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Before data acquisition (storage preparation)

DataLad must be version 0.19 or later

This project maintains data under version control thanks to DataLad1. For instructions on how to setup DataLad on your PC, please refer to the official documentation. When employing high-performance computing (HPC), we provide some specific guidelines.

Please read the DataLad Handbook, especially if you are new to this tool

Creating a DataLad dataset

  • Designate a host and folder where data will be centralized. In the context of this study, the primary copy of data will be downloaded into <hostname>, under the path /data/datasets/hcph-pilot-sourcedata for the piloting acquisitions and /data/datasets/hcph-sourcedata for the experimental data collection.
  • Install the bids DataLad procedure provided from this repository to facilitate the correct intake of data and metadata:

    PYTHON_SITE_PACKAGES=$( python -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])' )
    ln -s <path>/code/datalad/cfg_bids.py ${PYTHON_SITE_PACKAGES}/datalad/resources/procedures/
    
    DataLad's documentation does not recommend this approach

    For safety, you can prefer to use DataLad's recommendations and place the cfg_bids.py file in some of the suggested paths.

  • Check the new procedure is available as bids:

    $ datalad run-procedure --discover
    cfg_bids (/home/oesteban/.miniconda/lib/python3.9/site-packages/datalad/resources/procedures/cfg_bids.py) [python_script]
    cfg_yoda (/home/oesteban/.miniconda/lib/python3.9/site-packages/datalad/resources/procedures/cfg_yoda.py) [python_script]
    cfg_metadatatypes (/home/oesteban/.miniconda/lib/python3.9/site-packages/datalad/resources/procedures/cfg_metadatatypes.py) [python_script]
    cfg_text2git (/home/oesteban/.miniconda/lib/python3.9/site-packages/datalad/resources/procedures/cfg_text2git.py) [python_script]
    cfg_noannex (/home/oesteban/.miniconda/lib/python3.9/site-packages/datalad/resources/procedures/cfg_noannex.py) [python_script]
    

    Learn more about the YODA principles (DataLad Handbook)

  • Create a DataLad dataset for the original dataset:

    cd /data/datasets/
    datalad create -c bids hcph-dataset
    
  • Configure a RIA store, where large files will be pushed (and pulled from when installing the dataset in other computers)

    Creating a RIA sibling to store large files
    cd hcph-dataset
    datalad create-sibling-ria -s ria-storage --alias hcph-dataset \
            --new-store-ok --storage-sibling=only \
            "ria+ssh://<username>@<hostname>:<path>/dataset/"
    

  • Configure a GitHub sibling, to host the Git history and the annex metadata:

    Creating a GitHub sibling to store DataLad's infrastructure and dataset's metadata
    datalad siblings add --dataset . --name github \
            --pushurl git@github.com:<organization>/<repo_name>.git \
            --url https://github.com/<organization>/<repo_name>.git \
            --publish-depends ria-storage
    

Client side operations (when consuming the data)

Installing the DataLad dataset

Wherever you want to process the data, you'll need to datalad install it before you can pull down (datalad get) the data. To access the metadata (e.g., sidecar JSON files of the BIDS structure), you'll need to have access to the git repository that corresponds to the data (https://github.com/<organization>/<repo_name>.git) To fetch the dataset from the RIA store, you will need your SSH key be added to the authorized keys.

Getting access to the RIA store

These steps must be done just once before you can access the dataset's data:

  • Create a secure SSH key on the system(s) on which you want to install the dataset.
  • Send the SSH public key you just generated (e.g., ~/.ssh/id_ed25519.pub) over email to Oscar at *@****.
  • Install and get the dataset normally:

    datalad install https://github.com/<organization>/<repo_name>.git
    
    datalad install -g -J 8 https://github.com/<organization>/<repo_name>.git
    

Synchronizing your DataLad dataset

Once the dataset is installed, new sessions will be added as data collection goes on. When a new session is added, your DataLad dataset will remain at the same point in history (meaning, it will become out-of-date).

  • Pull new changes in the git history. DataLad will first fetch Git remotes and merge for you.

    cd hcph-dataset/  # <--- cd into the dataset's path
    datalad update -r --how merge
    
  • If you need the data, now you can get the data as usual:

    find sub-001/ses-pilot019 -name "*.nii.gz" | xargs datalad get -J 8
    

Adding data or metadata

  • Use datalad save indicating the paths you want to add, and include --to-git if the file contains only metadata (e.g., JSON files).

    find sub-001/ses-pilot019 -name "*.nii" -or -name "*.nii.gz" -or -name "*.tsv.gz" | \
        xargs datalad save -m '"add(pilot019): new session data (NIfTI and compressed TSV)"'
    
    find sub-001/ses-pilot019 -name "*.json" -or -name "*.tsv" -or -name "*.bvec" -or -name "*.bval" | \
        xargs datalad save -m '"add(pilot019): new session metadata (JSON, TSV, bvec/bval)"'
    

Registering containers

We use DataLad containers-run to execute software while keeping track of provenance. Prior to first use, containers must be added to DataLad as follows (example for MRIQC):

  • Register the MRIQC container to the dataset

    datalad containers-add \
        --call-fmt 'singularity exec --cleanenv -B {{${HOME}/tmp/}}:/tmp {img} {cmd}' \
        mriqc \
        --url docker://nipreps/mriqc:23.1.0
    
    Insert relevant arguments to the singularity command line with --call-fmt

    In the example above, we configure the container's call to automatically bind (-B flag to mount the filesystem) the temporary folder. MRIQC will store the working directory there by default. Please replace the path with the appropriate path for your settings (i.e., laptop, cluster, etc.).

    datalad containers-add \
        --call-fmt 'docker run -u $( id -u ) -it -v {{${HOME}/tmp/}}:/tmp {img} {cmd}' \
        mriqc \
        --url docker://nipreps/mriqc:23.1.0
    
    Pinning a particular version of MRIQC

    If a different version of MRIQC should be executed, replace the Docker image's tag (23.1.0) with the adequate version tag within the above command line.

HPC users - instructions to install DataLad

When HPC is planned for processing, DataLad will be required on that system(s).

  • Start an interactive session on the HPC cluster

    Do not run the installation of Conda and DataLad in the login node

    HPC systems typically recommend using their login nodes only for tasks related to job submission, data management, and preparing jobscripts. Therefore, the execution of resource-intensive tasks such as fMRIPrep or building containers on login nodes can negatively impact the overall performance and responsiveness of the system for all users. Interactive sessions are a great alternative when available and should be used when creating the DataLad dataset. For example, in the case of systems operating SLURM, the following command would open a new interactive session:

    srun --nodes=1 --ntasks-per-node=1 --time=01:00:00 --pty bash -i
    

  • Install DataLad. Generally, the most convenient and user-sandboxed installation (i.e., without requiring elevated permissions) can be achieved by using Conda, but other alternatives (such as lmod) can be equally valid:

    • Get and install Conda if it is not already deployed in the system:

      wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
      bash Miniconda3-latest-Linux-x86_64.sh
      
    • Install DataLad:

      conda install -c conda-forge -y "datalad>=0.19" datalad-container
      
    • Check the availability and dependencies for a specific Python version (here we check 3.8.2):

      module spider Python/3.8.2
      
    • Load Python (please note ml below is a shorthand for module load)

      ml GCCcore/9.3.0 Python/3.8.2
      
    • Update pip:

      python -m pip --user -U pip
      
    • Install DataLad:

      python -m pip install --user "datalad>=0.19" datalad-container
      
  • Check datalad is properly installed, for instance:

    $ datalad --version
    datalad 0.19.2
    
    DataLad crashes (Conda installations)

    DataLad may fail with the following error:

    ImportError: cannot import name 'getargspec' from 'inspect' (/home/users/cprovins/miniconda3/lib/python3.11/inspect.py)
    

    In such a scenario, create a Conda environment with a lower version of Python, and re-install datalad

    conda create -n "datalad" python=3.10
    conda activate datalad
    conda install -c conda-forge datalad datalad-container
    

  • Configure your Git identity settings.

    cd ~
    git config --global --add user.name "Jane Doe"
    git config --global --add user.email doe@example.com