A compact Docker container with a browser-accessible environment for reproducible neuroimaging analysis. Only the required software packages, already pre-installed, are downloaded from a public library (downloaded as containers).
You're welcome to complete the survey to help guide future additions to the software library: https://forms.gle/deKy85yniJLP4hDM8
For inquiries, please open a new issue, or contact Steffen Bollmann (https://github.com/stebo85) or Oren Civier (https://github.com/civier) or Aswin Narayanan (https://github.com/aswinnarayanan).
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Install Docker from here: https://docs.docker.com/get-docker/ (Mac, Windows, Linux; for HPC/supercomputer: https://github.com/NeuroDesk/neurodesk)
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Create a local folder where the downloaded software packages will be stored, e.g. ~/vnm in Mac and Linux, or C:\vnm in Windows
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Open a terminal, and type the folowing command to automatically download the VNM container and run it (Mac, Windows, Linux commands listed below)
- Mac:
docker run --privileged --name vnm -v ~/vnm:/vnm -e USER=neuro -p 6080:80 -p 5900:5900 vnmd/vnm:20210113
- Windows:
docker run --privileged --name vnm -v C:/vnm:/vnm -e USER=neuro -p 6080:80 -p 5900:5900 vnmd/vnm:20210113
- Linux:
sudo docker run --privileged --name vnm -v ~/vnm:/vnm -v /dev/shm:/dev/shm -e USER=neuro -p 6080:80 -p 5900:5900 vnmd/vnm:20210113
- Once VNM is downloaded i.e. "INFO success: novnc entered RUNNING state" is displayed in terminal, open a browser and go to:
http://localhost:6080
or open a VNC Client and connect to port 5900
- VNM is ready to use!
(The sudo default sudo password is "ubuntu")
Click on the Launcher icon in bottom-left corner and navigate to the "VNM Neuroimaging" menu, then select the application and version you wish to launch. If it is the first time you launch the application, it will be downloaded to your desktop environment. The application is ready to use when the "Singularity>" propmpt appears in the terminal window that opens. You can now run the GUI of the application (e.g., typing 'fsl') or any other utilities included with it.
Alternatively one can download an application from the command line, e.g.:
bash /neurodesk/local/fetch_and_run.sh fsl 6.0.3 20200905
(Notice: last argument is to be taken from https://github.com/NeuroDesk/neurodesk/blob/master/neurodesk/apps.json)
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Click on the terminal from which you ran VNM
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Press control-C
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Type:
docker stop vnm
- Type:
docker rm vnm
add the following parameter to the docker call:
-e RESOLUTION=1920x980
open in VNC viewer: http://localhost:5900
- Oracle OCI: https://mri.sbollmann.net/index.php/2020/12/08/run-neurodesk-on-oracle-cloud-free-tier/
- Microsoft Azure: https://henryjburg.medium.com/neurodesk-running-on-azure-3e38c590a152
- Git 2.25.1 (version control)
- Lmod 6.6 (for handling different versions of software)
- Nipype 1.5.0 (workflow system for neuro-imaging)
- Python 3.8.2 (programming language)
- Rsync 3.1.3 (synchronization of data)
- Singularity 3.7.0 (container runtime)
- Visual Studio Code 1.46.1 (code editor and development environment)
https://github.com/NeuroDesk/caid/packages
curl -s https://github.com/Neurodesk/caid/packages | sed -n "s/^.*\/NeuroDesk\/caid\/packages\/.*>\(.*\)\(\S*\)<\/a>$/\1/p"
https://github.com/NeuroDesk/neurodesk/blob/master/neurodesk/apps.json
curl -s https://raw.githubusercontent.com/NeuroDesk/neurodesk/master/neurodesk/apps.json
- Open a terminal window (there is a terminal icon in the bottom application bar)
- Examine the list of downloaded packages that shows up in the terminal window
- Use the 'module' command, giving the desired downloaded package as an argument, e.g.
module load fsl_6.0.3
- Call the programs/scripts included in the package as you would do if it was installed on your desktop, e.g.
fsleyes
- window tiling is set to: SHIFT-ALT-CTRL-{left,right,up,down}
