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  • Avoid using outdated software for new work.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; more may be available.
  • There might be different types of deployment per software package. IT is transitioning from afs to sc deployment.

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 on a network folder
  • 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 Package is installed on a network folder
  • Multiple releases are possible per computer generation.
  • Releases can be frozen which is cool, e.g. for long running studies.
  • 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 which can be run under user control (without root permissions)
  • Platform generation independence
  • Multiple releases of a software can coexist.
  • Central release repository can be used as well as group- or user-specific ones.
  • Package is portable, e.g. for using it on MPCDF's Slurm cluster.
  • For more information: SoftwareServiceLinux

Software categories

Analysis

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Function Neuroimage analysis tools afni AFNI afni
sc afni 		home chart-bar free 22.1.09 (nfs)
24.3.08 (sc)
18.2.17 (nfs) 		23.2.03 (nfs)
24.3.08 (sc)
19.1.05 (nfs)
22.0.03 (nfs)
22.1.09 (nfs)
 24.3.08 (sc)  
Normalisation tool ants ANTSENV ANTS
sc ants 		home chart-bar free 2.3.5 (nfs)
2.5.4 (sc)
2.3.1 (nfs)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
 2.3.5 (nfs)
2.5.4 (sc)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
 2.5.4 (sc)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
  
Bart bart   home MRI reconstruction toolbox free 0.4.02 (deb) 0.6.00 (deb) 0.8.00 (deb)  
Brain image processing brainvisa anatomist
sc brainvisa 		home chart-bar free 4.6.0 (afs)
5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		 
UCL Camino Diffusion MRI Toolkit camino CAMINO home chart-bar free 0.20180410 (afs)
1014 (afs)
1216 (afs)
 0.20180410 (afs) stop  
Caret caret   home Creating, viewing and manipulating surface reconstructions of the cerebral and cerebellar cortex.
This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects!
chart-bar 		free 5.65 (afs) stop stop  
MIPAV + some CBS specific plugins cbstools CBSTOOLS gui 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 (afs)
3.1 (afs) 		3.0 (afs)
3.1 (afs) 		stop  
Spatial normalization and atlas construction dtitk   home free 2.3.1 (afs) stop stop  
EEG data processing eeglab EEGLAB MATLAB matlab home free/dependent 14.1.2b (afs) 14.1.2b (afs) 14.1.2b (afs)  
EEP Tools eeptools EEPTOOLS chart-bar nodelocked stop 3.2.1 (afs) 3.2.1 (afs)  
Diffusion Model Analysis fastdm   home free 30.2 (afs) stop stop  
Toolbox for MEG and EEG analysis fieldtrip FIELDTRIP home chart-bar free 0.20180918 (afs) 0.20220623 (afs)
0.20240110 (afs) 		stop  
FMRI preprocessing pipeline fmriprep FMRIPREP
sc fmriprep 		home chart-bar free 1.5.0 (afs)
22.0.1/ (sc)
1.4.0 (afs)
1.4.1 (afs)
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)
 22.0.1/ (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)
 22.0.1/ (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)
  
Brain MRI image processing and analysis freesurfer FREESURFER home chart-bar free 6.0.0p1 (nfs)
7.4.1 (sc)
5.3.0 (nfs)
5.3.0 (sc)
7.0.0 (nfs)
7.1.0 (nfs)
 7.4.1 (nfs)
7.4.1 (sc)
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 (sc)
5.3.0 (sc) 		 
Analysis tools for fMRI, MRI and DTI brain imaging data fsl FSL
sc fsl 		home chart-bar
led-blue 		free 5.0.11 (nfs)
6.0.6 (sc)
5.0.9 (nfs)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (nfs)
6.0.3 (sc)
6.0.4 (sc)
 6.0.3 (nfs)
6.0.6 (sc)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (sc)
6.0.4 (sc)
6.0.7.7 (nfs)
6.0.7.11 (nfs)
 6.0.7.11 (nfs)
6.0.6 (sc)
5.0.9 (sc)
6.0.3 (sc)
6.0.4 (sc)
6.0.7.13 (nfs)
  
Brain ALE-analyser "Gingerale" gingerale   home chart-bar free 3.0 (afs)
2.3.6 (afs) 		3.0.2 (afs) stop  
3D image analysis itk ITK dtk chart-bar free 0.6.4.1 (afs) stop stop  
3D image segmentation itksnap ITKSNAP itksnap chart-bar free 3.8.0 (afs)
3.6.0 (afs) 		3.8.0 (afs) stop  
Heart beat analysis kubios   home chart-bar free 3.1.0 (afs) 3.5.0 (afs)
3.1.0 (afs) 		stop  
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 0.20190903 (afs)
0.20190206 (afs)
0.20190211 (afs)
0.20190306 (afs)
 0.20221118 (afs) 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  
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 (afs)
2.4 (afs)
2.5 (afs)
3.4 (afs)
3.5.1 (afs)
3.7 (afs)
4.0 (afs)
4.0.1 (afs)
 4.1 (afs) stop  
Brain image processing and visualisation medinria   home chart-bar free 3.0.0 (afs) 3.2.0 (afs) stop Medinria
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)  
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)  
Medical Image Registration ToolKit mirtk     free stop 0.20231123 (afs) stop  
MEG source localization mne MNE home chart-bar free stop 2.7.4 (afs) stop  
Python bindings for MNE mne-python MNE-PYTHON Please use the CUSTOMPYTHON environment and install mne using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 0.17.0 (afs)
0.16.2 (afs) 		stop stop  
Tools to perform diffusion-weighted MR white-matter tractography mrtrix MRTRIX mrview
sc mrtrix 		chart-bar free 3.0.0 (afs)
3.0.3 (sc)
3.0 (afs) 		3.0.3 (sc) 3.0.3 (sc)  
Software package of the Bennewitz Elekta MEG machine neuromag   chart-bar nodelocked stop 7 (afs)
6 (afs) 		stop  
Development, simmulation and test of magnetic resonance sequences odin     free stop 2.0.4 (deb) 2.0.5 (deb)  
Speech analysis praat   home Manual(de)
chart-bar 		free 6.0.43 (afs)
6.0.37 (deb) 		6.3.14 (afs)
6.1.38 (deb)
6.3.07 (afs) 		6.3.07 (deb)  
Preprocessing and analysis if q-space images qsiprep sc qsiprep 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)
  
Brain coordinate extraction "Scribe" scribe   home chart-bar free 3.8 (afs) stop stop  
3D spherical harmonic analyses of triangular mesh surfaces spharm SPHARM 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 1.13 (afs) stop stop  
Statistical analysis of brain imaging data in Matlab with "SPM" spm spm home chart-bar free/dependent 12.7771 (nfs) 12.7771 (nfs) 12.7771 (nfs)  
Fiber track data analysis in MR images trackvis TRACKVIS home chart-bar free 0.6.1 (afs) 0.6.1 (afs) stop  
White matter segmentation tool tractseg sc tractseg home free 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 Mathematica

Statistical analysis software

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Statistical analysis jasp sc jasp home chart-bar free 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) MS Office
Free alternative to SPSS - written explicitely as a replacement with compatibility in mind. pspp psppire
pspp 		home free 1.0.1 (deb) 1.4.1 (deb) stop  
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)
 4.4.1 (nfs)  
R statistical language GUI rstudio R+ rstudio home chart-bar free 2022.12.0 (deb) 2024.09.1 (deb) 2024.09.1 (deb)  
IBM SPSS Statistics spss   chart-bar floating 24fp1 (afs) 24fp1 (afs) stop  

Conversion tools

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
3D image conversion convert3d C3D chart-bar free 1.0.0 (afs) 1.0.0 (afs) stop  
Nifti-file reorganizer dcm2bids DCM2BIDS home This software was maintained centrally but is no more.
chart-bar 		free 2.1.4 (afs) stop stop  
Dicom to Nifti conversion dcm2niix dcm2niix   free stop 1.0.20240202 (deb) 1.0.20240202 (deb)  
Handling and conversion of scientific data in HDF5 format h5utils   home free 1.13 (deb) 1.13.1 (deb) 1.13.2 (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)  
Fast (Multi-Core) video conversion tool handbrake-gtk ghb home free 1.2.1 (deb) 1.4.1 (deb) stop  
DICOM converter heudiconv sc heudiconv
sc heudiconv 		home free 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)  
Multiformat MRI data processing isis-utils isisconv ...   free/cbs 0.7.17 (deb) 0.9.1 (deb) stop  
Dicom to Nifti conversion mricrogl dcm2niix home dcm2niix continues to be supported in G7 via the 'dcm2niix' package.
chart-bar 		free 20180623 (afs)
20181111 (afs) 		stop stop  
Dicom to Nifti conversion mricron MRICRON dcm2nii chart-bar free 20160222 (afs) 20160222 (afs) stop  

Software development

Development GUIs

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Development IDE for small computers (i.e. IOT) arduino ARDUINO home You'll need a software storage block in StorageUnified for this. If you don't have one, request it via a Ticket. free 1.8.10 (afs) stop stop  
Visual Studio Code, Development IDE code code home free stop 1.96.0 (deb) 1.96.0 (deb)  
Visual Studio Code fork without tracking and telemetry, Development IDE codium codium home free stop stop 1.91.1.24193 (deb)  
IDL GUI idl idlde home chart-bar floating 8.1 (afs) 8.1 (afs) stop  
Interactive python environment ipython3 ipython3 home free 5.5.0 (deb) 7.20.0 (deb) 8.5.0 (deb)  
Interactive python environment jupyter JUPYTER home free 1.0.0 (afs) 1.0.0 (afs) 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)
 9.16 (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)
 9.17 (nfs)
9.10 (nfs)
9.15 (nfs)
9.16 (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)
 stop  
Python development GUI pycharm pycharm+ home free 2022.1.1 (afs)
2022.1.1 (nfs)
2021.3.2 (afs)
2021.3.2 (nfs)
 2024.1 (afs)
2024.1 (nfs)
2021.3.2 (afs)
2021.3.2 (nfs)
2022.1.1 (afs)
2022.1.1 (nfs)
2023.3.2 (afs)
2023.3.2 (nfs)
2023.3.4 (afs)
2023.3.4 (nfs)
 2024.2.1 (afs)
2024.2.1 (nfs) 		 
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 (afs)
2022.1.1 (nfs)
2021.3.2 (afs)
2021.3.2 (nfs)
 2024.1 (afs)
2024.1 (nfs)
2021.3.2 (afs)
2021.3.2 (nfs)
2022.1.1 (afs)
2022.1.1 (nfs)
2023.1.4 (afs)
2023.1.4 (nfs)
2023.2.3 (afs)
2023.2.3 (nfs)
2023.3.2 (afs)
2023.3.2 (nfs)
2023.3.4 (afs)
2023.3.4 (nfs)
 2024.2.1 (afs)
2024.2.1 (nfs) 		 
R interactive GUI rstudio R+ rstudio home chart-bar free 2022.12.0 (deb) 2024.09.1 (deb) 2024.09.1 (deb)  
Python3 development GUI spyder spyder   free 3.2.6 (deb) 4.2.1 (deb) 5.4.2 (deb)  

Programming languages

Purpose Package ID Command(s) Info License G6 G7 G8 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) stop  
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)
 9.16 (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)
 9.17 (nfs)
9.10 (nfs)
9.15 (nfs)
9.16 (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)
 stop  
Psychology software for creating experiments pebl PEBL home chart-bar free 2.1 (afs) stop 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)  
Python programming language (Version 2) python python Do not use Python 2 anymore! It has reached End of life. Please use python3 .
This software is considered deprecated since it's no longer maintained. Do not use this software for new research projects! 		free 2.7.17 (deb) 2.7.18 (deb) stop  
Python programming language (Version 3) python3 python You might want to create your own python environment (incl. custom library version) using the CUSTOMPYTHON command. free 3.6.9 (deb) 3.9.2 (deb) 3.11.2 (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)
 4.4.1 (nfs)  

Software Libraries

Purpose Package ID Command(s) Info License G6 G7 G8 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  
Handling and conversion of scientific data in HDF5 format h5utils   home free 1.13 (deb) 1.13.1 (deb) 1.13.2 (deb)  
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)  
Python extension for numerical expression evaulation numexpr NUMEXPR Please use the CUSTOMPYTHON environment and install numexpr using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 2.2.2 (afs) stop stop  
Python extension for large arrays and matrices numpy NUMPY home Please use the CUSTOMPYTHON environment and install numpy using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 1.16.4 (afs)
1.9.2 (afs) 		stop stop  
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) 		 
Python extension for high performance data analysis pandas PANDAS Please use the CUSTOMPYTHON environment and install pandas using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 0.16.1 (afs) stop stop  
Python extension for stimuly presentation psychopy PSYCHOPY home chart-bar free 1.85.3 (deb)
2021.2.3 (nfs)
3.0.0 (nfs)
3.1.3 (nfs)
2020.1.2 (nfs)
2020.2.10 (nfs)
2021.1.3 (nfs)
 2023.2.3 (nfs)
2021.1.3 (nfs)
2021.2.3 (nfs)
2022.1.4 (nfs)
2022.2.4 (nfs)
2022.2.5 (nfs)
2023.1.0 (nfs)
2023.1.2 (nfs)
2023.1.3 (nfs)
2024.1.1 (nfs)
 stop  
Matlab based stimuli presentation library psychtoolbox PSYCHTOOLBOX home chart-bar free 3.0.15 (afs)
3.0.15 (nfs) 		3.0.18.13 (afs)
3.0.18.13 (nfs) 		stop  
Python extension to use grammars pyparsing PYPARSING Please use the CUSTOMPYTHON environment and install pyparsing using pip3.
This software was maintained centrally but is no more.
chart-bar 		free - - -  
Python binding for the HDF5 file format python-h5py   home Please use the CUSTOMPYTHON environment and install h5py using pip3. If you think, this package should be made available centrally, please Contact IT.
This software was maintained centrally but is no more. 		free 2.7.1 (deb) stop stop  
Python extention for handling data networks python-networkx   Please use the CUSTOMPYTHON environment and install networkx using pip3.
This software was maintained centrally but is no more. 		free 1.11 (deb) stop 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 data analysis and machine learning python-sklearn SKLEARN home Please use the CUSTOMPYTHON environment and install scikit-learn using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 0.20.0 (deb) stop stop  
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  
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)  
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)  
Python extension for accessing XNAT servers pyxnat PYXNAT home Please use the CUSTOMPYTHON environment and install pyxnat using pip3.
This software was maintained centrally but is no more. 		free - - -  
Python framework for mathematics and science scipy SCIPY Please use the CUSTOMPYTHON environment and install scipy using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 1.2.2 (afs) stop stop  
Tobii Eye tracker extension t2t T2T 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 0.7 (afs) stop stop  
Python extension for extraction data from Excel-files xlrd XLRD Please use the CUSTOMPYTHON environment and install xlrd using pip3.
This software was maintained centrally but is no more. 		free - - -  

Editors, Output-processing

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
PDF editor "Inkscape" inkscape inkscape home free stop 1.0.2 (deb) 1.2.2 (deb) 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 (afs)
2.4 (afs)
2.5 (afs)
3.4 (afs)
3.5.1 (afs)
3.7 (afs)
4.0 (afs)
4.0.1 (afs)
 4.1 (afs) stop  
PDF manipulation tool (commandline) qpdf     free 8.0.2 (deb) 10.1.0 (deb) 11.3.0 (deb)  
PDF annotation tool xournal     free stop 0.4.8.2016 (deb) 0.4.8.2016 (deb)  

Text Editing software

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Simple text editor gedit   Simple text editor free 3.28.1 (deb) 3.38.1 (deb) 44.2 (deb) 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)
5.5.0 (afs) 		stop Jedit
Feature-rich text editor kate     free 17.12.3 (deb) 20.12.2 (deb) 22.12.3 (deb) Notepad++
Simple text editor kwrite     free 17.12.3 (deb) 20.12.2 (deb) 22.12.3 (deb) Notepad

Shell environments

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Function Neuroimage analysis tools afni AFNI
sc afni 		home chart-bar free 22.1.09 (nfs)
24.3.08 (sc)
18.2.17 (nfs) 		23.2.03 (nfs)
24.3.08 (sc)
19.1.05 (nfs)
22.0.03 (nfs)
22.1.09 (nfs)
 24.3.08 (sc)  
Normalisation tool ants ANTSENV
sc ants 		home chart-bar free 2.3.5 (nfs)
2.5.4 (sc)
2.3.1 (nfs)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
 2.3.5 (nfs)
2.5.4 (sc)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
 2.5.4 (sc)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
  
Brain image processing brainvisa sc brainvisa home chart-bar free 4.6.0 (afs)
5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		 
UCL Camino Diffusion MRI Toolkit camino CAMINO home chart-bar free 0.20180410 (afs)
1014 (afs)
1216 (afs)
 0.20180410 (afs) stop  
MIPAV based analysis environent with 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 (afs)
3.1 (afs) 		3.0 (afs)
3.1 (afs) 		stop  
3D image conversion convert3d C3D chart-bar free 1.0.0 (afs) 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  
Nifti-file reorganizer dcm2bids DCM2BIDS home This software was maintained centrally but is no more.
chart-bar 		free 2.1.4 (afs) stop stop  
Toolbox for MEG and EEG analysis fieldtrip FIELDTRIP home chart-bar free 0.20180918 (afs) 0.20220623 (afs)
0.20240110 (afs) 		stop  
FMRI preprocessing pipeline fmriprep FMRIPREP
sc fmriprep 		home chart-bar free 1.5.0 (afs)
22.0.1/ (sc)
1.4.0 (afs)
1.4.1 (afs)
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)
 22.0.1/ (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)
 22.0.1/ (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)
  
Brain MRI image processing and analysis freesurfer FREESURFER home chart-bar free 6.0.0p1 (nfs)
7.4.1 (sc)
5.3.0 (nfs)
5.3.0 (sc)
7.0.0 (nfs)
7.1.0 (nfs)
 7.4.1 (nfs)
7.4.1 (sc)
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 (sc)
5.3.0 (sc) 		 
Analysis tools for fMRI, MRI and DTI brain imaging data fsl FSL
sc fsl 		home chart-bar
led-blue 		free 5.0.11 (nfs)
6.0.6 (sc)
5.0.9 (nfs)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (nfs)
6.0.3 (sc)
6.0.4 (sc)
 6.0.3 (nfs)
6.0.6 (sc)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (sc)
6.0.4 (sc)
6.0.7.7 (nfs)
6.0.7.11 (nfs)
 6.0.7.11 (nfs)
6.0.6 (sc)
5.0.9 (sc)
6.0.3 (sc)
6.0.4 (sc)
6.0.7.13 (nfs)
  
3D image analysis environment itk ITK chart-bar free 0.6.4.1 (afs) stop stop  
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 0.20190903 (afs)
0.20190206 (afs)
0.20190211 (afs)
0.20190306 (afs)
 0.20221118 (afs) 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)
 9.16 (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)
 9.17 (nfs)
9.10 (nfs)
9.15 (nfs)
9.16 (nfs)
  
MEG source localization mne MNE home chart-bar free stop 2.7.4 (afs) stop  
Python bindings for MNE mne-python MNE-PYTHON Please use the CUSTOMPYTHON environment and install mne using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 0.17.0 (afs)
0.16.2 (afs) 		stop stop  
Tools to perform diffusion-weighted MR white-matter tractography mrtrix MRTRIX
sc mrtrix 		chart-bar free 3.0.0 (afs)
3.0.3 (sc)
3.0 (afs) 		3.0.3 (sc) 3.0.3 (sc)  
Neural network simmulator nest NEST 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.
chart-bar 		free 2.16.0 (afs) stop stop  
Python extension for numerical expression evaulation numexpr NUMEXPR Please use the CUSTOMPYTHON environment and install numexpr using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 2.2.2 (afs) stop stop  
Python extension for large arrays and matrices numpy NUMPY home Please use the CUSTOMPYTHON environment and install numpy using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 1.16.4 (afs)
1.9.2 (afs) 		stop 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)
 stop  
Python extension for high performance data analysis pandas PANDAS Please use the CUSTOMPYTHON environment and install pandas using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 0.16.1 (afs) stop 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)  
Speech analysis with "Praat" praat PRAAT+
praat 		home Manual(de)
chart-bar 		free 6.0.43 (afs)
6.0.37 (deb) 		6.3.14 (afs)
6.1.38 (deb)
6.3.07 (afs) 		6.3.07 (deb)  
Stimuly presentation environment "Psychopy" psychopy PSYCHOPY home chart-bar free 1.85.3 (deb)
2021.2.3 (nfs)
3.0.0 (nfs)
3.1.3 (nfs)
2020.1.2 (nfs)
2020.2.10 (nfs)
2021.1.3 (nfs)
 2023.2.3 (nfs)
2021.1.3 (nfs)
2021.2.3 (nfs)
2022.1.4 (nfs)
2022.2.4 (nfs)
2022.2.5 (nfs)
2023.1.0 (nfs)
2023.1.2 (nfs)
2023.1.3 (nfs)
2024.1.1 (nfs)
 stop  
Matlab based stimuli presentation library psychtoolbox PSYCHTOOLBOX home chart-bar free 3.0.15 (afs)
3.0.15 (nfs) 		3.0.18.13 (afs)
3.0.18.13 (nfs) 		stop  
Python extension to use grammars pyparsing PYPARSING Please use the CUSTOMPYTHON environment and install pyparsing using pip3.
This software was maintained centrally but is no more.
chart-bar 		free - - -  
Python extension for data analysis and machine learning python-sklearn SKLEARN home Please use the CUSTOMPYTHON environment and install scikit-learn using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 0.20.0 (deb) stop 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)  
Python extension for accessing XNAT servers pyxnat PYXNAT home Please use the CUSTOMPYTHON environment and install pyxnat using pip3.
This software was maintained centrally but is no more. 		free - - -  
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)
 4.4.1 (nfs)  
Singularity builder scbuild SCBUILD Environment to build singularity containers in
chart-bar 		free stop stop stop  
Python framework for mathematics and science scipy SCIPY Please use the CUSTOMPYTHON environment and install scipy using pip3.
This software was maintained centrally but is no more.
chart-bar 		free 1.2.2 (afs) stop stop  
Spharm environment spharm SPHARM 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 1.13 (afs) stop stop  
SPM environment spm SPM MATLAB home This has to be used with matlab to be useful
chart-bar 		free/dependent 12.7771 (nfs) 12.7771 (nfs) 12.7771 (nfs)  
Tobii Eye tracker extension t2t T2T 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 0.7 (afs) stop stop  
Fiber track data analysis in MR images trackvis TRACKVIS home chart-bar free 0.6.1 (afs) 0.6.1 (afs) stop  
Python extension for extraction data from Excel-files xlrd XLRD Please use the CUSTOMPYTHON environment and install xlrd using pip3.
This software was maintained centrally but is no more. 		free - - -  

Access to external services

Purpose Package ID Command(s) Info License G6 G7 G8 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  

File management

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
File compression tool file-roller     free 3.28.0 (deb) 3.38.1 (deb) 43.0 (deb)  
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  
Image browser geeqie   home free 1.4 (deb) 1.6 (deb) 2.0.1 (deb)  
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)  
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)  
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)  
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)  
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 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 XFE

Internet access software

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Distributed data management datalad datalad home free 0.14.7 (deb) 0.19.5 (deb) 1.1.4 (deb)  
Filetransfer client filezilla   home free 3.28.0 (deb) 3.52.2 (deb) 3.63.0 (deb) Filezilla, Winscp
Web browser "Firefox" firefox     free 112.0 (deb) 128.5.0esr (deb) stop  
Globus Connect Personal globusconn globusconn home chart-bar free - - -  
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 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) Psi-Plus
Online collaboration rocketchat   home Online collaboration tool for teams free stop 4.0.0 (deb) 4.0.0 (deb) Rocketchat
File synchronisation tool rsync rsync -h home free 3.1.2 (deb) 3.2.3 (deb) 3.2.7 (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 102.10.0 (deb) 128.5.0esr (deb) 128.5.0esr (deb)  
Youtube-Downloader youtube-dl youtube-dl home free 2021.12.17 (deb) stop stop  
Video conference zoom zoom home Video conference tool. free 5.10.7.3311 (deb) stop 6.2.11.5069 (deb) Zoom

Internet file sharing (like Dropbox)

Purpose Package ID Command(s) Info License G6 G7 G8 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 Dropbox
Owncloud based sharing owncloud-client owncloud home This service is like Dropbox but the MPG offers this service under german jurisdiction free stop stop 5.3.1.14018 (deb) Dropbox

Infrastructure management

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
For managing SQL databases dbeaver-ce dbeaver-ce   freeware 22.1.0 (deb) 24.3.0 (deb) stop  

Multimedia

Audio processing and playback

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Wav(-eform) editor "Audacity" audacity     free 2.2.1 (deb) 2.4.2 (deb) 3.2.4 (deb) Adobe Premiere
Command line volume normalizer normalize-audio     free 0.7.7 (deb) 0.7.7 (deb) 0.7.7 (deb)  
Sound mixer pavucontrol     free 3.0 (deb) 4.0 (deb) 5.0 (deb) Windows Mixer
Speech analysis praat   home Manual(de)
chart-bar 		free 6.0.43 (afs)
6.0.37 (deb) 		6.3.14 (afs)
6.1.38 (deb)
6.3.07 (afs) 		6.3.07 (deb)  
Music sequencer software "Rosegarden" rosegarden   home free 17.12.1 (deb) 20.12 (deb) stop Cakewalk
Command line audio editor sox   home free 14.4.2 (deb) 14.4.2 (deb) 14.4.2 (deb)  

Image processing

Purpose Package ID Command(s) Info License G6 G7 G8 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 Visio
Mind Map Editor freemind   home chart-bar free 1.0.1 (afs) stop stop  
Bitmap image viewer geeqie   home free 1.4 (deb) 1.6 (deb) 2.0.1 (deb)  
Bitmap editing application gimp gimp home free stop 2.10.22 (deb) 2.10.34 (deb) Adobe Photoshop
Graphical morphing tool gtkmorph   home free 20140707 (deb) 20140707 (deb) 20150712 (deb)  
Plattform-independent image manipulation "ImageJ" imagej   home free stop 1.53 (afs) 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)  
Vector graphics application "Inkscape" inkscape inkscape home free stop 1.0.2 (deb) 1.2.2 (deb) 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)  
CAD application librecad   home free 2.1.2 (deb) 2.1.3 (deb) 2.2.0 (deb) Autocad
DTP application scribus   home free 1.4.6 (deb) 1.5.6.1 (deb) 1.5.8 (deb) Adobe Illustrator
Screenshot and annotation tool shutter shutter home free 0.94 (deb) 0.99.2 (deb) 0.99.2 (deb)  

Video processing and playback

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Video editor (Linear) avidemux   home free stop 2.7.8 (deb) stop Virtualdub
Plattform independent modeller, renderer, etc. blender blender home led-blue free stop 2.83.5 (deb) 3.4.1 (deb)  
Video annotation elan elan   free stop 6.8 (nfs) stop  
Command line video conversion tool ffmpeg ffmpeg ffmpeg was sometimes known as 'avconv' free 3.4.11 (deb) 4.4.5 (deb) 5.1.6 (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)  
Fast (Multi-Core) video conversion tool handbrake-gtk ghb home free 1.2.1 (deb) 1.4.1 (deb) stop  
Video editor (Non-linear) kdenlive   home free 17.12.3 (deb) 21.04.3 (deb) 22.12.3 (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)  
Video (avi,mkv,mp4,...) player "Mplayer" mplayer   home free 1.3.0 (deb) 1.4.0 (deb) 1.5 (deb) Windows Media Player
Screen video recorder simplescreenrecorder   home free 0.3.8 (deb) 0.4.2 (deb) 0.4.4 (deb)  
Plattform independent Video player "VLC" vlc   home free 3.0.8 (deb) 3.0.21 (deb) 3.0.21 (deb) VLC

Document processing

Purpose Package ID Command(s) Info License G6 G7 G8 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 Visio
Reference and document management docear docear home chart-bar free 1.2.0.0 (afs) 1.2.0.0 (afs) stop  
Mind Map Editor freemind   home chart-bar free 1.0.1 (afs) stop stop  
Reference management jabref   question home chart-bar free 4.3.1 (afs) stop stop Endnote
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) MS Office
Reference and document management mendeley-rm mendeley-refman chart-bar free stop 2.90.0 (nfs)
2.122.0 (nfs) 		2.122.0 (nfs)  
Review Manager "RevMan 5" revman revman home Software for writing reviers for "Cochrane"
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 - - -  
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  
LaTeX-GUI "Texmaker" texmaker   question free 5.0.2 (deb) stop stop Texniccenter
LaTeX-GUI "Texstudio" texstudio   question free - - - Texniccenter
Bibliometric network tool vosviewer   home chart-bar free stop 1.6.20 (afs)
1.6.19 (afs) 		stop  
Personal Wiki zim   home free 0.68 (deb) 0.73.5 (deb) 0.75.1 (deb)  
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 (afs)
6.0.5 (nfs)
5.0.89 (afs)
5.0.89 (nfs)
5.0.92 (afs)
5.0.92 (nfs)
5.0.95 (afs)
5.0.95 (nfs)
5.0.96.3 (afs)
5.0.96.3 (nfs)
 7.0.10 (afs)
6.0.23 (nfs)
5.0.96.3 (afs)
5.0.96.3 (nfs)
6.0.5 (afs)
6.0.5 (nfs)
6.0.13 (afs)
6.0.13 (nfs)
6.0.23 (afs)
 7.0.10 (afs) Endnote

PDF viewers and editors

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

Revision/Change management

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
GIT revision management git     free 2.24.0 (deb) 2.30.2 (deb) 2.39.5 (deb)  
GIT revision browser gitk     free 2.24.0 (deb) 2.30.2 (deb) 2.39.5 (deb)  
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)  
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  
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) 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)  

Singularity software containers

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Function Neuroimage analysis tools afni sc afni
sc afni 		home chart-bar free 22.1.09 (nfs)
24.3.08 (sc)
18.2.17 (nfs) 		23.2.03 (nfs)
24.3.08 (sc)
19.1.05 (nfs)
22.0.03 (nfs)
22.1.09 (nfs)
 24.3.08 (sc)  
Normalisation tool ants sc ants latest
sc ants 		home chart-bar free 2.3.5 (nfs)
2.5.4 (sc)
2.3.1 (nfs)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
 2.3.5 (nfs)
2.5.4 (sc)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
 2.5.4 (sc)
2.3.4 (sc)
2.3.5 (sc)
2.4.0 (sc)
2.4.1 (sc)
2.4.2 (sc)
2.4.3 (sc)
  
Brain image processing brainvisa sc brainvisa home chart-bar free 4.6.0 (afs)
5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		5.1.1 (sc)
5.0.4 (sc) 		 
FMRI preprocessing pipeline fmriprep sc fmriprep home chart-bar free 1.5.0 (afs)
22.0.1/ (sc)
1.4.0 (afs)
1.4.1 (afs)
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)
 22.0.1/ (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)
 22.0.1/ (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)
  
Analysis tools for fMRI, MRI and DTI brain imaging data fsl sc fsl home chart-bar
led-blue 		free 5.0.11 (nfs)
6.0.6 (sc)
5.0.9 (nfs)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (nfs)
6.0.3 (sc)
6.0.4 (sc)
 6.0.3 (nfs)
6.0.6 (sc)
5.0.9 (sc)
6.0.1 (nfs)
6.0.3 (sc)
6.0.4 (sc)
6.0.7.7 (nfs)
6.0.7.11 (nfs)
 6.0.7.11 (nfs)
6.0.6 (sc)
5.0.9 (sc)
6.0.3 (sc)
6.0.4 (sc)
6.0.7.13 (nfs)
  
Reproducible fMRI analysis" halfpipe sc halfpipe home free 1.2.2 (sc) 1.2.2 (sc) 1.2.2 (sc)  
DICOM converter heudiconv sc heudiconv home free 0.9.0 (sc) 0.9.0 (sc) 0.9.0 (sc)  
Statistical analysis jasp sc jasp home chart-bar free 0.16.4 (sc) 0.16.4 (sc) 0.16.4 (sc)  
Tools to perform diffusion-weighted MR white-matter tractography mrtrix sc mrtrix chart-bar free 3.0.0 (afs)
3.0.3 (sc)
3.0 (afs) 		3.0.3 (sc) 3.0.3 (sc)  
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)  
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) 		 
Preprocessing and analysis if q-space images qsiprep sc qsiprep 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)
  
White matter segmentation tool tractseg sc tractseg latest
sc tractseg 		home free 2.8 (sc) 2.8 (sc) 2.8 (sc)  

Scientific software, mouse operated

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Neuroimaging visualisation and discovery connectome-workbench wb_view
wb_command 		home free 2.0.0 (deb) 2.0.1 (deb) 2.0.1 (deb)  
3D-finite element mesh generator gmsh gmsh home free 3.0.6 (deb) 4.7.1 (deb) 4.8.4 (deb)  
Neural network simmulator nest NEST nest
NEST sli 		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.
chart-bar 		free 2.16.0 (afs) stop stop  
Video analyser opendbm OPENDBM home chart-bar free 0.20210204 (afs) stop stop  
Simulation of Non-invasive Brain Stimulation simnibs SIMNIBS home chart-bar free 2.1.1 (afs)
3.1.0 (afs) 		4.0.1 (afs)
3.2.6 (afs) 		stop  

Security

Purpose Package ID Command(s) Info License G6 G7 G8 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)  
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)  

Stimuly preparation

Purpose Package ID Command(s) Info License G6 G7 G8 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  
Speech manipulation praat   home Manual(de)
chart-bar 		free 6.0.43 (afs)
6.0.37 (deb) 		6.3.14 (afs)
6.1.38 (deb)
6.3.07 (afs) 		6.3.07 (deb)  
Conversion and cleanup tool for video clips prepare-video     free stop stop stop  
Stimuli presentation GUI psychopy PSYCHOPY gui home chart-bar free 1.85.3 (deb)
2021.2.3 (nfs)
3.0.0 (nfs)
3.1.3 (nfs)
2020.1.2 (nfs)
2020.2.10 (nfs)
2021.1.3 (nfs)
 2023.2.3 (nfs)
2021.1.3 (nfs)
2021.2.3 (nfs)
2022.1.4 (nfs)
2022.2.4 (nfs)
2022.2.5 (nfs)
2023.1.0 (nfs)
2023.1.2 (nfs)
2023.1.3 (nfs)
2024.1.1 (nfs)
 stop  
Matlab based stimuli presentation library psychtoolbox psychtoolbox home chart-bar free 3.0.15 (afs)
3.0.15 (nfs) 		3.0.18.13 (afs)
3.0.18.13 (nfs) 		stop  
Multilingual pseudoword generator wuggy   home chart-bar free 0.2.2b2 (afs) stop stop  

Various tools

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
CD/DVD burn tool brasero     free 3.12.1 (deb) 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  
Desktop productivity tool cerebro   home Desktop productivity tool
chart-bar 		free - - -  
Client to access the CentralWindows service (windows application server farm via Citrix Selfservice). citrixrec centralwindows chart-bar freeware 21.8.0.40 (nfs) 24.2.0.65 (afs)
24.2.0.65 (nfs)
21.8.0.40 (afs)
21.8.0.40 (nfs)
22.7.0.20 (afs)
22.7.0.20 (nfs)
23.8.0.39 (afs)
23.8.0.39 (nfs)
 24.2.0.65 (afs)
24.2.0.65 (nfs) 		 
GPU memory test cudamemtest cudamemtest Memory test for Cuda supported Nvidia GPUs. free 1.2.3 (afs) 1.2.3 (afs) stop  
Desktop calculator tool galculator     free 2.1.4 (deb) 2.1.4 (deb) 2.1.4 (deb) 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  
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) Partition Manager
GPU-Burn gpu-burn gpu-burn home For creating load on locally connected GPUs, to test their stability and thermal management free 0.1 (afs) 0.1 (afs) stop  
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  
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)  
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  
Prime 95 prime95 prime95 -t CPU stress test tool. free 30.7b9 (afs) 30.8b17 (afs) 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  
RDP remode desktop access client rdesktop rdesktop   free 1.8.3 (deb) 1.9.0 (deb) 1.9.0 (deb)  
Container startup interface sc sc Tool for running MPI/CBS IT provided Singularity containers free stop stop stop  
Singularity builder scbuild SCBUILD Environment to build singularity containers in
chart-bar 		free 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)  
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)  
Software container tool singularity-container singularity   free 2.6.1 (deb) stop stop  

Software to view file contents

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Dicom Viewer aeskulap   home free 0.2.2b1 (deb) 0.2.2 (deb) 0.2.2 (deb)  
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  
BrainNet Viewer brainnetviewer   home chart-bar free 1.70 (afs) 1.70 (afs) stop  
PDF Viewer "Evince" evince   home free stop 3.38.2 (deb) 43.1 (deb) Adobe Reader
ZIP/RAR/7z/LHA/... archive viewer file-roller     free 3.28.0 (deb) 3.38.1 (deb) 43.0 (deb)  
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)  
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 (afs)
2.4 (afs)
2.5 (afs)
3.4 (afs)
3.5.1 (afs)
3.7 (afs)
4.0 (afs)
4.0.1 (afs)
 4.1 (afs) stop  
Text comparision (graphical diff) meld   home free 3.18.0 (deb) 3.20.2 (deb) 3.22.0 (deb)  
Nifti Viewer mricrogl mricrogl home dcm2niix continues to be supported in G7 via the 'dcm2niix' package.
chart-bar 		free 20180623 (afs)
20181111 (afs) 		stop stop  
Nifti Viewer mricron MRICRON mricron chart-bar free 20160222 (afs) 20160222 (afs) stop  
PDF Viewer "qpdfview" qpdfview     free stop 0.4.18 (deb) 0.5.0 (deb) Adobe Reader
Dicom Viewer slicer Slicer home chart-bar free 4.8.1 (nfs) 5.2.2 (nfs)
5.0.3 (nfs) 		stop  
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  

Data visualisation/presentation

Purpose Package ID Command(s) Info License G6 G7 G8 Comparable windows software
Graph generator gnuplot   home free 5.2.2 (deb) 5.4.1 (deb) 5.4.4 (deb)  
Mathamatical function plotter kmplot     free 17.12.3 (deb) 20.12.0 (deb) 22.12.3 (deb) 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) MS Office
Brain image processing and visualisation medinria   home chart-bar free 3.0.0 (afs) 3.2.0 (afs) stop Medinria
Scientific Client-Server-Visualisation paraview   home chart-bar
led-blue 		free 5.4.1 (deb) 5.9.0 (deb) 5.11.0 (deb)  

One or more packages haven't been classified, yet: anatomist bcbtk bips bit cartool catfish ciftity cpac custom dipy dsistudio fl-toolbox freecad jags jupyterlab libmr matplotlib mdt micapipe mpv mriqc nengo netpyne nibabies opsi-configed pymc python-dicom python-enthoughtbase python-mvpa2 python-surfer scirun sconv seaborn solarecl spinach uanwander xtightvncviewer

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Topic revision: 30 Dec 2024, Burk2
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