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‎provenance_fmriprep/.bidsignore‎

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sub-001/*

‎provenance_fmriprep/README.md‎

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This example aims at showing provenance metadata for a preprocessing with [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). Provenance metadata was generated manually ; this acts as a guideline for minimal provenance description at dataset level.
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!!! warning
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Validation of the `sub-001/` directory is ignored through a `.bidsignore` file, as the aim of the example is to focus on provenance metadata.
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## Original dataset
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This dataset is a subset of the `fmriprep` derivative dataset from [ds001734](https://openneuro.org/datasets/ds001734/versions/1.0.5), which contains raw and preprocessed fMRI data of two versions of the mixed gambles task, from the Neuroimaging Analysis Replication and Prediction Study (NARPS). **Only data for subject `sub-001` is kept in this example.** All `.nii.gz` files were replaced by empty files.
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This dataset is a derivative dataset of the [ds001734](https://openneuro.org/datasets/ds001734/versions/1.0.5) dataset. ds001734 contains raw and preprocessed fMRI data of two versions of the mixed gambles task, from the Neuroimaging Analysis Replication and Prediction Study (NARPS). **Only raw data for subject `sub-001` was preprocessed for this example.** All `.nii.gz` files were replaced by empty files.
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## Directory tree
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After preprocessing, and adding provenance traces, the directory tree is as follows.
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After preprocessing, and adding provenance metadata, the directory tree is as follows.
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Files marked with ✍️ were generated manually, other files were generated by the preprocessing step.
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Legend:
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- ✳️ files that were generated manually;
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- ✍️ files that were originally available in the ds001734 dataset, but edited for this example;
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- ⭐ files that were originally available in the ds001734 dataset as is.
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!!! note
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Note that the `docs/` directory contains explanatory data (see [Provenance as a RDF graph](#provenance-as-a-rdf-graph)) that is not required to encode provenance.
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```
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.
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├── dataset_description.json
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├── derivatives
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│ └── fmriprep
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│ └── sub-001
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│ ├── anat
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│ │ ├── sub-001_T1w_brainmask.nii.gz
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│ │ ├── sub-001_T1w_dtissue.nii.gz
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│ │ ├── sub-001_T1w_label-aparcaseg_roi.nii.gz
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│ │ ├── sub-001_T1w_label-aseg_roi.nii.gz
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│ │ ├── sub-001_T1w_preproc.nii.gz
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│ │ ├── sub-001_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
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│ │ ├── sub-001_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
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│ │ └── sub-001_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
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│ └── func
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│ ├── sub-001_task-MGT_run-01_bold_confounds.tsv
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│ ├── sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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│ ├── sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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│ ├── sub-001_task-MGT_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
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│ ├── sub-001_task-MGT_run-01_bold_space-T1w_label-aseg_roi.nii.gz
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│ ├── sub-001_task-MGT_run-02_bold_confounds.tsv
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│ ├── sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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│ ├── sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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│ ├── sub-001_task-MGT_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz
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│ ├── sub-001_task-MGT_run-02_bold_space-T1w_label-aseg_roi.nii.gz
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│ ├── sub-001_task-MGT_run-03_bold_confounds.tsv
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│ ├── sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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│ ├── sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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│ ├── sub-001_task-MGT_run-03_bold_space-T1w_label-aparcaseg_roi.nii.gz
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│ ├── sub-001_task-MGT_run-03_bold_space-T1w_label-aseg_roi.nii.gz
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│ ├── sub-001_task-MGT_run-04_bold_confounds.tsv
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│ ├── sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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│ ├── sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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│ ├── sub-001_task-MGT_run-04_bold_space-T1w_label-aparcaseg_roi.nii.gz
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│ └── sub-001_task-MGT_run-04_bold_space-T1w_label-aseg_roi.nii.gz
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├── docs
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│ ├── prov-fmriprep.jsonld
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│ └── prov-fmriprep.png
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├── participants.tsv
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├── prov
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│ ├── ✳️ prov-fmriprep_act.json
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│ ├── ✳️ prov-fmriprep_ent.json
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│ ├── ✳️ prov-fmriprep_env.json
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│ └── ✳️ prov-fmriprep_soft.json
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├── README.md
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├── sub-001
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│ ├── anat
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│ │ └── sub-001_T1w.nii.gz
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│ └── func
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│ ├── sub-001_task-MGT_run-01_bold.nii.gz
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│ ├── sub-001_task-MGT_run-01_events.tsv
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│ ├── sub-001_task-MGT_run-01_sbref.nii.gz
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│ ├── sub-001_task-MGT_run-02_bold.nii.gz
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│ ├── sub-001_task-MGT_run-02_events.tsv
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│ ├── sub-001_task-MGT_run-02_sbref.nii.gz
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│ ├── sub-001_task-MGT_run-03_bold.nii.gz
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│ ├── sub-001_task-MGT_run-03_events.tsv
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│ ├── sub-001_task-MGT_run-03_sbref.nii.gz
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│ ├── sub-001_task-MGT_run-04_bold.nii.gz
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│ ├── sub-001_task-MGT_run-04_events.tsv
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│ └── sub-001_task-MGT_run-04_sbref.nii.gz
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├── T1w.json
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├── task-MGT_bold.json
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└── task-MGT_sbref.json
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├── ✍️ dataset_description.json
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├── ✍️ docs
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│ ├── ✍️ prov-fmriprep.jsonld
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│ └── ✍️ prov-fmriprep.png
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├── ✍️ prov
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│ ├── ✍️ prov-fmriprep_act.json
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│ ├── ✍️ prov-fmriprep_ent.json
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│ ├── ✍️ prov-fmriprep_env.json
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│ └── ✍️ prov-fmriprep_soft.json
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├── ✍️ README.md
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└── sub-001
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├── anat
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│ ├── sub-001_T1w_brainmask.nii.gz
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│ ├── sub-001_T1w_dtissue.nii.gz
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│ ├── sub-001_T1w_label-aparcaseg_roi.nii.gz
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│ ├── sub-001_T1w_label-aseg_roi.nii.gz
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│ ├── sub-001_T1w_preproc.nii.gz
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│ ├── sub-001_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
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│ ├── sub-001_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
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│ └── sub-001_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
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└── func
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├── sub-001_task-MGT_run-01_bold_confounds.tsv
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├── sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
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├── sub-001_task-MGT_run-01_bold_space-T1w_label-aseg_roi.nii.gz
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├── sub-001_task-MGT_run-02_bold_confounds.tsv
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├── sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz
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├── sub-001_task-MGT_run-02_bold_space-T1w_label-aseg_roi.nii.gz
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├── sub-001_task-MGT_run-03_bold_confounds.tsv
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├── sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-03_bold_space-T1w_label-aparcaseg_roi.nii.gz
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├── sub-001_task-MGT_run-03_bold_space-T1w_label-aseg_roi.nii.gz
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├── sub-001_task-MGT_run-04_bold_confounds.tsv
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├── sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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├── sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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├── sub-001_task-MGT_run-04_bold_space-T1w_label-aparcaseg_roi.nii.gz
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└── sub-001_task-MGT_run-04_bold_space-T1w_label-aseg_roi.nii.gz
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```
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## Provenance as a RDF graph

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