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Example container configuration YAML files

Here we provide a few example container configuration YAML files for different use cases. With customization, these YAML files can be applied to both SGE and Slurm clusters. Note that because of inevitable differences across clusters, these YAML files require customization before you apply it to your cluster. We provide hints in the YAML files (e.g., [FIX ME]) for how to customize it. For more, please refer to the documentation for how to prepare a container configuration YAML file.

Please also note that, these YAML files were prepared for specific versions of the BIDS Apps. If there are changes in the BIDS App itself (e.g., argument names) in different BIDS App versions, please change the YAML files accordingly. In addition, please check if the function of the YAML files (especially the singularity_run section) fits your purpose.

  • Naming convention: eg_<bidsapp-0-0-0>_<task>.yaml
    • <bidsapp-0-0-0>: BIDS App name and version
    • <task>: How this BIDS App is applied? Regular application? Or some specific use case?
example YAML file BIDS App BIDS App version for what input BIDS dataset(s) Notes
link toy BIDS App 0.0.7 for testing BABS on a raw BIDS dataset one raw BIDS dataset This is used in the example walkthrough; please refer to that doc for how to customize this YAML file.
link toy BIDS App 0.0.7 for testing BABS on a zipped BIDS derivatives dataset one zipped BIDS derivatives dataset
link QSIPrep 0.18.1 regular use of QSIPrep one raw BIDS dataset This does not include qsirecon workflow
link fMRIPrep 23.1.3 regular use of fMRIPrep one raw BIDS dataset
link fMRIPrep 23.1.3 fMRIPrep --anat-only one raw BIDS dataset
link fMRIPrep 23.1.3 fMRIPrep with FreeSurfer results ingressed one raw BIDS dataset + one zipped BIDS derivatives dataset of FreeSurfer results For 2nd input dataset, you may use results from fMRIPrep --anat-only (see example YAML here)
link fMRIPrep 20.2.3 regular use of fMRIPrep one raw BIDS dataset
link fMRIPrep 20.2.3 fMRIPrep --anat-only one raw BIDS dataset Only freesurfer folder is saved.
link fMRIPrep 20.2.3 fMRIPrep with FreeSurfer results ingressed one raw BIDS dataset + one zipped BIDS derivatives dataset of FreeSurfer results For 2nd input dataset, you may use results from fMRIPrep --anat-only (see example YAML here)
link XCP-D 0.4.0 for NIfTI images (i.e., without --cifti) one zipped BIDS derivatives dataset of fMRIPrep results The 0.4.0 version of XCP-D is labeled as 04.0 on Docker Hub.

Note that because fMRIPrep changed its default output layout in version 21.0, here we provide example YAML files for both a recent version (23.1.3) and an older version (20.2.3). The recent version uses BIDS output layout, whereas the older one uses legacy output layout. This difference reflects in the zip_folernames section.

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