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DOI

Preprocessed structural data from the studyforrest project

This dataset contains the results of an fMRIprep-based, anatomical preprocessing workflow of structural studyforrest data (studyforrest.org).

All results are fully and automatically reproducible with datalad. The details of this workflow are described at https://github.com/psychoinformatics-de/processing-workflow.

How to recompute

Make sure to fulfill the Software Requirements listed below. Then, clone this dataset with DataLad. Next, take a look at the Git history of the data and identify the 40-character long commit shasum of a single-subject computation, then use this shasum in a datalad rerun command:

$ datalad rerun a95484c793793b7274dbef5239e0cc3d315ca0fe

How to obtain data without recomputation

First, clone this dataset with DataLad. Next, retrieve any file(s) of your choice with the datalad get command.

Software requirements for automatic recomputation

Software requirements for the worflow are described in detail here.

If you're not planning to use any job scheduling / batch processing system (e.g. HTCondor, SLURM), but would simply like to run the example below, make sure to have the following software installed:

  • DataLad: Please make sure that you have installed a recent version of DataLad (0.14.3 or higher), as well as recent versions of its dependencies (git, 2.24.0 or higher; git-annex, 8.20* or higher). Installation instructions are available at: http://handbook.datalad.org.

  • Singularity: In principle, no specific version of Singularity is required. If you're not sure what version to use, simply install the most recent one. Installation instructions can be found here.

Make sure to have your Git identity set up.

Installation tips for MacOS

An installation of Singularity on MacOS requires using a virtual machine. It is recommended to use VirtualBox and (optionally) Vagrant software. This software can be installed via Homebrew package manager.

$ brew install --cask virtualbox && \
    brew install --cask vagrant && \
    brew install --cask vagrant-manager

The easiest way to start is to browse the public Vagrant box catalog for a Vagrant box matching your use case. Here, a box can be undestood as a base image of an operating system environment.

First, create and enter a directory to be used with your virtual machine:

$ mkdir vm-tutorial && \
    cd vm-tutorial

Next, initialise your virtual machine. Please substitute the value of the $VM variable with a name of your Vagrant box (debian/buster64 in this example).

    IMPORTANT NOTE: The Singularity community maintains a set of Vagrant boxes too. These boxes have Singularity software already included and ready to use.
$ export VM=debian/buster64 && \
    vagrant init $VM

Make sure to allocate enough memory for your virtual machine. This can be done by editing the vb.memory parameter in the corresponding Vagrantfile (Vagrant configuration file). This file is automatically created in you virtual machine's directory.

Next, issue the following commands to bring your virtual machine up:

$ vagrant up && \
    vagrant ssh

Lastly, install the required software in your VM, as if your operating system was Linux. Please follow instructions described in the "Software requirements for automatic recomputation" section above.

Acknowledgements

This development was supported by European Union’s Horizon 2020 research and innovation programme under grant agreement Human Brain Project SGA3 (H2020-EU.3.1.5.3, grant no. 945539).

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A tutorial for decentralized, reproducible processing with DataLad, based on fMRIprep and structural studyforrest data

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