Release History

Previous releases of neurodesktop
Latest Version


  • add new CVMFS CDN servers
  • add jupyter_scheduler and ipycanvas
  • update guacamole version to 1.5.5 and tomcat to 9.0.87
  • add rise extension for presentations
  • fixed brkraw by @stebo85 in #268
  • QSMxT: v6.4.1 by @astewartau in #270
  • update mrtrix3 by @stebo85 in #271
  • QSMxT: v6.4.2 by @astewartau in #272
  • QSMxT: v6.4.3 by @astewartau in #274
  • update bidscoin to 4.3.2 by @stebo85 in #275
  • update fmriprep by @stebo85 in #277
  • add julia 1.9.4 by @stebo85 in #280
  • update dsi_studio by @stebo85 in #283
  • add glmsingle by @stebo85 in #284
  • ants 2.5.1 20240429 by @stebo85 in #285
  • QSMxT: v6.4.4 by @astewartau in #287


  • Switched from singularity to apptainer
  • added (brkraw) and fixed multiple tools (mrtrix3, julia)


  • fixed fsl GUI error, when starting fsl in VNC mode (the USER was not exported)
  • removed c.ServerApp.root_dir setting because it was causing an error when clicking on the Home button. Now it’s not possible to navigate outside of the homedirectory anymore in the side panel.


  • fixed a bug where the /proc/cpuinfo file under ARM did not contain a MHz entry, which stopped Matlab from starting up
  • fixed a bug where the SINGULARITY_BINDPATH was not send in a jupyter notebook file


  • bugfix: conda and mamba environments are now initialized correctly when neurodesktop starts up (not just in jupyter)


  • the neurodesktop image is now multi-arch and supports x86 and ARM64
  • fixed recursive link creation in /data
  • switched to new cvmfs server geolocation DNS steering policy system: cvmfs[1,2,3] resolve to 3 servers per region which are compared for speed by the client on startup
  • fixed recursive execution of bash shell inside a singularity container
  • fixed empty username
  • switched release tag naming scheme to YYYY-MM-DD instead of YYYYMMDD for better readability


  • directories can now be deleted in jupyter interface even if they contain files
  • moved startup configurations out of .bashrc
  • removed redundant chown of homedirectory (e.g. affecting windows startup time)
  • added git extension to juputerlab
  • more robust handling of CVMFS edge cases


  • included neurodesktop version in hostname
  • removed apt lists
  • triggered automount externally


  • used jupyter based image
  • fixed environment variables for nipype
  • fixed RDP upload permission errors
  • added symlink on home if /data is mounted



  • updated qsmxt to 1.1.13 (contributed by Ashley)
  • added nipype 1.8.3 (contributed by Steffen)
  • added mneextended 1.1.0 (contributed by David)
  • added new tool category “workflows”
  • added new CVMFS mirror server in Phoenix
  • added mimetypes so that nii/minc files now open in the respective applications
  • matlab licenses can now be saved from the activation GUI
  • update rstudio to 2022.07.2 (and R version to 4.1.2 with new additional packages, like brms)


  • updated qsmxt to 1.1.12 (contributed by Ashley)
  • updated 3D Slicer to 5.0.3 and included MONAI Label (contributed by Xincheng)
  • added Matlab 2022a (contributed by Oren)
  • updated AFNI to 22.1.14 (contributed by Steffen)
  • updated Spinal Cord Toolbox to 5.7 (contributed by Steffen)
  • updated Oshyx to 0.4 (contributed by Jeryn)
  • updated freesurfer to 7.3.2 (contributed by Steffen)
  • added CVMFS mirror server in Perth and cleaned up server list to account for DNS geo location steering (contributed by Steffen)


  • added laynii 2.2.1 - layer fMRI toolbox (contributed by Renzo Huber)
  • added fieldtrip 20220617 - eeg processing (contributed by David White)


  • added bidscoin 3.7.0 (converting data to bids) contributed by Oren
  • added sigviewer 0.6.4 (viewing electrophysiological data) contributed by Tom
  • added niftyreg 1.4.0 (image registration tool) contributed by Steffen
  • added mne 1.0.0 (EEG processing pipeline) contributed by David


  • update of ROMEO (phase unwrapping) to latest version 3.2.8
  • update of QSMxT (automated end-to-end QSM processing) to latest version 1.1.10
  • added mritools 3.3.0 (includes clearswi 1.0.1, mcpc3ds 0.1.0, romeo 3.2.8 as compiled binaries)


  • update for PhysIO toolbox (physiological noise correction for fMRI) to r2021a including the latest SPM r8224
  • update of lcmodel to include basis sets for 1.5-9.4T
  • added a memory display plugin to illustrate how much memory is available to the container and how much is consumed
  • added a version checker to help with identifying if a new version is available
  • added file upload via guacamole (+ update of guacamole to 1.4) - users can now drag and drop their files onto guacamole and they get copied to the desktop


  • update of Spinalcordtoolbox to 5.5
  • update of CAT12 to r1933


  • MNE Python 0.23.4 container including VScode and extensions
  • VScode container including Python/Julia Extensions and singularity to test “Inception Mode” (Running singularity containers within singularity containers)
  • update of fsl to
  • added CAT12 (a software that allows estimation of tissue volumes (and additional surface parameters such as cortical thickness, gyrification or fractal dimension) for different volume and surface-based atlas maps)


  • a deep learning based vessel segmentation algorithm “vesselapp” was added in version 0.3.1
  • palm - Permutation Analysis of Linear Models - was added in version alpha119
  • niistat running in octave was added with version 1.0.20191216
  • MRIcroGL was updated to a version with included python support, so the scripting is now working
  • rabies - Rodent Automated Bold Improvement of EPI Sequences was added with version 0.3.5
  • oshyx was updated to 0.3


  • neurodesktop can now be accessed via native RDP client as well (e.g. for multi-monitor support):
  • there is a new Help button in the menu :)
  • updates of ants 2.3.4 (now includes Scripts as well, including + newly added version 2.3.5
  • new version of QSMxT 1.1.9 20211219
  • new version of Spinal Cord Toolbox 5.4
  • new tools: MRIcroGL and surfice - fantastic viewers for neuroimaging data


  • Physio toolbox compiled and added to SPM + update of SPM
  • added brainstorm
  • new neurodesktop container management scripts for Linux, Mac and Windows:
  • added fieldtrip
  • Datalad is now in the main image, so datalad run should work
  • added Oshy-X segmentation tool
  • updated freesurfer 7.2.0


  • added EEGLAB


  • added Rstudio, R and multiple R packages (plotly, car, tidyverse, …)
  • added ClearSWI and ROMEO for MRI phase processing (including new Tutorials:
  • added more categories in applications menu (Body, Electrophysiology, Hippocampus, Phase Processing, Rodent Imaging, Shape Analysis, Spine, Statistics)
  • bugfix: improved startup time of the desktop container (miniconda in homedirectory was causing chmod slowdown)
  • bugfix: ssh, vnc and rdp servers are now restarted in case the container was stopped and started again (e.g. on Standby)


  • fixed naming of aidmri to aidamri and added new category “Rodent Imaging”
  • updated all tool icons and updated neurodesk icon including background image
  • VScode now stores settings in persistent storage /neurodesktop-storage and with this keeps extensions and settings across different neurodesktop versions
  • docker layers are now cached, so updating the desktop to the next version is very fast and consumes less disk space locally
  • default theme of terminal changed from Solarized to Tango as the old theme was hiding information in tools like htop (same font colour on same background…)


  • removed faulty mriqc 0.15.2 container
  • is now starting page in firefox browser


  • added mriqc 0.16.1 and mrtrix 3.0.3


  • included more tools for connecting to cloud storage services (rclone, owncloud, nextcloud, davfs2, globus). For more info: Storage
  • styling of desktop interface, including background wallpaper and colour scheme in terminal window
  • new categories in menu system (visualization) and added more categories to tools


  • This is the first version of the newly renamed and rebuild neurodesktop (previously vnm and neuromachine)
  • containers are mounted by default from CVMFS, but this can be deactivated by adding -e CVMFS_DISABLE=true to the docker call