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Neurodesk

Release History

Latest Version: 2026-04-28

Please consult this page for the template for new releases.

2026-04-28 Latest

New Features

Section titled “New Features”
  • added slurm
  • added opencode, codex, claude agent apps
  • vscode server
  • added webapps
  • added donation banner

Improvements

Section titled “Improvements”
  • VNC and RDP desktops are now secured by random passwords
  • added pytest testing under /opt/tests
  • startup time optimisation
  • size optimisation

Bug Fixes

Section titled “Bug Fixes”
  • fixed NBI default model and instructions for notebooks
2025-12-20

New Features

Section titled “New Features”
  • added pydra
  • add jupyter-sshd-proxy to allow ssh and vscode connections
  • add nbdev
  • add nipoppy

Improvements

Section titled “Improvements”
  • update examples
  • update ipyniivue

Bug Fixes

Section titled “Bug Fixes”
  • pin ipywidgets version to 7.8.5 in Dockerfile to get niivue to work in rise slideshow
2025-06-10

New Features

Section titled “New Features”

Improvements

Section titled “Improvements”
  • updated niivue (with breaking interface change)
  • updated jupyter-lmod (with breaking interface change)
  • moved cvmfs cache to home directory
  • updated background to new Neurodesk logo
  • updated ants to 2.6.0

Bug Fixes

Section titled “Bug Fixes”
  • split cvmfs in 3 different regions
2025-04-08

New Features

Section titled “New Features”

Improvements

Section titled “Improvements”
  • Replaced BIDScoin 4.6.0 with 4.6.1 to fix GUI bug
  • Updated qsiprep to 1.0.1

Bug Fixes

Section titled “Bug Fixes”
  • Improved internet test by using DNS lookup instead of ping
2025-03-14

Bug Fixes

Section titled “Bug Fixes”
  • Startup process was setting variables in different places
2025-03-12

New Features

Section titled “New Features”
  • Added neurodesk copilot dependencies

Bug Fixes

Section titled “Bug Fixes”
  • Apptainer didn’t mount binfmt, which was resulting in simg files not working in offline mode on apple silicon
2025-03-07

Bug Fixes

Section titled “Bug Fixes”
  • CVMFS_DISABLED=false also disabled it.
2025-03-06

Improvements

Section titled “Improvements”
  • Add overlay directory on startup

Bug Fixes

Section titled “Bug Fixes”
  • Only link from cvmfs if cvmfs is not disabled
2025-03-05

New Features

Section titled “New Features”
  • Added support for downloading containers offline, can be activated by setting CVMFS_DISABLE=true
  • Add synthstrip 7.4.1
  • Add pydeface 2.0.2
  • Add fmriprep 24.1.1 20250214

Improvements

Section titled “Improvements”
  • update BIDScoin to 4.5.0
  • update aslprep to 0.7.5
  • update QSMxT to v7.3.1
  • update QSMxT to v7.3.2
  • changed from apptainer -w flag to overlay directory because it works with SIMG files
  • disable automatic GPU flag —nv because it is causing problems on newer host OSs like Ubuntu 24.04
  • automate zenodo doi creation and update to applist.json
  • tweaks in chown of files in homedirectory (#268 #269)
2025-02-04

New Features

Section titled “New Features”
  • Add latency check for cvmfs direct vs CDN
  • Add fsl 6.0.7.16
  • Add dicomtools container

Improvements

Section titled “Improvements”
2025-01-29

New Features

Section titled “New Features”

Bug Fixes

Section titled “Bug Fixes”
  • In JVM, parameters only worked for arm64, not x86
2025-01-24

New Features

Section titled “New Features”
  • add Matlab 2023b
  • add Matlab 2022b
  • new Quay.io jupyter baseimage

Improvements

Section titled “Improvements”
  • update version in neurodesk.yml
  • Change TinyRange share path to /data instead of /share
  • updated deepRetinotopy version
  • update Matlab 2024b

Bug Fixes

Section titled “Bug Fixes”
  • Added workaround for JVM bug on Apple M4
  • added docker fix for macOS to desktop
2024-12-06
  • updated QSMxT: v7.2.2
  • add heudiconv 1.3.1
  • add mriqc 24.0.2 20241108
  • add samsrfx v10.003
  • add palmettobug 0.0.1 20241119
  • add neurodock/pydesigner
  • Update dcm2niix version to 20241125
  • changed CVMFS servers
  • added -w workaround for docker on apple silicon into dockerfile
  • add static strace to /opt for container debugging
  • enabled VNC again and fix RDP auto resizing
2024-10-22
  • use cloudfront distribution only
  • workaround for kernel bug on arm64
  • add ipywidgets ipyvolume jupyterlab_widgets
  • add fsl 6.0.7.14
  • add QSMxT v7.2.1
2024-10-16
  • add jupyter-resource-usage plugin
  • disable VNC
  • remove updating of example directory on startup
  • update jupyter-server-proxy
  • add more CVMFS servers
  • Added relion 4.0.1.sm61 20240528
  • update aslprep to 0.7.0
  • update deepretinotpy to 1.0.5
  • add quickshear
  • add nighres 1.5.1
  • update BIDScoin 4.3.3 and 4.4.0
  • Added bart 0.9.00
  • updated QSMxT to 7.1.0
  • Added mrtrix3src (latest version)
  • update VesselBoost to ver 1.0.0 by @KMarshallX in #301
  • add qmrlab
  • added niimath
  • updated fsl to 6.0.7.8
  • update aslprep to 0.7.2
  • update ants to 2.5.3
  • updated spinalcordtoolbox to 6.4
  • Update afni to 24.2.07
  • add dcm2niix
  • add micapipe 0.2.3
  • added brainnetviewer
  • Added brainlifecli
  • update fmriprep to 24.1.0
  • Update dsistudio 2024.06.12
  • add vmtk 1.5.0
2024-05-25
  • 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
  • https://github.com/neurodesk/neurocommand/releases/tag/2024-05-25
  • 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
2024-03-27
  • Switched from singularity to apptainer
  • added (brkraw) and fixed multiple tools (mrtrix3, julia)
2024-01-12
  • 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 home directory anymore in the side panel.
2023-11-28
  • 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 sent in a jupyter notebook file
2023-10-29
  • bugfix: conda and mamba environments are now initialised correctly when neurodesktop starts up (not just in jupyter)
2023-09-20
  • 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].neurodesk.org 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
20230628
  • directories can now be deleted in jupyter interface even if they contain files
  • moved startup configurations out of .bashrc
  • removed redundant chown of home directory (e.g. affecting windows startup time)
  • added git extension to jupyterlab
  • more robust handling of CVMFS edge cases
20230531
  • included neurodesktop version in hostname
  • removed apt lists
  • triggered automount externally
20230525
  • used jupyter based image
  • fixed environment variables for nipype
  • fixed RDP upload permission errors
  • added symlink on home if /data is mounted
20221216
20221129
  • 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)
20220813
  • 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)
20220701
  • added laynii 2.2.1, layer fMRI toolbox (contributed by Renzo Huber)
  • added fieldtrip 20220617, eeg processing (contributed by David White)
20220329
  • 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
20220302
  • 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)
20220222
  • 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
20220128
  • update of Spinalcordtoolbox to 5.5
  • update of CAT12 to r1933
20220121
  • 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 6.0.5.1
  • 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)
20220111
  • 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
20211220
  • neurodesktop can now be accessed via native RDP client as well (e.g. for multi-monitor support): Windows guide
  • there is a new Help button in the menu
  • updates of ants 2.3.4 (now includes Scripts as well, including antsCookTemplatePriors.sh) + 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
20211207
  • Physio toolbox compiled and added to SPM + update of SPM
  • added brainstorm
  • new neurodesktop container management scripts for Linux, Mac and Windows: https://github.com/neurodesk/neurodesktop
  • added fieldtrip
  • Datalad is now in the main image, so datalad run should work
  • added Oshy-X segmentation tool
  • updated freesurfer 7.2.0
20211028
  • added EEGLAB
20211018
  • added Rstudio, R and multiple R packages (plotly, car, tidyverse, …)
  • added ClearSWI and ROMEO for MRI phase processing
  • 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 home directory 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)
20210929
  • 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)
20210923
  • removed faulty mriqc 0.15.2 container
  • neurodesk.github.io is now starting page in firefox browser
20210918
  • added mriqc 0.16.1 and mrtrix 3.0.3
20210917
  • 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 (visualisation) and added more categories to tools
20210916
  • This is the first version of the newly renamed and rebuilt 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