Supported linux software

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Summary: This is a table of supported Linux applications and environments in the MPI CBS internal network. Default operating system of newly installed or upgraded institute workstations is G7 (Generation 7) currently. Older computers with G6 setup are still in use.

Hints on how to use this page

  • This overview is auto-generated by the institute's software management system.
  • Use Ctrl+F find software on this page.
  • A stop symbol indicates no version for a certain platform generation.
  • For missing software or packages, submit a trouble ticket.
  • Linux software can be generally downloaded and evaluated/used without asking IT.
    • Choose an appropriate filesystem path for installation - e.g. /data/u_myusername_software
    • Consider requesting storage if needed.
  • Contact IT to permanently add a package to institute computers for reproducible research results.
  • IT can't test all software; report issues with a trouble ticket.
  • Avoid using outdated software for new work. See also DeathOfSoftware.
  • For home use, prefer software with 'free' in the license.
  • Default software release versions are shown separately per generation per SoftwareLinux. Additional ones might be available (see "more..." link).
  • There might be different types of deployment per software package. IT is favoring deb , scwrap and sc deployment types. afs is currently moved to nfs for performances reasons.

Deployment types

Type Description Advantages
deb Package is installed directly on the computer
  • Automatically embedded in the current environment
  • Easily installable on mobile computers
afs Package is installed in a network folder. This method will be retired in favor of nfs
  • Multiple releases are possible per computer generation.
  • Releases can be frozen which is cool, e.g. for long running studies.
  • For more information: SoftwareServiceLinux
nfs Like afs but faster
  • nfs is way faster than afs (programs start delay is low). All afs deployments will move to nfs over time.
  • For more information: SoftwareServiceLinux
sc Package installed in a software container in a network folder which can be run under user control (without root permissions).
Software is enabled or run via
user@host > sc [softwareid]
  • Platform generation independend
  • Multiple releases of a software can coexist.
  • Package is portable, e.g. for using it on MPCDF's Slurm cluster.
  • For more information: SoftwareServiceLinux
scwrap Identical to sc plus a wrapping mechanism ( SCWRAP ) which enables easily directly calling command families in a container from outside the container.
Enable containerized commands via
user@host > SCWRAP [softwareid]
  • Platform generation independent
  • Can be combined with other command families.

Software categories

Analysis

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Function Neuroimage analysis tools afni sc afni
SCWRAP afni 		home chart-bar free 22.1.09 (nfs)
24.3.08 (scwrap)
18.2.17 (nfs) 		23.2.03 (nfs)
24.3.08 (scwrap)
19.1.05 (nfs)
22.0.03 (nfs)
22.1.09 (nfs)
 24.3.08 (scwrap) 24.3.08 (scwrap)  
Normalisation tool ants sc ants
SCWRAP ants 		home chart-bar free 2.3.5 (nfs)
2.6.0 (sc)
2.6.0 (scwrap)
2.3.1 (nfs)
2.3.4 (sc)
2.3.5 (scwrap)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
2.5.4 (scwrap)
 2.3.5 (nfs)
2.6.0 (sc)
2.6.0 (scwrap)
2.3.4 (sc)
2.3.5 (scwrap)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
2.5.4 (scwrap)
 2.6.0 (sc)
2.6.0 (scwrap)
2.3.4 (sc)
2.3.5 (scwrap)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
2.5.4 (scwrap)
 2.6.0 (sc)
2.6.0 (scwrap)
2.3.4 (sc)
2.3.5 (scwrap)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
2.5.4 (scwrap)
  
Bart bart   home MRI reconstruction toolbox
chart-bar 		free 0.4.02 (deb)
0.9.00 (scwrap)
0.8.00 (scwrap)
0.8.00 (scwrap)
 0.9.00 (scwrap)
0.8.00 (scwrap)
0.8.00 (scwrap)
 0.9.00 (scwrap)
0.8.00 (scwrap)
0.8.00 (scwrap)
 0.9.00 (scwrap)
0.8.00 (scwrap)
0.8.00 (scwrap)
  
Brain image processing brainvisa sc brainvisa home chart-bar free 5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		 
MIPAV + some CBS specific plugins cbstools cbstools This software is maintained by Dr. Nico Scherf.
Warning: There's no revision management for this software. Results might not be reproducible.
chart-bar 		free/cbs 3.0 (nfs)
3.0 (sc)
3.1 (nfs) 		3.0 (nfs)
3.0 (sc)
3.1 (nfs) 		3.0 (sc) 3.0 (sc)  
Diffusion MRI Analysis dsistudio sc dsistudio home chart-bar free 2023.03.28 (sc)
2021.07 (sc)
2021.10.05 (sc)
2021.12.03 (sc)
2022.01.11 (sc)
 2023.03.28 (sc)
2021.07 (sc)
2021.10.05 (sc)
2021.12.03 (sc)
2022.01.11 (sc)
 2023.03.28 (sc)
2021.07 (sc)
2021.10.05 (sc)
2021.12.03 (sc)
2022.01.11 (sc)
 2023.03.28 (sc)
2021.07 (sc)
2021.10.05 (sc)
2021.12.03 (sc)
2022.01.11 (sc)
  
EEG data processing eeglab EEGLAB MATLAB matlab home chart-bar free/dependent stop stop 14.1.2b (nfs) stop  
EEP Tools eeptools EEPTOOLS This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar 		nodelocked stop 3.2.1 (afs) 3.2.1 (afs) stop  
Toolbox for MEG and EEG analysis fieldtrip FIELDTRIP home chart-bar free stop 0.20220623 (nfs)
0.20240110 (nfs) 		0.20250420 (nfs) stop  
FMRI preprocessing pipeline fmriprep sc fmriprep latest
sc fmriprep 		home chart-bar free 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
  
Brain MRI image processing and analysis freesurfer FREESURFER home chart-bar free 6.0.0p1 (nfs)
7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (nfs)
5.3.0 (sc)
7.0.0 (nfs)
7.1.0 (nfs)
 7.4.1 (nfs)
7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (nfs)
5.3.0 (sc)
6.0.0p1 (nfs)
7.1.0 (nfs)
7.2.0 (nfs)
7.3.2 (nfs)
 7.4.1 (nfs)
7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (sc)
7.1.0 (nfs)
 7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (sc) 		 
Analysis tools for fMRI, MRI and DTI brain imaging data fsl FSL
sc fsl
FSL 		home chart-bar
led-blue 		free 5.0.11 (nfs)
6.0.6 (sc)
6.0.6 (scwrap)
5.0.9 (nfs)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (nfs)
6.0.3 (scwrap)
6.0.4 (sc)
 6.0.3 (nfs)
6.0.6 (sc)
6.0.6 (scwrap)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (scwrap)
6.0.4 (sc)
6.0.7.7 (nfs)
6.0.7.11 (nfs)
 6.0.7.11 (nfs)
6.0.6 (sc)
6.0.6 (scwrap)
5.0.9 (sc)
6.0.3 (nfs)
6.0.3 (scwrap)
6.0.4 (sc)
6.0.7.13 (nfs)
 6.0.6 (sc)
6.0.6 (scwrap)
5.0.9 (sc)
6.0.3 (scwrap)
6.0.4 (sc)
  
Brain ALE-analyser "Gingerale" gingerale   home chart-bar free 3.0.2 (sc) 3.0.2 (sc) 3.0.2 (sc) 3.0.2 (sc)  
Reproducible fMRI analysis" halfpipe sc halfpipe home free 1.2.2 (sc) 1.2.2 (sc) 1.2.2 (sc) 1.2.2 (sc)  
3D image segmentation itksnap itksnap chart-bar free 3.8.0 (nfs)
4.2.2 (sc)
3.6.0 (nfs) 		3.8.0 (nfs)
4.2.2 (sc) 		4.2.2 (sc) 4.2.2 (sc)  
Commandline tools for fMRI analysis lipsia LIPSIA home Lipsia is a collection of tools for the analysis of fMRI data. Its main focus is on new algorithms such as statistical inference (LISA), Eigenvector centrality mapping (ECM) and network detection in task-fMRI (TED).
This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar 		free stop 0.20221118 (afs) stop stop  
SPM customizer make-spm-private make-spm-private Tool for quickly setting up a private SPM installation which can easily be modified free stop stop stop stop  
Volumetric image viewer/editor/analyzer mango   home This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar 		free 4.1 (sc) 4.1 (sc) 4.1 (sc) 4.1 (sc)  
MNI medical image format tools minc-tools dpkg -L minc-tools | grep bin home free 2.3.00 (deb) 2.3.00 (deb) 2.3.00 (deb) stop  
Medical Image Processing mipav mipav chart-bar free 8.0.2 (nfs)
11.3.2 (sc) 		11.0.3 (nfs)
11.3.2 (sc) 		11.3.2 (sc) 11.3.2 (sc)  
Medical Image Registration ToolKit mirtk     free stop 0.20231123 (afs) stop stop  
MEG source localization mne MNE home chart-bar free stop 2.7.4 (nfs) 2.7.4 (nfs) stop  
IQM extraction from MRI images mriqc sc mriqc latest
sc mriqc 		home chart-bar free 24.0.2 (sc)
0.16.1 (sc) 		24.0.2 (sc)
0.16.1 (sc) 		24.0.2 (sc)
0.16.1 (sc) 		24.0.2 (sc)
0.16.1 (sc) 		 
Software package of the Bennewitz Elekta MEG machine neuromag   chart-bar nodelocked 7 (scwrap) 7 (scwrap) 7 (scwrap) 7 (scwrap)  
Development, simmulation and test of magnetic resonance sequences odin     free stop 2.0.4 (deb) 2.0.5 (deb) stop  
Speech analysis praat   home Manual(de) free 6.0.37 (deb) 6.1.38 (deb) 6.3.07 (deb) 6.4.27 (deb)  
Preprocessing and analysis if q-space images qsiprep sc dsistudio home chart-bar free 0.16.0RC3/ (sc)
0.14.3 (sc)
0.15.4 (sc)
0.16.0RC3 (sc)
 0.16.0RC3/ (sc)
0.14.3 (sc)
0.15.4 (sc)
0.16.0RC3 (sc)
 0.16.0RC3/ (sc)
0.14.3 (sc)
0.15.4 (sc)
0.16.0RC3 (sc)
 0.16.0RC3/ (sc)
0.14.3 (sc)
0.15.4 (sc)
0.16.0RC3 (sc)
  
Statistical analysis of brain imaging data in Matlab with "SPM" spm spm home chart-bar free/dependent stop 12.7771 (nfs) 12.7771 (nfs) 12.7771 (nfs)  
White matter segmentation tool tractseg sc tractseg home chart-bar free 2.8 (sc) 2.8 (sc) 2.8 (sc) 2.8 (sc)  
Symbolic algebra tool wxmaxima   home Software is no longer provided centrally since there seems to be no interest on the users' end. Please tell us, if we're wrong. free 18.02.0 (deb) 20.12.1 (deb) stop stop Mathematica

Statistical analysis software

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Statistical analysis jasp jasp home chart-bar free 0.16.4 (sc) 0.16.4 (sc) 0.16.4 (sc) 0.16.4 (sc)  
Spread sheet processing libreoffice   home Find a guide on effective writing with Libreoffice at https://designingwithlibreoffice.com/
chart-bar 		free stop 7.0.4 (deb) 7.4.7 (deb) stop MS Office
R statistical language r R+ home chart-bar free 4.2.0 (nfs)
4.1.2 (nfs) 		4.4.0 (nfs)
4.1.2 (nfs)
4.2.0 (nfs)
4.2.2 (nfs)
4.3.2 (nfs)
4.3.3 (nfs)
 4.5.0 (nfs)
4.0.0 (nfs)
4.4.1 (nfs)
4.4.3 (nfs)
4.5.1 (nfs)
 stop  
R statistical language GUI rstudio R+ rstudio home chart-bar free 2022.12.0 (deb) 2024.12.1 (deb) 2025.05.1 (deb) stop  
IBM SPSS Statistics spss   chart-bar floating 24fp1 (sc) 24fp1 (sc) 24fp1 (sc) 24fp1 (sc)  

Conversion tools

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
3D image conversion convert3d C3D chart-bar free stop stop 1.0.0 (afs) stop  
Dicom to Nifti conversion dcm2niix dcm2niix   free stop 1.0.20240202 (deb) 1.0.20240202 (deb) stop  
Handling and conversion of scientific data in HDF5 format h5utils   home free 1.13 (deb) 1.13.1 (deb) 1.13.2 (deb) stop  
Fast (Multi-Core) video conversion tool (CLI) handbrake-cli handbrake-cli home free 1.2.1 (deb) 1.4.1 (deb) 1.6.1 (deb) stop  
Fast (Multi-Core) video conversion tool handbrake-gtk ghb home free 1.2.1 (deb) 1.4.1 (deb) stop 1.9.2 (deb)  
DICOM converter heudiconv sc heudiconv
sc heudiconv 		home free 0.9.0 (sc) 0.9.0 (sc) 0.9.0 (sc) 0.9.0 (sc)  
2D Image batch convertion tool "convert" imagemagick convert source.gif target.png home free 6.9.7.4 (deb) 6.9.11.60 (deb) 6.9.11.60 (deb) stop  
Multiformat MRI data processing isis-utils isisconv ...   free/cbs 0.7.17 (deb) 0.9.1 (deb) 0.10.2 (deb) stop  
Dicom to Nifti conversion (deprecated) mricron dcm2nii chart-bar free 20160222 (nfs)
20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		20160222 (nfs)
20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		 

Software development

Development GUIs

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Visual Studio Code, Development IDE. Please use 'codium' instead. code code home This software is only available for compatibility reasons but should not be used at the @MPI/CBS. Please use an alternative package! free stop 1.98.1 (deb) stop stop  
Visual Studio Code fork without tracking and telemetry, Development IDE codium codium home free stop stop 1.103.15418 (deb) stop  
IDL GUI idl idlde home chart-bar floating 8.1 (afs) 8.1 (afs) 8.1 (afs) 8.1 (afs)  
Interactive python environment ipython3 ipython3 home free 5.5.0 (deb) 7.20.0 (deb) 8.5.0 (deb) stop  
Matlab interactive GUI matlab MATLAB matlab home chart-bar floating 9.12 (nfs)
7.14 (nfs)
9.0 (nfs)
9.1 (nfs)
9.2 (nfs)
9.3 (nfs)
9.4 (nfs)
9.5 (nfs)
9.6 (nfs)
9.7 (nfs)
9.8 (nfs)
9.9 (nfs)
9.10 (nfs)
9.11 (nfs)
 24.1 (nfs)
8.3 (nfs)
9.0 (nfs)
9.1 (nfs)
9.2 (nfs)
9.3 (nfs)
9.4 (nfs)
9.5 (nfs)
9.6 (nfs)
9.7 (nfs)
9.8 (nfs)
9.9 (nfs)
9.10 (nfs)
9.11 (nfs)
9.12 (nfs)
9.13 (nfs)
9.14 (nfs)
9.14u3 (nfs)
9.15 (nfs)
9.16 (nfs)
23.2 (nfs)
 25.1 (nfs)
9.4 (nfs)
9.10 (nfs)
9.11 (nfs)
9.12 (nfs)
9.13 (nfs)
9.15 (nfs)
9.16 (nfs)
9.17 (nfs)
23.2 (nfs)
24.1 (nfs)
24.2 (nfs)
 25.1 (nfs)  
Octave interactive GUI octave OCTAVE+ octave --force-gui home chart-bar free 4.2.2 (deb) 6.2.0 (deb)
8.2.0 (nfs)
5.1.0 (nfs)
6.4.0 (nfs)
 10.2.0 (nfs) stop  
Python development GUI pycharm pycharm+ home free 2022.1.1 (nfs)
2021.3.2 (nfs) 		2024.1 (nfs)
2021.3.2 (nfs)
2022.1.1 (nfs)
2023.3.2 (nfs)
2023.3.4 (nfs)
 2025.1.3 (nfs)
2024.2.1 (nfs) 		stop  
Python development GUI (Pro edition) pycharm-pro pycharm-pro home Please be aware that this only includes the software installation. No license is provided by the institute. personal 2022.1.1 (nfs)
2021.3.2 (nfs) 		2024.1 (nfs)
2021.3.2 (nfs)
2022.1.1 (nfs)
2023.1.4 (nfs)
2023.2.3 (nfs)
2023.3.2 (nfs)
2023.3.4 (nfs)
 2025.1.3 (nfs)
2024.2.1 (nfs) 		stop  
R interactive GUI rstudio R+ rstudio home chart-bar free 2022.12.0 (deb) 2024.12.1 (deb) 2025.05.1 (deb) stop  
Python3 development GUI spyder spyder   free 3.2.6 (deb) 4.2.1 (deb) 5.4.2 (deb) stop  

Programming languages

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Custom python environment custompython CUSTOMPYTHON Starts a custom python environment (custom library versions). This environment will be stored in a personal software-specific storage block. free - - - -  
IDL idl idl home chart-bar floating 8.1 (afs) 8.1 (afs) 8.1 (afs) 8.1 (afs)  
Julia programming language julia JULIA home chart-bar free 1.11.5 (sc) 1.5.3 (deb)
1.11.5 (sc) 		1.11.5 (sc) 1.11.5 (sc)  
Matlab programming language matlab MATLAB matlab -nojvm home chart-bar floating 9.12 (nfs)
7.14 (nfs)
9.0 (nfs)
9.1 (nfs)
9.2 (nfs)
9.3 (nfs)
9.4 (nfs)
9.5 (nfs)
9.6 (nfs)
9.7 (nfs)
9.8 (nfs)
9.9 (nfs)
9.10 (nfs)
9.11 (nfs)
 24.1 (nfs)
8.3 (nfs)
9.0 (nfs)
9.1 (nfs)
9.2 (nfs)
9.3 (nfs)
9.4 (nfs)
9.5 (nfs)
9.6 (nfs)
9.7 (nfs)
9.8 (nfs)
9.9 (nfs)
9.10 (nfs)
9.11 (nfs)
9.12 (nfs)
9.13 (nfs)
9.14 (nfs)
9.14u3 (nfs)
9.15 (nfs)
9.16 (nfs)
23.2 (nfs)
 25.1 (nfs)
9.4 (nfs)
9.10 (nfs)
9.11 (nfs)
9.12 (nfs)
9.13 (nfs)
9.15 (nfs)
9.16 (nfs)
9.17 (nfs)
23.2 (nfs)
24.1 (nfs)
24.2 (nfs)
 25.1 (nfs)  
Octave programming language octave OCTAVE+ octave --no-gui home chart-bar free 4.2.2 (deb) 6.2.0 (deb)
8.2.0 (nfs)
5.1.0 (nfs)
6.4.0 (nfs)
 10.2.0 (nfs) stop  
Perl programming language perl perl This language is great for crunching large amounts of text using simple and small scripts. However, it should not be used for computations or bigger projects. Use python3 for that. free 5.26.1 (deb) 5.32.1 (deb) 5.36.0 (deb) 5.40.1 (deb)  
Python programming language (Version 3) python3 python Some things are to consider when handling python packages - esp. when it comes to reproducibility. Read more at SoftwarePython . free 3.6.9 (deb) 3.9.2 (deb) 3.11.2 (deb) 3.13.5 (deb)  
R statistical language r R+ R home chart-bar free 4.2.0 (nfs)
4.1.2 (nfs) 		4.4.0 (nfs)
4.1.2 (nfs)
4.2.0 (nfs)
4.2.2 (nfs)
4.3.2 (nfs)
4.3.3 (nfs)
 4.5.0 (nfs)
4.0.0 (nfs)
4.4.1 (nfs)
4.4.3 (nfs)
4.5.1 (nfs)
 stop  

Software Libraries

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Cuda environment cuda CUDA This environment enables Cuda usage and development if your computer has the necessary hardware in it.
Version selection is possible but it's connected to hardware capabilities - not the the software platform.
chart-bar 		free stop stop stop stop  
Handling and conversion of scientific data in HDF5 format h5utils   home free 1.13 (deb) 1.13.1 (deb) 1.13.2 (deb) stop  
Nightres nighres sc nighres home Nighres is a Python package for processing of high-resolution neuroimaging data free 1.3.0 (sc) 1.3.0 (sc) 1.3.0 (sc) 1.3.0 (sc)  
Human pose detection openpose sc openpose home Realtime multi person pose detection free 1.7.1 (sc)
1.7.1 (sc) 		1.7.1 (sc)
1.7.1 (sc) 		1.7.1 (sc)
1.7.1 (sc) 		1.7.1 (sc)
1.7.1 (sc) 		 
Python extension for stimuly presentation psychopy PSYCHOPY home chart-bar free 1.85.3 (deb)
2021.2.3 (nfs)
2024.2.5 (sc)
3.0.0 (nfs)
3.1.3 (nfs)
2020.1.2 (nfs)
2020.2.10 (nfs)
2021.1.3 (nfs)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
 2023.2.3 (nfs)
2024.2.5 (sc)
2021.1.3 (nfs)
2021.2.3 (nfs)
2021.2.3 (sc)
2022.1.4 (nfs)
2022.2.3 (sc)
2022.2.4 (nfs)
2022.2.4 (sc)
2022.2.5 (nfs)
2023.1.0 (nfs)
2023.1.2 (nfs)
2023.1.3 (nfs)
2023.2.3 (sc)
2024.1.1 (nfs)
2024.2.5 (nfs)
2025.1.1 (sc)
 2024.2.5 (nfs)
2024.2.5 (sc)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
 2024.2.5 (sc)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
  
Matlab based stimuli presentation library psychtoolbox PSYCHTOOLBOX home chart-bar free 3.0.15 (nfs) 3.0.18.13 (nfs)
3.0.20.4 (nfs) 		3.0.20.4 (nfs) stop  
Python extention for computer vision and machine learning via Open CV python-opencv   Please use the CUSTOMPYTHON environment and install opencv-python using pip3.
This software was maintained centrally but is no more. 		free - - - -  
Python extension for efficiently handling sparse matrices python-sparse   home Please use the CUSTOMPYTHON environment and install sparse using pip3.
This software was maintained centrally but is no more. 		free 1.1.1 (deb) stop stop stop  
Python3 image processing python3-pil   This package is only mentioned here to have the local version on record. Feel free install you own release via the CUSTOMPYTHON method. free 5.1.0 (deb) 8.1.2 (deb) 9.4.0 (deb) 11.1.0 (deb)  
Python3 Package manager python3-pip   With PIP, users are able to install python packages with IT intervention. Use the CUSTOMPYTHON commant! free 9.0.1 (deb) 20.3.4 (deb) 23.0.1 (deb) stop  

Editors, Output-processing

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
PDF editor "Inkscape" inkscape inkscape home free stop 1.0.2 (deb) 1.2.2 (deb) stop Core Draw, Inkscape
Volumetric image viewer/editor/analyzer mango   home This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar 		free 4.1 (sc) 4.1 (sc) 4.1 (sc) 4.1 (sc)  
PDF manipulation tool (commandline) qpdf     free 8.0.2 (deb) 10.1.0 (deb) 11.3.0 (deb) stop  
PDF annotation tool xournal     free stop 0.4.8.2016 (deb) 0.4.8.2016 (deb) stop  

Text Editing software

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Simple text editor gedit   Simple text editor free 3.28.1 (deb) 3.38.1 (deb) 44.2 (deb) stop Notepad
Plattform feature-rich idependent editor jedit   home This editor is available for Linux,Mac and Windows.
Software is no longer provided centrally since there seems to be no interest on the users' end. Please tell us, if we're wrong.
chart-bar 		free stop 5.6.0 (afs) 5.7.0 (afs)
5.6.0 (afs) 		stop Jedit
Feature-rich text editor kate     free 17.12.3 (deb) 20.12.2 (deb) 22.12.3 (deb) stop Notepad++
Simple text editor kwrite     free 17.12.3 (deb) 20.12.2 (deb) 22.12.3 (deb) stop Notepad

Shell environments

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Function Neuroimage analysis tools afni SCWRAP afni home chart-bar free 22.1.09 (nfs)
24.3.08 (scwrap)
18.2.17 (nfs) 		23.2.03 (nfs)
24.3.08 (scwrap)
19.1.05 (nfs)
22.0.03 (nfs)
22.1.09 (nfs)
 24.3.08 (scwrap) 24.3.08 (scwrap)  
Brain image processing brainvisa   home chart-bar free 5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		 
3D image conversion convert3d C3D chart-bar free stop stop 1.0.0 (afs) stop  
Cuda environment cuda CUDA This environment enables Cuda usage and development if your computer has the necessary hardware in it.
Version selection is possible but it's connected to hardware capabilities - not the the software platform.
chart-bar 		free stop stop stop stop  
Toolbox for MEG and EEG analysis fieldtrip FIELDTRIP home chart-bar free stop 0.20220623 (nfs)
0.20240110 (nfs) 		0.20250420 (nfs) stop  
Brain MRI image processing and analysis freesurfer FREESURFER home chart-bar free 6.0.0p1 (nfs)
7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (nfs)
5.3.0 (sc)
7.0.0 (nfs)
7.1.0 (nfs)
 7.4.1 (nfs)
7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (nfs)
5.3.0 (sc)
6.0.0p1 (nfs)
7.1.0 (nfs)
7.2.0 (nfs)
7.3.2 (nfs)
 7.4.1 (nfs)
7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (sc)
7.1.0 (nfs)
 7.4.1 (sc)
7.4.1 (scwrap)
5.3.0 (sc) 		 
Commandline tools for fMRI analysis lipsia LIPSIA home Lipsia is a collection of tools for the analysis of fMRI data. Its main focus is on new algorithms such as statistical inference (LISA), Eigenvector centrality mapping (ECM) and network detection in task-fMRI (TED).
This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar 		free stop 0.20221118 (afs) stop stop  
Matlab programming environment matlab MATLAB home chart-bar floating 9.12 (nfs)
7.14 (nfs)
9.0 (nfs)
9.1 (nfs)
9.2 (nfs)
9.3 (nfs)
9.4 (nfs)
9.5 (nfs)
9.6 (nfs)
9.7 (nfs)
9.8 (nfs)
9.9 (nfs)
9.10 (nfs)
9.11 (nfs)
 24.1 (nfs)
8.3 (nfs)
9.0 (nfs)
9.1 (nfs)
9.2 (nfs)
9.3 (nfs)
9.4 (nfs)
9.5 (nfs)
9.6 (nfs)
9.7 (nfs)
9.8 (nfs)
9.9 (nfs)
9.10 (nfs)
9.11 (nfs)
9.12 (nfs)
9.13 (nfs)
9.14 (nfs)
9.14u3 (nfs)
9.15 (nfs)
9.16 (nfs)
23.2 (nfs)
 25.1 (nfs)
9.4 (nfs)
9.10 (nfs)
9.11 (nfs)
9.12 (nfs)
9.13 (nfs)
9.15 (nfs)
9.16 (nfs)
9.17 (nfs)
23.2 (nfs)
24.1 (nfs)
24.2 (nfs)
 25.1 (nfs)  
MEG source localization mne MNE home chart-bar free stop 2.7.4 (nfs) 2.7.4 (nfs) stop  
Octave programming language octave OCTAVE+ home chart-bar free 4.2.2 (deb) 6.2.0 (deb)
8.2.0 (nfs)
5.1.0 (nfs)
6.4.0 (nfs)
 10.2.0 (nfs) stop  
Scientific Client-Server-Visualisation paraview PARAVIEW+ home chart-bar
led-blue 		free 5.4.1 (deb) 5.9.0 (deb) 5.11.0 (deb) stop  
Speech analysis with "Praat" praat   home Manual(de) free 6.0.37 (deb) 6.1.38 (deb) 6.3.07 (deb) 6.4.27 (deb)  
Stimuly presentation environment "Psychopy" psychopy PSYCHOPY home chart-bar free 1.85.3 (deb)
2021.2.3 (nfs)
2024.2.5 (sc)
3.0.0 (nfs)
3.1.3 (nfs)
2020.1.2 (nfs)
2020.2.10 (nfs)
2021.1.3 (nfs)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
 2023.2.3 (nfs)
2024.2.5 (sc)
2021.1.3 (nfs)
2021.2.3 (nfs)
2021.2.3 (sc)
2022.1.4 (nfs)
2022.2.3 (sc)
2022.2.4 (nfs)
2022.2.4 (sc)
2022.2.5 (nfs)
2023.1.0 (nfs)
2023.1.2 (nfs)
2023.1.3 (nfs)
2023.2.3 (sc)
2024.1.1 (nfs)
2024.2.5 (nfs)
2025.1.1 (sc)
 2024.2.5 (nfs)
2024.2.5 (sc)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
 2024.2.5 (sc)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
  
Matlab based stimuli presentation library psychtoolbox PSYCHTOOLBOX home chart-bar free 3.0.15 (nfs) 3.0.18.13 (nfs)
3.0.20.4 (nfs) 		3.0.20.4 (nfs) stop  
Python3 Package manager python3-pip   With PIP, users are able to install python packages with IT intervention. Use the CUSTOMPYTHON commant! free 9.0.1 (deb) 20.3.4 (deb) 23.0.1 (deb) stop  
R environment r R+ home This environment is required, if you need a newer R-release than installed on your computer. Just type R+ .
chart-bar 		free 4.2.0 (nfs)
4.1.2 (nfs) 		4.4.0 (nfs)
4.1.2 (nfs)
4.2.0 (nfs)
4.2.2 (nfs)
4.3.2 (nfs)
4.3.3 (nfs)
 4.5.0 (nfs)
4.0.0 (nfs)
4.4.1 (nfs)
4.4.3 (nfs)
4.5.1 (nfs)
 stop  
Singularity builder scbuild SCBUILD Environment to build singularity containers in
chart-bar 		free stop stop stop stop  
SPM environment spm SPM MATLAB home This has to be used with matlab to be useful. The per-platform version list is not complete for SPM - only default versions are shown. Use SPM --versions to show all available releases.
chart-bar 		free/dependent stop 12.7771 (nfs) 12.7771 (nfs) 12.7771 (nfs)  

Access to external services

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Lookup journal papers by brain region sleuth   home chart-bar free 2.4 (afs)
2.3 (afs)
3.0.4 (afs)
 3.0.4 (afs) stop stop  

File management

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
File compression tool file-roller     free 3.28.0 (deb) 3.38.1 (deb) 43.0 (deb) stop  
Graphical storage usage analyzer filelight   home A tool for cleaning up storage areas.
Software is no longer provided centrally since there seems to be no interest on the users' end. Please tell us, if we're wrong. 		free 17.12.3 (deb) 20.12.0 (deb) stop stop  
Image browser geeqie   home free 1.4 (deb) 1.6 (deb) 2.0.1 (deb) stop  
Text based Filemanager "Midnight Commander" mc   home This is the fastest file manager out there. It's text based, mouse controllable and has a lot of easy to learn keyboard shortcuts. There's a CBS-Cheatsheet available. free 4.8.19 (deb) 4.8.26 (deb) 4.8.29 (deb) 4.8.33 (deb)  
Graphical storage usage analyzer qdirstat   home A tool for cleaning up storage areas by identifying big folders/files inside of directory structures. free 1.4 (deb) 1.7 (deb) 1.8.1 (deb) stop  
Graphical file manager "Thunar" thunar   If you need a graphical file manager on a G5+ computer, use this one! free 1.6.15 (deb) 4.16.8 (deb) 4.18.4 (deb) 4.20.2 (deb)  
Command line tools to handle the trash folder trash-cli trash-empty Several tools for managing the virtual trash folder. trash-empty (being the most important one) empties the trash free 0.12.9.14 (deb) 0.17.1.14 (deb) 0.17.1.14 (deb) stop  
Transparent file encryptor veracrypt veracrypt home Veracrypt is an application for transparently using encrypted file containers or whole disks/USB-sticks/... . It's available on Linux, Windows and MacOSX + the format can be used on MacOSX and IOS. free 1.25.4 (deb) 1.26.7 (deb) stop stop Veracrypt
Graphical file manager "XFE" xfe   home Very feature-rich file manager.
Software is no longer provided centrally since there seems to be no interest on the users' end. Please tell us, if we're wrong. 		free 1.42 (deb) stop stop stop XFE

Internet access software

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Distributed data management datalad datalad home free 0.14.7 (deb) 0.19.5 (deb) 1.1.5 (deb) stop  
Filetransfer client filezilla   home free 3.28.0 (deb) 3.52.2 (deb) 3.63.0 (deb) stop Filezilla, Winscp
Web browser "Firefox" firefox     free 113.0.2 (deb) 128.13.0esr (deb) stop stop  
Instant Messaging via Jabber/XMPP psi   home Please use Psi-Plus instead.
This software is no longer provided centrally since it has been replaced. 		free 1.3 (deb) stop stop stop Psi-Plus
Instant Messaging via Jabber/XMPP psi-plus   home There's an institute-provided instant messaging service available to chat with your co-workers and with IT. free stop 1.4.554 (deb) 1.4.554 (deb) stop Psi-Plus
Online collaboration rocketchat   home Online collaboration tool for teams free stop 4.0.0 (deb) 4.0.0 (deb) stop Rocketchat
File synchronisation tool rsync rsync -h home free 3.1.2 (deb) 3.2.3 (deb) 3.2.7 (deb) 3.4.1 (deb)  
Mail client thunderbird   home A local mail client is useful, if multiple accounts must be handled or if specific functions are to be used via plugins. If in doubt, use the institute's webmail: https://mail.cbs.mpg.de . free 102.11.0 (deb) 128.13.0esr (deb) 128.13.0esr (deb) stop  
Youtube-Downloader youtube-dl youtube-dl home free 2021.12.17 (deb) stop stop stop  
Video conference zoom zoom home Video conference tool. free 5.10.7.3311 (deb) stop 6.5.9.3723 (deb) stop Zoom

Internet file sharing (like Dropbox)

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Owncloud based sharing nextcloud-desktop   home A local client for using Nextcloud servers. This program only makes sense in a desktop environment. Run it via the Start menu. free stop 3.1.1 (deb) stop 3.16.4 (deb) Dropbox
Owncloud based sharing owncloud-client owncloud home This service is like Dropbox but the MPG offers this service under german jurisdiction free - - - - Dropbox

Infrastructure management

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
For managing SQL databases dbeaver-ce dbeaver-ce   freeware 22.1.0 (deb) 25.0.0 (deb) stop stop  

Multimedia

Audio processing and playback

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Wav(-eform) editor "Audacity" audacity     free 2.2.1 (deb) 2.4.2 (deb) 3.3.3 (deb) 3.7.5 (deb) Adobe Premiere
Command line volume normalizer normalize-audio     free 0.7.7 (deb) 0.7.7 (deb) 0.7.7 (deb) stop  
Sound mixer pavucontrol     free 3.0 (deb) 4.0 (deb) 5.0 (deb) 6.1 (deb) Windows Mixer
Speech analysis praat   home Manual(de) free 6.0.37 (deb) 6.1.38 (deb) 6.3.07 (deb) 6.4.27 (deb)  
Music sequencer software "Rosegarden" rosegarden   home free 17.12.1 (deb) 20.12 (deb) stop stop Cakewalk
Command line audio editor sox   home free 14.4.2 (deb) 14.4.2 (deb) 14.4.2 (deb) stop  

Image processing

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Diagram editor dia   Software is no longer provided centrally since there seems to be no interest on the users' end. Please tell us, if we're wrong. free 0.97.3 (deb) 0.97.3 (deb) stop stop Visio
Bitmap image viewer geeqie   home free 1.4 (deb) 1.6 (deb) 2.0.1 (deb) stop  
Bitmap editing application gimp gimp home free stop 2.10.22 (deb) 2.10.34 (deb) 3.0.4 (deb) Adobe Photoshop
Graphical morphing tool gtkmorph   home free 20140707 (deb) 20140707 (deb) 20150712 (deb) stop  
2D Image batch convertion tool "convert" imagemagick convert source.gif target.png home free 6.9.7.4 (deb) 6.9.11.60 (deb) 6.9.11.60 (deb) stop  
Vector graphics application "Inkscape" inkscape inkscape home free stop 1.0.2 (deb) 1.2.2 (deb) stop Core Draw, Inkscape
Digital bitmap painting "Krita" krita   home Krita supports graphic tablets with pressure sensitive pen input free stop 4.4.2 (deb) 5.1.5 (deb) stop  
CAD application librecad   home free 2.1.2 (deb) 2.1.3 (deb) 2.2.0 (deb) stop Autocad
DTP application scribus   home free 1.4.6 (deb) 1.5.6.1 (deb) 1.5.8 (deb) stop Adobe Illustrator
Screenshot and annotation tool shutter shutter home free 0.94 (deb) 0.99.2 (deb) 0.99.2 (deb) stop  

Video processing and playback

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Video editor (Linear) avidemux   home free stop 2.7.8 (deb) stop stop Virtualdub
Video annotation elan elan   free stop 6.8 (nfs) 6.9 (nfs) stop  
Command line video conversion tool ffmpeg ffmpeg ffmpeg was sometimes known as 'avconv' free 3.4.11 (deb) 4.4.6 (deb) 6.0.1 (deb) 7.1.1 (deb)  
Fast (Multi-Core) video conversion tool (CLI) handbrake-cli handbrake-cli home free 1.2.1 (deb) 1.4.1 (deb) 1.6.1 (deb) stop  
Fast (Multi-Core) video conversion tool handbrake-gtk ghb home free 1.2.1 (deb) 1.4.1 (deb) stop 1.9.2 (deb)  
Video editor (Non-linear) kdenlive   home free 17.12.3 (deb) 21.04.3 (deb) 23.04.2 (deb) 25.04.3 (deb) Final Cut Pro
Shows extensive metadata about video files mediainfo mediainfo video.avi home free 17.12 (deb) 20.09 (deb) 23.04 (deb) 25.04 (deb)  
Video (avi,mkv,mp4,...) player "Mplayer" mplayer   home free 1.3.0 (deb) 1.4.0 (deb) 1.5.0 (deb) 1.5.0 (deb) Windows Media Player
Screen video recorder simplescreenrecorder   home free 0.3.8 (deb) 0.4.2 (deb) 0.4.4 (deb) stop  
Plattform independent Video player "VLC" vlc   home free 3.0.8 (deb) 3.0.21 (deb) 3.0.21 (deb) 3.0.21 (deb) VLC

Document processing

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Diagram editor dia   Software is no longer provided centrally since there seems to be no interest on the users' end. Please tell us, if we're wrong. free 0.97.3 (deb) 0.97.3 (deb) stop stop Visio
Reference management kbibtex   question free - - - -  
LaTeX-GUI "Kile" kile   question free - - - -  
Word processing libreoffice   home Find a guide on effective writing with Libreoffice at https://designingwithlibreoffice.com/
chart-bar 		free stop 7.0.4 (deb) 7.4.7 (deb) stop MS Office
Reference and document management mendeley-rm mendeley-refman chart-bar free stop stop 2.135.0 (nfs) stop  
Lookup journal papers by brain region sleuth   home chart-bar free 2.4 (afs)
2.3 (afs)
3.0.4 (afs)
 3.0.4 (afs) stop stop  
LaTeX-GUI "Texmaker" texmaker   question free 5.0.2 (deb) stop stop stop Texniccenter
LaTeX-GUI "Texstudio" texstudio   question free - - - - Texniccenter
Personal Wiki zim   home free 0.68 (deb) 0.73.5 (deb) 0.75.1 (deb) stop  
Reference management zotero zotero home This is the standalone program "Zotero". Please install the Firefox browser plugin by yourself (if needed).
chart-bar 		free 6.0.5 (nfs)
7.0.24 (sc) 		7.0.15 (nfs)
7.0.24 (sc)
6.0.5 (nfs) 		7.0.15 (nfs)
7.0.24 (sc) 		7.0.24 (sc) Endnote

PDF viewers and editors

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
PDF Viewer "Evince" evince   home free stop 3.38.2 (deb) 43.1 (deb) stop Adobe Reader
PDF editor "Inkscape" inkscape inkscape home free stop 1.0.2 (deb) 1.2.2 (deb) stop Core Draw, Inkscape
PDF manipulation tool (commandline) qpdf     free 8.0.2 (deb) 10.1.0 (deb) 11.3.0 (deb) stop  
PDF Viewer "qpdfview" qpdfview     free stop 0.4.18 (deb) 0.5.0 (deb) stop Adobe Reader
PDF annotation tool xournal     free stop 0.4.8.2016 (deb) 0.4.8.2016 (deb) stop  

Revision/Change management

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
GIT revision management git     free 2.24.0 (deb) 2.30.2 (deb) 2.39.5 (deb) 2.47.2 (deb)  
GIT revision browser gitk     free 2.24.0 (deb) 2.30.2 (deb) 2.39.5 (deb) stop  
GUI for managing data in SVN kdesvn kdesvn home Although a GUI is not necessary, it makes handling data in SVN revision controlled repositories more comfortable. free 2.0.0 (deb) 2.1.0 (deb) 2.1.0 (deb) stop  
Revision management GUI (for SVN) "RappidSVN" rapidsvn   This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects! free 0.12.1dfsg (deb) stop stop stop  
Revision management GUI (for SVN) "Smartsvn" smartsvn   This software is only available for a specific group of users. Please use kdesvn .
chart-bar 		user stop 9.3.0 (afs) 9.3.0 (afs) stop  
Subversion (aka SVN) revision management subversion svn Tool for accessing the institut's revision management server. See RevisionControl(de) for more information free 1.9.7 (deb) 1.14.1 (deb) 1.14.2 (deb) stop  

Singularity software containers

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
FMRI preprocessing pipeline fmriprep sc fmriprep home chart-bar free 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
 25.1.3 (sc)
20.2.0 (sc)
20.2.3 (sc)
20.2.6 (sc)
21.0.0 (sc)
21.0.1 (sc)
21.0.2 (sc)
21.0.3 (sc)
22.0.1 (sc)
24.1.1 (sc)
  
DICOM converter heudiconv sc heudiconv home free 0.9.0 (sc) 0.9.0 (sc) 0.9.0 (sc) 0.9.0 (sc)  
IQM extraction from MRI images mriqc sc mriqc home chart-bar free 24.0.2 (sc)
0.16.1 (sc) 		24.0.2 (sc)
0.16.1 (sc) 		24.0.2 (sc)
0.16.1 (sc) 		24.0.2 (sc)
0.16.1 (sc) 		 
White matter segmentation tool tractseg sc tractseg latest
sc tractseg 		home chart-bar free 2.8 (sc) 2.8 (sc) 2.8 (sc) 2.8 (sc)  

Scientific software, mouse operated

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Neuroimaging visualisation and discovery connectome-workbench wb_view
wb_command 		home free 2.0.1 (deb) 2.1.0 (deb) 2.1.0 (deb) stop  
3D-finite element mesh generator gmsh gmsh home free 3.0.6 (deb) 4.7.1 (deb) 4.8.4 (deb) stop  
Video analyser opendbm OPENDBM home chart-bar free 2.0/ (sc)
2.0 (sc) 		2.0/ (sc)
2.0 (sc) 		2.0/ (sc)
2.0 (sc) 		2.0/ (sc)
2.0 (sc) 		 
Simulation of Non-invasive Brain Stimulation simnibs SIMNIBS home chart-bar free stop 4.0.1 (afs) stop stop  

Security

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Password manager "Keepassx" keepassx   home Password manager based on an encrypted container. free 2.0.3 (deb) 2.0.3 (deb) 2.0.3 (deb) stop  
Password manager "Pass" pass   home Securitywise this password manager is the theoretical optimum of any password manager. Contact IT, if you want to know more. free 1.7.1 (deb) 1.7.3 (deb) 1.7.4 (deb) stop  

Stimuly preparation

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Stimuly randomisation "Conan" conan   This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects! free stop stop stop stop  
Speech manipulation praat   home Manual(de) free 6.0.37 (deb) 6.1.38 (deb) 6.3.07 (deb) 6.4.27 (deb)  
Conversion and cleanup tool for video clips prepare-video     free stop stop stop stop  
Stimuli presentation GUI psychopy PSYCHOPY gui home chart-bar free 1.85.3 (deb)
2021.2.3 (nfs)
2024.2.5 (sc)
3.0.0 (nfs)
3.1.3 (nfs)
2020.1.2 (nfs)
2020.2.10 (nfs)
2021.1.3 (nfs)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
 2023.2.3 (nfs)
2024.2.5 (sc)
2021.1.3 (nfs)
2021.2.3 (nfs)
2021.2.3 (sc)
2022.1.4 (nfs)
2022.2.3 (sc)
2022.2.4 (nfs)
2022.2.4 (sc)
2022.2.5 (nfs)
2023.1.0 (nfs)
2023.1.2 (nfs)
2023.1.3 (nfs)
2023.2.3 (sc)
2024.1.1 (nfs)
2024.2.5 (nfs)
2025.1.1 (sc)
 2024.2.5 (nfs)
2024.2.5 (sc)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
 2024.2.5 (sc)
2021.2.3 (sc)
2022.2.3 (sc)
2022.2.4 (sc)
2023.2.3 (sc)
2025.1.1 (sc)
  
Matlab based stimuli presentation library psychtoolbox psychtoolbox home chart-bar free 3.0.15 (nfs) 3.0.18.13 (nfs)
3.0.20.4 (nfs) 		3.0.20.4 (nfs) stop  

Various tools

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
CD/DVD burn tool brasero     free 3.12.1 (deb) stop stop stop  
Environment handling cbsenv cbsenv -L This tool shows information about active CAPITAL-ONLY-environments (i.e. MATLAB or SPM) free/cbs stop stop stop stop  
Client to access the CentralWindows service (windows application server farm via Citrix Selfservice). citrixrec centralwindows chart-bar freeware stop 25.3.0.66 (afs)
25.3.0.66 (nfs)
24.2.0.65 (afs) 		25.3.0.66 (afs)
25.3.0.66 (nfs)
24.2.0.65 (afs) 		stop  
GPU memory test cudamemtest cudamemtest Memory test for Cuda supported Nvidia GPUs. free 1.2.3 (afs) 1.2.3 (afs) stop stop  
Desktop calculator tool galculator     free 2.1.4 (deb) 2.1.4 (deb) 2.1.4 (deb) stop Calc
Get a usable compute server getserver getserver -sL
getserver --help 		This tool returns the name of a usable compute server. Usable means "online", "you have permissions to access it" and "in the same town" free/cbs stop stop stop stop  
Disk management tool i.e. for formatting external HDDs and Sticks. gnome-disk-utility gnome-disks   free 3.28.3 (deb) 3.38.2 (deb) 43.0 (deb) 46.1 (deb) Partition Manager
Show homedir storage usage homedirusage homedirusage The homedirectory in the instiute is very small by design (see https://topic.cbs.mpg.de/details#smallhome ). This command shows tips about how to make room there. free stop stop stop stop  
English/german translation tool libwww-dict-leo-org-perl leo test home Command line tool for quick translations between english and german words free/cbs 2.02 (deb) 2.02 (deb) 2.02 (deb) stop  
Phone and Room number query tool for MPI/CBS staff phone phone john doe
phone 111 		This tool queries the user database for phone numbers user names and room numbers. free/cbs stop stop stop stop  
Prime 95 prime95 prime95 -t CPU stress test tool. free 30.7b9 (afs) 30.8b17 (afs) stop stop  
Show privatly allocated and available ("Quota") storage space q Q This tool shows all quota information of yours in the MPI/CBS network. free/cbs stop stop stop stop  
RDP remode desktop access client rdesktop rdesktop   free 1.8.3 (deb) 1.9.0 (deb) 1.9.0 (deb) stop  
Container startup interface sc sc Tool for running MPI/CBS IT provided Singularity containers free stop stop stop stop  
Singularity builder scbuild SCBUILD Environment to build singularity containers in
chart-bar 		free stop stop stop stop  
Terminal multiplexer screen screen home This program is very useful, esp. if you need to handle a lot of shells on a remote computer (e.g. a compute server) free 4.6.2 (deb) 4.8.0 (deb) 4.9.0 (deb) 4.9.1 (deb)  
Password manager frontend seahorse seahorse Browser/graphical frontend for the password manager keeping track of credentials for Owncloud, Psi and other programs. free 3.20.0 (deb) 3.38.0.1 (deb) 43.0 (deb) stop  
Software container tool singularity-container singularity   free 2.6.1 (deb) stop stop stop  

Software to view file contents

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Dicom Viewer aeskulap   home free 0.2.2b1 (deb) 0.2.2 (deb) 0.2.2 (deb) stop  
Brain viewer braingl   This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar
led-blue 		free/cbs 0.20170310 (afs) 0.20170310 (afs) stop stop  
BrainNet Viewer brainnetviewer   home chart-bar free stop 1.70 (afs) stop stop  
PDF Viewer "Evince" evince   home free stop 3.38.2 (deb) 43.1 (deb) stop Adobe Reader
ZIP/RAR/7z/LHA/... archive viewer file-roller     free 3.28.0 (deb) 3.38.1 (deb) 43.0 (deb) stop  
Nifti Viewer fslview   home Fslview is no longer being developed. Please use fsleyes via the FSL environment.
This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects! 		free - - - -  
2D-Image (jpg,png,...) viewer geeqie   home free 1.4 (deb) 1.6 (deb) 2.0.1 (deb) stop  
HDF data viewer hdfview   home chart-bar freeware 3.3.2 (sc) 3.3.2 (sc) 3.3.2 (sc) 3.3.2 (sc)  
Volumetric image viewer/editor/analyzer mango   home This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar 		free 4.1 (sc) 4.1 (sc) 4.1 (sc) 4.1 (sc)  
Text comparision (graphical diff) meld   home free 3.18.0 (deb) 3.20.2 (deb) 3.22.0 (deb) stop  
Nifti Viewer mricron mricron
sc mricron 		chart-bar free 20160222 (nfs)
20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		20160222 (nfs)
20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		20190902 (sc)
20190902 (scwrap)
20160222 (scwrap) 		 
PDF Viewer "qpdfview" qpdfview     free stop 0.4.18 (deb) 0.5.0 (deb) stop Adobe Reader
Dicom Viewer slicer Slicer home chart-bar free 4.8.1 (nfs)
5.8.1 (sc) 		5.2.2 (nfs)
5.8.1 (sc) 		5.8.1 (sc) 5.8.1 (sc)  
Dicom Viewer xmedcon   home Software is no longer provided centrally since there seems to be no interest on the users' end. Please tell us, if we're wrong. free 0.14.1 (deb) 0.16.3 (deb) stop stop  

Data visualisation/presentation

Purpose Package ID Command(s) Info License G6 G7 G8 G9 Comparable windows software
Graph generator gnuplot   home free 5.2.2 (deb) 5.4.1 (deb) 5.4.4 (deb) stop  
Mathamatical function plotter kmplot     free 17.12.3 (deb) 20.12.0 (deb) 22.12.3 (deb) stop Winfunktion
Presentation software (like Powerpoint) libreoffice   home Find a guide on effective writing with Libreoffice at https://designingwithlibreoffice.com/
chart-bar 		free stop 7.0.4 (deb) 7.4.7 (deb) stop MS Office
Scientific Client-Server-Visualisation paraview   home chart-bar
led-blue 		free 5.4.1 (deb) 5.9.0 (deb) 5.11.0 (deb) stop  

One or more packages haven't been classified, yet: bips bit blender cartool catfish cpac custom dcm2bids dipy docear dtitk fl-toolbox freecad gpu-burn imagej jabref jags jymmin kubios libmr matplotlib mdt mne-python mpv mricrogl mrtrix netpyne numexpr numpy oldreleases opsi-configed pandas pspp pymc pyparsing python python-dicom python-enthoughtbase python-h5py python-mvpa2 python-networkx python-sklearn python-surfer pyxnat scribe spinach uanwander xlrd xtightvncviewer

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Topic revision: 18 Aug 2025, Burk2
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