Neurocontainers

• 1: CVMFS
• 2: DataLad
• 3: Docker
• 4: OpenRecon
• 5: Singularity/Apptainer
• 6: Windows 11 and Windows Subsystem for Linux

1 - CVMFS

Install the CernVM File System (CVMFS)

To begin, install CVMFS. Follow the official instructions here: https://cvmfs.readthedocs.io/en/stable/cpt-quickstart.html#getting-the-software

An example installation for Ubuntu in Windows Subsystem for Linux (WSL) would look like this:

sudo apt-get install lsb-release
wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb
sudo dpkg -i cvmfs-release-latest_all.deb
rm -f cvmfs-release-latest_all.deb
sudo apt-get update
sudo apt-get install build-essential
sudo apt-get install cvmfs

Ubuntu 24.04 might have an issue with this, so try installing dependies manually:

sudo apt install libattr1=1:2.5.2-1build1 libuuid1=2.39.3-9ubuntu6

Configure CVMFS

Once installed create the keys and configure the servers used:

sudo mkdir -p /etc/cvmfs/keys/ardc.edu.au/


echo "-----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAwUPEmxDp217SAtZxaBep
Bi2TQcLoh5AJ//HSIz68ypjOGFjwExGlHb95Frhu1SpcH5OASbV+jJ60oEBLi3sD
qA6rGYt9kVi90lWvEjQnhBkPb0uWcp1gNqQAUocybCzHvoiG3fUzAe259CrK09qR
pX8sZhgK3eHlfx4ycyMiIQeg66AHlgVCJ2fKa6fl1vnh6adJEPULmn6vZnevvUke
I6U1VcYTKm5dPMrOlY/fGimKlyWvivzVv1laa5TAR2Dt4CfdQncOz+rkXmWjLjkD
87WMiTgtKybsmMLb2yCGSgLSArlSWhbMA0MaZSzAwE9PJKCCMvTANo5644zc8jBe
NQIDAQAB
-----END PUBLIC KEY-----" | sudo tee /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub

echo "CVMFS_USE_GEOAPI=yes" | sudo tee /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf

echo 'CVMFS_SERVER_URL="http://cvmfs-geoproximity.neurodesk.org/cvmfs/@fqrn@;http://cvmfs.neurodesk.org/cvmfs/@fqrn@;http://s1osggoc-cvmfs.openhtc.io:8080/cvmfs/@fqrn@;http://s1fnal-cvmfs.openhtc.io:8080/cvmfs/@fqrn@;http://s1sampa-cvmfs.openhtc.io:8080/cvmfs/@fqrn@;http://s1brisbane-cvmfs.openhtc.io/cvmfs/@fqrn@;http://s1nikhef-cvmfs.openhtc.io/cvmfs/@fqrn@;http://s1bnl-cvmfs.openhtc.io/cvmfs/@fqrn@;http://s1perth-cvmfs.openhtc.io/cvmfs/@fqrn@"' | sudo tee -a /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf 

echo 'CVMFS_KEYS_DIR="/etc/cvmfs/keys/ardc.edu.au/"' | sudo tee -a /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf

echo "CVMFS_HTTP_PROXY=DIRECT" | sudo tee  /etc/cvmfs/default.local
echo "CVMFS_QUOTA_LIMIT=5000" | sudo tee -a  /etc/cvmfs/default.local

sudo cvmfs_config setup

You can use the list above, but you can also pick a subset of servers that are close to you or fit your usecase better. To better understand what to choose, we use the following CVMFS server setup:

These CVMFS Stratum 1 servers are hosted by the Open Science Grid and every server has a Cloudflare CDN alias that is correctly geo-located through the Maxmind GEOAPI service in the CVMFS client:

• Illinois, USA: s1fnal-cvmfs.openhtc.io:8080 -> cvmfs-s1fnal.opensciencegrid.org:8000
• Nebraska, USA: s1osggoc-cvmfs.openhtc.io:8080 -> cvmfs-s1goc.opensciencegrid.org:8000
• New York, US: s1bnl-cvmfs.openhtc.io:8080 -> cvmfs-s1bnl.opensciencegrid.org:8000
• Oxford, UK: s1ral-cvmfs.openhtc.io:8080 -> cvmfs-egi.gridpp.rl.ac.uk:8000
• Netherlands, Europe: s1nikhef-cvmfs.openhtc.io:8080 -> cvmfs01.nikhef.nl:8000

This server is currently down:

• Sao Paulo, Brazil: s1sampa-cvmfs.openhtc.io:8080 -> sampacs01.if.usp.br:8000

These CVMFS Stratum 1 servers are hosted by ARDC Nectar Cloud and also has a Cloudflare CDN alias.

• Brisbane, Queensland, Australia: s1brisbane-cvmfs.openhtc.io -> cvmfs-brisbane.neurodesk.org
• Sydney, New South Wales, Australia: s1sydney-cvmfs.openhtc.io -> cvmfs-sydney.neurodesk.org
• Melbourne, Victoria, Australia: s1melbourne-cvmfs.openhtc.io -> cvmfs-melbourne.neurodesk.org
• Perth, Western Australia, Australia: s1perth-cvmfs.openhtc.io -> cvmfs-perth.neurodesk.org

This CVMFS Stratum 1 server is hosted by AWS:

• Frankfurt, Germany: cvmfs-frankfurt.neurodesk.org -> ec2-3-72-92-91.eu-central-1.compute.amazonaws.com

This CMVFS Stratum 1 server is hosted by Jetstream:

• Indiana, US: cvmfs-jetstream.neurodesk.org -> 149.165.172.188

Then we have a one geolocation-steered domain: cvmfs-geoproximity.neurodesk.org

• 153.02 (Longitude),-27.46 (Latitude) -> cvmfs-brisbane.neurodesk.org

• 151.2073, -33.8678 -> cvmfs-sydney.neurodesk.org

• 115.86,-31.95 -> cvmfs-perth.neurodesk.org

• -88.30,41.84 -> cvmfs-s1fnal.opensciencegrid.org

• -96.66,40.83 -> cvmfs-s1goc.opensciencegrid.org

• -1.26, 51.75 -> cvmfs-egi.gridpp.rl.ac.uk

• 4.90,52.37 -> cvmfs01.nikhef.nl

• 8.68,50.11 -> ec2-3-72-92-91.eu-central-1.compute.amazonaws.com

• -46.63,-23.54 -> sampacs01.if.usp.br

• -86.45,39.22 -> cvmfs-jetstream.neurodesk.org

• 145.13,-37.92 -> cvmfs-melbourne.neurodesk.org

• Every location has a health check attached to it and doesn’t forward to it if the destination is not working.

Then we have 3 direct URLS without CDNs as well that are geolocation-steered: cvmfs1.neurodesk.org: South America -> sampacs01.if.usp.br North America -> cvmfs-s1fnal.opensciencegrid.org Default -> cvmfs-brisbane.neurodesk.org Europe -> ec2-3-72-92-91.eu-central-1.compute.amazonaws.com Asia -> cvmfs-perth.neurodesk.org

cvmfs2.neurodesk.org: North America -> cvmfs-s1goc.opensciencegrid.org Europe -> cvmfs01.nikhef.nl Default -> cvmfs-s1goc.opensciencegrid.org

cvmfs3.neurodesk.org: North America -> cvmfs-s1bnl.opensciencegrid.org Asia -> cvmfs-brisbane.neurodesk.org Default -> cvmfs-s1bnl.opensciencegrid.org Oceania -> cvmfs-perth.neurodesk.org

These servers are currently NOT working and are NOT YET mirroring our repository (we are waiting for RAL to come back online, then the others will mirror that):

• Swinburne, Australia: s1swinburne-cvmfs.openhtc.io:8080 -> cvmfs-s1.hpc.swin.edu.au:8000
• China: s1ihep-cvmfs.openhtc.io:8080 -> cvmfs-stratum-one.ihep.ac.cn:8000

For WSL users

You will need to run this for each new WSL session:

sudo cvmfs_config wsl2_start

Test if the connection works:

sudo cvmfs_config chksetup

ls /cvmfs/neurodesk.ardc.edu.au

sudo cvmfs_talk -i neurodesk.ardc.edu.au host info

cvmfs_config stat -v neurodesk.ardc.edu.au

For Ubuntu 22.04 users

If configuring CVMFS returns the following error:

Error: failed to load cvmfs library, tried: './libcvmfs_fuse3_stub.so' '/usr/lib/libcvmfs_fuse3_stub.so' '/usr/lib64/libcvmfs_fuse3_stub.so' './libcvmfs_fuse_stub.so' '/usr/lib/libcvmfs_fuse_stub.so' '/usr/lib64/libcvmfs_fuse_stub.so'
./libcvmfs_fuse3_stub.so: cannot open shared object file: No such file or directory
/usr/lib/libcvmfs_fuse3_stub.so: cannot open shared object file: No such file or directory
/usr/lib64/libcvmfs_fuse3_stub.so: cannot open shared object file: No such file or directory
./libcvmfs_fuse_stub.so: cannot open shared object file: No such file or directory
libcrypto.so.1.1: cannot open shared object file: No such file or directory
/usr/lib64/libcvmfs_fuse_stub.so: cannot open shared object file: No such file or directory


Failed to read CernVM-FS configuration

A temporary workaround is:

wget https://mirror.umd.edu/ubuntu/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1f-1ubuntu2.15_amd64.deb
dpkg -i libssl1.1_1.1.1f-1ubuntu2.15_amd64.deb

Install singularity/apptainer

e.g for Ubuntu/Debian install apptainer:

sudo apt-get install -y software-properties-common
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt-get update
sudo apt-get install -y apptainer
sudo apt-get install -y apptainer-suid

e.g. for Ubuntu/Debian install singularity:

export VERSION=1.18.3 OS=linux ARCH=amd64 && \
    wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
    sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
    rm go$VERSION.$OS-$ARCH.tar.gz

echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
    echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
    source ~/.bashrc

go get -d github.com/sylabs/singularity

export VERSION=v3.10.0 # or another tag or branch if you like && \
    cd $GOPATH/src/github.com/sylabs/singularity && \
    git fetch && \
    git checkout $VERSION # omit this command to install the latest bleeding edge code from master

export VERSION=3.10.0 && # adjust this as necessary \
    mkdir -p $GOPATH/src/github.com/sylabs && \
    cd $GOPATH/src/github.com/sylabs && \
    wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
    tar -xzf singularity-ce-${VERSION}.tar.gz && \789
    cd ./singularity-ce-${VERSION} && \
    ./mconfig --without-seccomp --without-conmon

./mconfig --without-seccomp --without-conmon && \
    make -C ./builddir && \
    sudo make -C ./builddir install

export PATH="/usr/local/singularity/bin:${PATH}"

Use of Neurodesk CVMFS containers

The containers are now available in /cvmfs/neurodesk.ardc.edu.au/containers/ and can be started with:

singularity shell /cvmfs/neurodesk.ardc.edu.au/containers/itksnap_3.8.0_20201208/itksnap_3.8.0_20201208.simg

make sure that SINGULARITY_BINDPATH includes the directories you want to work with:

export SINGULARITY_BINDPATH='/cvmfs,/mnt,/home'

For WSL users

The homedirectory might not be supported. Avoid mounting it with

singularity shell --no-home /cvmfs/neurodesk.ardc.edu.au/containers/itksnap_3.8.0_20201208/itksnap_3.8.0_20201208.simg

or configure permanently:

sudo vi /etc/singularity/singularity.conf

set

mount home = no

Install module system

sudo yum install lmod

or

sudo apt install lmod

Use of containers in the module system

Configuration for module system

Create a the new file /usr/share/module.sh with the content (NOTE: update the version, here 6.6, with your lmod version, e.g. 6.6 (Ubuntu 20.04/22.04), 8.6.19 (Ubuntu 24.04)):

# system-wide profile.modules                                          #
# Initialize modules for all sh-derivative shells                      #
#----------------------------------------------------------------------#
trap "" 1 2 3

case "$0" in
    -bash|bash|*/bash) . /usr/share/lmod/YOURLMODVERSION_HERE/init/bash ;;
       -ksh|ksh|*/ksh) . /usr/share/lmod/YOURLMODVERSION_HERE/init/ksh ;;
       -zsh|zsh|*/zsh) . /usr/share/lmod/YOURLMODVERSION_HERE/init/zsh ;;
          -sh|sh|*/sh) . /usr/share/lmod/YOURLMODVERSION_HERE/init/sh ;;
                    *) . /usr/share/lmod/YOURLMODVERSION_HERE/init/sh ;;  # default for scripts
esac

trap - 1 2 3

Make the module system usable in the shell

Add the following lines to your ~/.bashrc file or to /etc/bash.bashrc for a global install:

if [ -f '/usr/share/module.sh' ]; then source /usr/share/module.sh; fi

if [ -d /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules ]; then
        # export MODULEPATH="/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules"
        module use /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*
else
        export MODULEPATH="/neurodesktop-storage/containers/modules"              
        module use $MODULEPATH
        export CVMFS_DISABLE=true
fi

if [ -f '/usr/share/module.sh' ]; then
        echo 'Run "ml av" to see which tools are available - use "ml <tool>" to use them in this shell.'
        if [ -v "$CVMFS_DISABLE" ]; then
                if [ ! -d $MODULEPATH ]; then
                        echo 'Neurodesk tools not yet downloaded. Choose tools to install from the Application menu.'
                fi
        fi
fi

Restart the current shell or run

source ~/.bashrc

Use of containers in the module system

export SINGULARITY_BINDPATH='/cvmfs,/mnt,/home'
module use /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*
ml fsl
fslmaths

Troubleshooting and diagnostics

# Check servers
sudo cvmfs_talk -i neurodesk.ardc.edu.au host probe
sudo cvmfs_talk -i neurodesk.ardc.edu.au host info

# Change settings
sudo touch /var/log/cvmfs_debug.log.cachemgr
sudo chown cvmfs /var/log/cvmfs_debug.log.cachemgr
sudo touch /var/log/cvmfs_debug.log
sudo chown cvmfs /var/log/cvmfs_debug.log

sudo vi /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf
echo -e "\nCVMFS_DEBUGLOG=/var/log/cvmfs_debug.log" | sudo tee -a /etc/cvmfs/default.local
cat /etc/cvmfs/default.local
sudo cvmfs_config umount
sudo service autofs stop
sudo mount -t cvmfs neurodesk.ardc.edu.au /cvmfs/neurodesk.ardc.edu.au
# check if new settings are applied correctly:
cvmfs_config showconfig neurodesk.ardc.edu.au

cat /var/log/cvmfs_debug.log
cat /var/log/cvmfs_debug.log.cachemgr 

2 - DataLad

Using Neurodesk Containers with DataLad

This page explains how to use DataLad and the ReproNim containers with Neurodesk tools.

Install DataLad, datalad-container, and the ReproNim containers repository

conda install datalad
pip install datalad_container
datalad install https://github.com/ReproNim/containers.git
cd containers

List all default available containers

datalad containers-list

Download and run the latest container version

datalad containers-run -n neurodesk-romeo

Change version of container

You can change which version of a container is used in two ways:

Option 1: change version in .datalad/config

vi .datalad/config
# now change the version of the container you like
# all available containers can be seen via `ls images/neurodesk`
datalad save -m 'downgraded version of romeo to x.x.x'
datalad containers-run -n neurodesk-romeo

Option 2: change version using freeze_versions script

# all available containers can be seen via `ls images/neurodesk`
scripts/freeze_versions neurodesk-romeo=3.2.4
datalad save -m 'downgraded version of romeo to 3.2.4'
datalad containers-run -n neurodesk-romeo

3 - Docker

Our containers are automatically built in https://github.com/neurodesk/neurocontainers/ and hosted on dockerhub and on github

Pull Docker containers

e.g. for a julia container docker

docker pull vnmd/julia_1.6.1

You an also build singularity images from dockerhub

singularity build julia_1.6.1.simg docker://vnmd/julia_1.6.1

Replace julia_1.6.1 with your selected application. You can find the available containers here: https://neurodesk.org/applications/

4 - OpenRecon

Building an OpenRecon Container

These instructions were tested on GitHub Codespaces, and we recommend Codespaces as a starting point.

For a local setup, install Docker, Python 3, and neurodocker. If neurodocker is not already on your PATH, add it:

python -m pip install neurodocker

# Check whether neurodocker is already on PATH:
which neurodocker

# If not, add the appropriate local install path.
# The path depends on your local setup.
export PATH=$PATH:~/.local/lib/python3.12/site-packages/bin
export PATH=$PATH:~/.local/bin

1. Add the Python MRD server to a Neurocontainers recipe

Add the OpenRecon macro to any recipe in the neurocontainers recipes directory:

- include: macros/openrecon/neurodocker.yaml

Make sure to adjust invertcontrast.py for your pipeline, or replace it with the files your pipeline needs from the Python MRD server.

Here is an example Neurocontainers recipe.

Then build the recipe:

sf-login openreconexample --architecture x86_64
# Or:
./builder/build.py generate openreconexample --recreate --build --login --architecture x86_64 --offline_mode true

2. Test the tool inside the container and then through the MRD server

Convert data to MRD test data

Note: enhanced DICOM and NIfTI-to-MRD conversion scripts are not yet merged into the main branch of python-ismrmrd-server.

In the meantime, get the scripts here:

• enhanceddicom2mrd.py
• nifti2mrd.py

Then add them to the image in build.yaml:

        - copy: enhanceddicom2mrd.py /opt/code/python-ismrmrd-server/enhanceddicom2mrd.py
        - copy: nifti2mrd.py /opt/code/python-ismrmrd-server/nifti2mrd.py

The directory that the container is built from is mounted automatically under /buildhostdirectory.

cd /opt/code/python-ismrmrd-server

# For legacy DICOM data:
python3 dicom2mrd.py -o input_data.h5 PATH_TO_YOUR_DICOM_FILES

# For enhanced DICOM data:
python /opt/code/python-ismrmrd-server/enhanceddicom2mrd.py -o /buildhostdirectory/input.h5 /buildhostdirectory/enhanced_dicom_data

# For converting NIfTI data to MRD:
python3 nifti2mrd.py -i /buildhostdirectory/input_Se1_Res0.8_0.8_Spac0.8.nii -o /buildhostdirectory/input_fromNIFTI.h5

Start the server and client, then test the application:

python3 /opt/code/python-ismrmrd-server/main.py -v -r -H=0.0.0.0 -p=9002 -s -S=/tmp/share/saved_data &
sleep 2
python3 /opt/code/python-ismrmrd-server/client.py -G dataset -o openrecon_output.h5 input_data.h5 -c openreconexample

3. Submit the container recipe to Neurocontainers

Submit the container recipe to the neurocontainers repository.

Here is an example: openreconexample.

The container is built automatically. If the build is successful, a pull request will be opened automatically for step 4.

4. Submit the container to OpenRecon

Submit the container to the openrecon repository.

Here is an example: openreconexample.

Detailed instructions for building on GitHub directly

Contributed by Kerrin Pine.

Prerequisites

You need a public GitHub account so the container can be submitted to the public Neurodesk OpenRecon repository and built.

Process

1. Fork neurodesk/neurocontainers to your personal GitHub account. In the upper-right corner, click Fork. If prompted, fork to your personal GitHub account.

2. After forking, go to your forked repository, for example github.com/YOUR_GITHUB_USERNAME/neurocontainers.

3. Create a new codespace. In your forked repository, click the green <> Code button, then select Create codespace on main.

4. In the terminal, run neurodocker --version. You should see a version such as 2.0.0.

5. Still in the terminal, run cd recipes, create a project directory with mkdir projectname, and copy the files from recipes/openreconexample into this new directory.

6. In build.yaml and test.yaml, change all occurrences of openreconexample to your own project name, and change openreconexample.py to projectname.py.

7. Follow the instructions in build.yaml to build.

8. Building drops you into the container itself. Follow the instructions in test.yaml to import your own test DICOM data into an .h5 file for testing. In Codespaces, you can drag data from another window into the folder.

9. Continue following the instructions in test.yaml to start the server and send demo data to it. For example:

   python3 /opt/code/python-ismrmrd-server/client.py \
     -G dataset \
     -o /buildhostdirectory/output.h5 \
     /buildhostdirectory/b0map.h5 \
     -c openreconexample

   You should see the expected number of images sent from the client to the server and returned by the server. The output in output.h5 can be viewed with the built-in H5Web viewer.

10. To check intermediate outputs for troubleshooting, open Extensions with Ctrl+Shift+X or the Extensions icon on the left, then install niivue for NIfTI image viewing in Codespaces.

11. Once the container has been thoroughly tested and you are happy with it, commit the new files and push them if you were not working on github.com. Do not include your demo data.

12. To build a container ready for the scanner, first open a pull request. For example: Add projectname container for OpenRecon MRD server. In the pull request description, include the neurodocker.yaml build instructions, the customized MRD Python scripts, and the Codespaces testing notes.

13. The second step is to write a recipe for neurodesk/openrecon. Because it is a separate repository, fork it, navigate to recipes, create a folder for your project, and add OpenReconLabel.json and params.sh with the version number. OpenReconLabel.json defines how the container description and UI options appear on the scanner. Then open a pull request. Updating the version number will trigger the container to be rebuilt, and instructions for downloading and installing the container will appear as an issue in that repository.

Tips, tricks, and troubleshooting for OpenRecon

Installing and testing a new OpenRecon package

Make sure that no protocol is open, because an open protocol can prevent installation of a new package.

Copy the OpenRecon zip file into C:\Program Files\Siemens\Numaris\OperationalManagement\FileTransfer\incoming.

Wait for the file to disappear.

Check whether it is being installed by watching C:\ProgramData\Siemens\Numaris\log\syngo.MR.HostInfra.OpenRecon.Watcher.

It should first create a 0 KB text file with the container name and version.

The text file then fills to about 100-200 KB.

Once the log file is written, you can open a protocol and check whether the package is available.

Run the sequence with OpenRecon enabled and check for errors in the log viewer at C:\ProgramData\Siemens\Numaris\log\OpenRecon.utr.

Do not use Prio Recon with OpenRecon

This option has to be disabled in an OpenRecon sequence:

Right-click Sequence in the Scan Queue, then select Edit Properties (Alt+Enter) and Execution.

CUDA version

Make sure that you install the correct CUDA version in the container and that it does not get overwritten by a pip install. OpenRecon only supports CUDA 11.x.

Always double-check in the container with:

# Check that the CUDA version is valid for MARS; it must be CUDA 11.x.
python -c "import torch; print(torch.version.cuda)"

Versioning of containers

OpenRecon requires container versions. For example, on the scanner, version 1.2.3 only shows the major version in the selection box, but hovering over the name shows the full version:

OpenRecon will not install an update to a container with the same version.

High-performance computing license side effects

For OpenRecon to work, the N_High_End_Computing license must be active on the scanner.

Activating this license takes memory away from the main ICE recon system, so normal recons might run out of memory sooner. If you need this memory back, you can temporarily disable this license and OpenRecon.

Turn the license off by commenting it out. Add # in front of the relevant lines in C:\Program Files\Siemens\Numaris\bin\Common\Licensing\license.dat.

Restart the whole system. Restarting the workspace is not enough.

Cleaning up package on the scanner

After installing a few different versions the container library can get full.

Download the tool “wip_OpenRecon_PackageRemover_Tool.exe” from the Siemens magnetom.net forum. Make sure to follow the installation instructions. Then run wip_OpenRecon_PackageRemover_Tool.exe -p to cleanup old versions.

For the deletion to work (and for the tool to see your OpenRecon package), the package needs to be labeled as Research - it will not touch OpenRecon tools labels as Product.

so check, that you have this in your OpenReconLabel.json file:

    "content_qualification_type": "RESEARCH"

5 - Singularity/Apptainer

Our docker containers are converted to singularity/apptainer containers and stored on Object storage.

Download Singularity Containers

First get an overview of which containers are available as Singularity containers: https://github.com/neurodesk/neurocommand/blob/main/cvmfs/log.txt

curl -s https://raw.githubusercontent.com/neurodesk/neurocommand/main/cvmfs/log.txt

assign the container name to a variable:

export container=itksnap_3.8.0_20201208

Then download the containers. One way is to use CURL:

curl -X GET https://neurocontainers.s3.us-east-2.amazonaws.com/$container.simg -O

Singularity Containers and GPUs

Some of our containers contain GPU-accelerated applications. Here is an example that tests the GPU accelerated program eddy in FSL:

curl -X GET https://neurocontainers.s3.us-east-2.amazonaws.com/fsl_6.0.5.1_20221016.simg -O
git clone https://github.com/neurolabusc/gpu_test.git
singularity shell --nv fsl_6.0.5.1_20221016.simg
cd gpu_test/etest/
bash runme_gpu.sh

Transparent Singularity

The singularity containers can be also be used in combination with our Transparent Singularity Tool, which wraps the executables inside a container to make them easily available for pipelines. More information can be found here:

one example to do this is:

curl -s https://raw.githubusercontent.com/neurodesk/neurocommand/main/cvmfs/log.txt
export container=itksnap_3.8.0_20201208
git clone https://github.com/neurodesk/transparent-singularity ${container}
cd ${container}
./run_transparent_singularity.sh ${container}

6 - Windows 11 and Windows Subsystem for Linux

1. Install WSL

Follow the instructions to enable Windows Subsystem for Linux 2 in Windows 11: https://docs.microsoft.com/en-us/windows/wsl/install

2. Configure CVMFS, Singularity and LMOD (only needs to be done once)

Install build tools

sudo apt update
sudo apt install make gcc

Install singularity

export SINGULARITY_VERSION=3.9.3 VERSION=1.17.2 OS=linux ARCH=amd64
wget -q https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz 
sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz 
rm go$VERSION.$OS-$ARCH.tar.gz 
export GOPATH=${HOME}/go 
export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin 
mkdir -p $GOPATH/src/github.com/sylabs 
cd $GOPATH/src/github.com/sylabs 
wget -q https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz 
tar -xzvf singularity-ce-${SINGULARITY_VERSION}.tar.gz 
cd singularity-ce-${SINGULARITY_VERSION} 
./mconfig --prefix=/usr/local/singularity 
make -C builddir 
sudo make -C builddir install 
cd .. 
sudo rm -rf singularity-ce-${SINGULARITY_VERSION} 
sudo rm -rf /usr/local/go $GOPATH

Setup Bindpaths for Singularity (e.g. in .bashrc)

export PATH="/usr/local/singularity/bin:${PATH}"
export SINGULARITY_BINDPATH='/cvmfs,/mnt,/home'

CVMFS

Follow the instructions here: https://neurodesk.org/docs/getting-started/neurocontainers/cvmfs/

LMOD

sudo apt install lmod

3. Use Neurodesk containers

sudo cvmfs_config wsl2_start

module use /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*

Example usage of fsleyes:

ml fsl
fsleyes

List the available programs:

ml av