debian Science typesetting packages
Versions of package science-typesetting
ReleaseVersionArchitectures
trixie1.14.6all
bullseye1.14.2all
buster1.10all
stretch1.7all
jessie1.4all
sid1.14.6all
bookworm1.14.5all
Debtags of package science-typesetting:
rolemetapackage
suitedebian
Popcon: 2 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

This metapackage will install Debian Science packages related to typesetting. You might also be interested in the use::typesetting debtag.

Debian packages in contrib or non-free

fsl
transitional dummy package
Versions of package fsl
ReleaseVersionArchitectures
buster5.0.8-6 (non-free)all
jessie5.0.7-4 (non-free)all
Debtags of package fsl:
fieldmedicine:imaging
interfacecommandline, x11
roleprogram
uitoolkittk
useanalysing
x11application
Popcon: 0 users (0 upd.)*
Versions and Archs
License: non-free
Git

The only purpose of this package is to enable upgrades to the new 'fsl-core' package which replaces 'fsl'. This package can safely be removed.

Users aiming to perform a complete FSL installation (including all data components) are advised to install the 'fsl-complete' package from NeuroDebian.

Please cite: Mark Jenkinson, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich and Stephen M. Smith: FSL. (PubMed) NeuroImage 62(2):782-790 (2012)

Packaging has started and developers might try the packaging code in VCS

bioimagesuite
integrated image analysis software suite
Versions of package bioimagesuite
ReleaseVersionArchitectures
VCS2.0-1all
Versions and Archs
License: GPL-2+
Debian package not available
Git
Version: 2.0-1

BioImage Suite has extensive capabilities for both neuro/cardiac and abdominal image analysis and state of the art visualization. Many packages are available that are highly extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. It can be integrated with other biomedical image processing software, such as FSL and SPM. This site provides information, downloads, documentation, and other resources for users of the software.

BioImage Suite was developed at Yale University and has been extensively used at different labs at Yale since 2004.

Please cite: X. Papademetris, M. Jackowski, N. Rajeevan, R. T. Constable and L. Staib: BioImage Suite: An integrated medical image analysis suite. (eprint) Insight Journal (2005)
Remark of Debian Science team: How to work together with upstream

There is a forum at BioImage Suite site for discussion of compiling it from source and packaging issues at http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0

debruijn
De Bruijn cycle generator
Versions of package debruijn
ReleaseVersionArchitectures
VCS1.6-2all
Versions and Archs
License: BSD-4-clause
Git
Version: 1.6-2

Stimulus counter-balance is important for many experimental designs. This command-line software creates De Bruijn cycles, which are pseudo-random sequences with arbitrary levels of counterbalance. "Path-guided" de Bruijn cycles may also be created. These sequences encode a hypothesized neural modulation at specified temporal frequencies, and have enhanced detection power for BOLD fMRI experiments.

freesurfer
analysis and visualization of functional brain imaging data
Versions of package freesurfer
ReleaseVersionArchitectures
VCS5.1.0+dev+cvs20120104-1all
Versions and Archs
License: FreeSurfer-Software-License-Agreement
Git
Version: 5.1.0+dev+cvs20120104-1

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. It contains a fully automatic structural stream for processing cross sectional and longitudinal data.

FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with an sterotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures, etc.

This package depends upon the latest version of freesurfer.

Please cite: A. M. Dale, B. Fischl and M. I. Sereno: Cortical surface-based analysis. I. Segmentation and surface reconstruction. (PubMed) Neuroimage 9(2):179-94 (1999)
Remark of Debian Science team: The 'tktools' (tkmedit, tksurfer and tkregister2) under the
 CorTechs license are not readily redistributable thus excluded.
openmeeg-tools
openmeeg library -- command line tools
Versions of package openmeeg-tools
ReleaseVersionArchitectures
VCS2.4.2-1all
Versions and Archs
License: CeCILL-B
Debian package not available
Git
Version: 2.4.2-1

OpenMEEG consists of state-of-the art solvers for forward problems in the field of MEG and EEG. Solvers are based on the symmetric Boundary Element method [Kybic et al, 2005], providing excellent accuracy, particularly for superficial cortical sources. OpenMEEG can compute four types of lead fields (EEG, MEG, Internal Potential and Electrical Impedence Tomography).

This package provides command line interface to openmeeg functionality.

Please cite: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi and Maureen Clerc: OpenMEEG: opensource software for quasistatic bioelectromagnetics. (PubMed,eprint) BioMedical Engineering OnLine 9:45 (2010)
slicer
software package for visualization and image analysis - main application
Versions of package slicer
ReleaseVersionArchitectures
VCS4.10.2-1all
Versions and Archs
License: free
Debian package not available
Git
Version: 4.10.2-1

Slicer is an application for computer scientists and clinical researchers. The platform provides functionality for segmentation, registration and three-dimensional visualization of multi-modal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software and image informatics frameworks.

3D Slicer main application.

Please cite: Steven Pieper, Michael Halle, Ron Kikinis: 3D SLICER. (2004)
xnat
platform for data management and productivity tasks in neuroimaging
Versions of package xnat
ReleaseVersionArchitectures
VCS1.7.5.1-1all
Versions and Archs
License: XNAT_SLA
Debian package not available
Git
Version: 1.7.5.1-1

The primary functionality of XNAT is to provide a place to store and control access to neuroimaging data. This includes sophisticated user control, search and retrieval, and archiving capabilities. As open-source software, XNAT also supports a wide variety of research-based processing pipelines, and is able to link up with supercomputer processing power to dramatically shorten image processing time.

Please cite: Daniel S. Marcus, Timothy R. Olsen, Mohana Ramaratnam and Randy L. Buckner: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data.. (PubMed,eprint) Neuroinformatics 5(1):11-34 (2007)

Unofficial packages built by somebody else

eeglab
toolbox for processing and visualization of electrophysiological data
Responsible: NeuroDebian Team
License: GPL-2+
Language: C, Matlab/Octave

EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.

Please register by following this link if you are using eeglab.
Please cite: Delorme A and Makeig S: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics (2004)
mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
Responsible: Michael Hanke
License: no-free, but GPLed parts

This package provides a version of the MNI Average Brain (an average of 305 T1-weighted MRI scans, linearly transformed to Talairach space) specially adapted for use with the MNI Linear Registration Package.

  • average_305.mnc - a version of the average MRI that covers the whole brain (unlike the original Talairach atlas), sampled with 1mm cubic voxels
  • average_305_mask.mnc - a mask of the brain in average_305.mnc
  • average_305_headmask.mnc - another mask, required for nonlinear mode

Remark: Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg and http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg-model to Debian Med svn and start group maintenance.

mni-n3
MNI Non-parametric Non-uniformity Normalization
Responsible: Michael Hanke
License: BSDish

MNI Non-parametric Non-uniformity Normalization (N3). This package provides the 'nu_correct' tool for unsupervised correction of radio frequency (RF) field inhomogenities in MR volumes. Two packages are provided:

  • mni-n3 - provides 'nu_correct'
  • libebtks-dev - MNI support library with numerical types and algorithms

Remark: Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-n3 to Debian Med svn and start group maintenance.

No known packages available but some record of interest (WNPP bug)

fieldtrip - wnpp
toolbox for MEG and EEG analysis
License: GPL-2+
Debian package not available
Language: Matlab/Octave

The software includes algorithms for simple and advanced analysis of MEG and EEG data, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing. It supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of the most popular EEG systems, and new formats can be added easily. FieldTrip contains high-level functions that you can use to construct your own analysis protocols in Matlab. Furthermore, it easily allows developers to incorporate low-level algorithms for new EEG/MEG analysis methods.

Remark of Debian Science team: The NIMH distributes a "port" of fieldtrip to Octave (at

http://kurage.nimh.nih.gov/meglab/Meg/Software). It needs to be figured out whether this port can be incorporated into the official version, and to what degree it is complete. Packaging fieldtrip is required to complete the packaging of SPM8.

pysurfer - wnpp
visualize Freesurfer's data in Python
Responsible: NeuroDebian Team
License: BSD-3
Debian package not available
Language: Python

This is a Python package for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data.

PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets.

spm8 - wnpp
analysis of brain imaging data sequences
Responsible: NeuroDebian team
License: GPL-2+
Debian package not available

Statistical Parametric Mapping (SPM) refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. It is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.

Please register by following this link if you are using spm8.
Please cite: Karl J. Friston, John T. Ashburner, Stephen Kiebel, Thomas E. Nichols and William D. Penny: Statistical Parametric Mapping: The Analysis of Functional Brain Images.. (2007)
Remark of Debian Science team: This software is written for matlab, but initial tests indicate that

some (significant) portion of it might also work with octave. More tests are pending...

No known packages available

brainvisa
image processing factory for MR images
License: Free? (CeCill License)
Debian package not available

BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of treatments on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are built the assembly lines of the factory. BrainVISA is distributed with a toolbox of building blocks dedicated to the segmentation of T1-weighted MR images. The product of the main assembly line made up from this toolbox is the following: grey/white classification for Voxel Based Morphometry, Meshes of each hemisphere surface for visualization purpose, Spherical meshes of each hemisphere white matter surface, a graph of the cortical folds, a labeling of the cortical folds according to a nomenclature of the main sulci.

hid
database management system for clinical imaging
License: BSD, BIRN
Debian package not available
Language: java

The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.

Please register by following this link if you are using hid.
Please cite: Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P.: A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN) (2008)
iqr
large-scale multi-level neuronal systems simulator
Responsible: NeuroDebian team
License: GPL-3+
Debian package not available

This graphical environment allows for designing large-scale multi-level neuronal systems that can control real-world devices, such as cameras and mobile robots, in real-time. iqr is an extensible framework with the ability to handle new, user-provided, neuron and synapse types, as well as custom interfaces to other hardware systems. iqr employes an XML-based format for system descriptions.

Please cite: Ulysses Bernardet, Paul F.M.J. Verschure: iqr: A tool for the construction of multi-level simulations of brain and behaviour.. (2010)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 246146