diff --git a/README.md b/README.md index 53f625d61..40ef0ff13 100644 --- a/README.md +++ b/README.md @@ -372,5 +372,6 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|--------|---------------|-------------|------------|---------------------|-----------------| +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------|:------------|:-----------|:--------------------|:----------------| +| [provenance_fmriprep Provenance records for a derivative dataset after functional MRI preprocessing performed with [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). This example is build upon [ds001734](https://openneuro.org/datasets/ds001734/versions/1.0.5) data. [@bclenet](https://github.com/bclenet) anat, func, prov](https://github.com/bids-standard/bids-examples/tree/master/provenance_fmriprep Provenance records for a derivative dataset after functional MRI preprocessing performed with [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). This example is build upon [ds001734](https://openneuro.org/datasets/ds001734/versions/1.0.5) data. [@bclenet](https://github.com/bclenet) anat, func, prov) | T1w, bold, act, ent, soft, env | n/a | n/a | n/a | n/a | diff --git a/dataset_listing.tsv b/dataset_listing.tsv index f9c2db4f2..95251c8cc 100644 --- a/dataset_listing.tsv +++ b/dataset_listing.tsv @@ -86,3 +86,4 @@ xeeg_hed_score EEG and iEEG data with annotations of artifacts, seizures and mod dwi_deriv exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform. dwi dwi pheno004 Minimal dataset with subjects with imaging and/or phenotype data [@ericearl](https://github.com/ericearl) phenotype, anat T1w mri_chunk Example MRI dataset to illustrate BIDS chunk entity. A single subject, two chunks. [@valosekj](https://github.com/valosekj) anat T1w +provenance_fmriprep Provenance records for a derivative dataset after functional MRI preprocessing performed with [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). This example is build upon [ds001734](https://openneuro.org/datasets/ds001734/versions/1.0.5) data. [@bclenet](https://github.com/bclenet) anat, func, prov T1w, bold, act, ent, soft, env \ No newline at end of file diff --git a/provenance_fmriprep/README.md b/provenance_fmriprep/README.md new file mode 100644 index 000000000..8d203f952 --- /dev/null +++ b/provenance_fmriprep/README.md @@ -0,0 +1,52 @@ +# BEP028 example dataset - Provenance records for `fMRIPrep` + +This example aims at showing provenance records for a preprocessing, performed by [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). Provenance records were created manually ; they act as a guideline for minimal provenance description at dataset level. + +We use [ds001734](https://openneuro.org/datasets/ds001734/versions/1.0.5) as source dataset, it 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 001 is used in this example. + +After preprocessing, and adding provenance traces, the directory tree is as follows: +``` +. +├── ✍️ dataset_description.json +├── ✍️ prov/ +│ ├── ✍️ prov-fmriprep_act.json +│ ├── ✍️ prov-fmriprep_ent.json +│ ├── ✍️ prov-fmriprep_env.json +│ └── ✍️ prov-fmriprep_soft.json +├── ✍️ README.md +└── ⭐ sub-001/ + ├── ⭐ anat + │ ├── ⭐ sub-001_T1w_brainmask.nii.gz + │ ├── ⭐ sub-001_T1w_dtissue.nii.gz + │ ├── ⭐ sub-001_T1w_label-aparcaseg_roi.nii.gz + │ ├── ⭐ sub-001_T1w_label-aseg_roi.nii.gz + │ ├── ⭐ sub-001_T1w_preproc.nii.gz + │ ├── ⭐ sub-001_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz + │ ├── ⭐ sub-001_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz + │ └── ⭐ sub-001_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz + └── ⭐ func + ├── ⭐ sub-001_task-MGT_run-01_bold_confounds.tsv + ├── ⭐ sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz + ├── ⭐ sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz + ├── ⭐ sub-001_task-MGT_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz + ├── ⭐ sub-001_task-MGT_run-01_bold_space-T1w_label-aseg_roi.nii.gz + ├── ⭐ sub-001_task-MGT_run-02_bold_confounds.tsv + ├── ⭐ sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz + ├── ⭐ sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz + ├── ⭐ sub-001_task-MGT_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz + ├── ⭐ sub-001_task-MGT_run-02_bold_space-T1w_label-aseg_roi.nii.gz + ├── ⭐ sub-001_task-MGT_run-03_bold_confounds.tsv + ├── ⭐ sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz + ├── ⭐ sub-001_task-MGT_run-03_bold_space-MNI152NLin2009cAsym_preproc.nii.gz + ├── ⭐ sub-001_task-MGT_run-03_bold_space-T1w_label-aparcaseg_roi.nii.gz + ├── ⭐ sub-001_task-MGT_run-03_bold_space-T1w_label-aseg_roi.nii.gz + ├── ⭐ sub-001_task-MGT_run-04_bold_confounds.tsv + ├── ⭐ sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz + ├── ⭐ sub-001_task-MGT_run-04_bold_space-MNI152NLin2009cAsym_preproc.nii.gz + ├── ⭐ sub-001_task-MGT_run-04_bold_space-T1w_label-aparcaseg_roi.nii.gz + └── ⭐ sub-001_task-MGT_run-04_bold_space-T1w_label-aseg_roi.nii.gz +``` + +About symbols: +* files with a ⭐ were generated by `fMRIPrep` ; +* files with a ✍️ were generated manually. diff --git a/provenance_fmriprep/dataset_description.json b/provenance_fmriprep/dataset_description.json new file mode 100644 index 000000000..3f98962ed --- /dev/null +++ b/provenance_fmriprep/dataset_description.json @@ -0,0 +1,19 @@ +{ + "Name": "Outputs from fMRIPrep preprocessing", + "BIDSVersion": "1.10.0", + "DatasetType": "derivative", + "License": "CC0", + "Authors": [ + "Boris Clénet" + ], + "DatasetLinks": { + "ds001734": "https://openneuro.org/datasets/ds001734/versions/1.0.5" + }, + "SourceDatasets": [ + { + "URL": "ds001734", + "Version": "1.0.5" + } + ], + "GeneratedBy": "bids::prov#preprocessing-xMpFqB5q" +} diff --git a/provenance_fmriprep/prov/prov-fmriprep.jsonld b/provenance_fmriprep/prov/prov-fmriprep.jsonld new file mode 100644 index 000000000..5a5373bc4 --- /dev/null +++ b/provenance_fmriprep/prov/prov-fmriprep.jsonld @@ -0,0 +1,47 @@ +{ + "BIDSProvVersion": "0.0.1", + "@context": "https://purl.org/nidash/bidsprov/context.json", + "Records": { + "Software": [ + { + "Id": "bids::prov#fmriprep-awf6cvk6", + "Label": "fMRIPrep", + "Version": "1.1.4", + "AltIdentifier": "RRID:SCR_016216" + } + ], + "Activities": [ + { + "Id": "bids::prov#preprocessing-xMpFqB5q", + "Label": "Preprocessing", + "Command": "docker run --rm -it -v /soft/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /dev/BEP028_BIDSprov/examples/fmriprep/ds001734:/data:ro -v /data/ds001734_fmriprep:/out -v /data/ds001734_fmriprep/work:/scratch poldracklab/fmriprep:1.1.4 /data /out participant --participant-label=001 --reports-only --write-graph -w /scratch", + "AssociatedWith": [ + "bids::prov#fmriprep-awf6cvk6" + ], + "Used": [ + "bids::prov#poldracklab/fmriprep-mHl7Dqa0", + "bids:ds001734" + ] + } + ], + "Entities": [ + { + "Id": "bids:ds001734", + "Label": "NARPS" + }, + { + "Id": "bids:current_dataset", + "Label": "Outputs from fMRIPrep preprocessing", + "GeneratedBy": [ + "bids::prov#preprocessing-xMpFqB5q" + ] + } + ], + "Environments": [ + { + "Id": "bids::prov#poldracklab/fmriprep-mHl7Dqa0", + "Label": "poldracklab/fmriprep:1.1.4" + } + ] + } +} \ No newline at end of file diff --git a/provenance_fmriprep/prov/prov-fmriprep.png b/provenance_fmriprep/prov/prov-fmriprep.png new file mode 100644 index 000000000..76b1c6245 Binary files /dev/null and b/provenance_fmriprep/prov/prov-fmriprep.png differ diff --git a/provenance_fmriprep/prov/prov-fmriprep_act.json b/provenance_fmriprep/prov/prov-fmriprep_act.json new file mode 100644 index 000000000..1223365da --- /dev/null +++ b/provenance_fmriprep/prov/prov-fmriprep_act.json @@ -0,0 +1,16 @@ +{ + "Activities": [ + { + "Id": "bids::prov#preprocessing-xMpFqB5q", + "Label": "Preprocessing", + "Command": "docker run --rm -it -v /soft/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /dev/BEP028_BIDSprov/examples/fmriprep/ds001734:/data:ro -v /data/ds001734_fmriprep:/out -v /data/ds001734_fmriprep/work:/scratch poldracklab/fmriprep:1.1.4 /data /out participant --participant-label=001 --reports-only --write-graph -w /scratch", + "AssociatedWith": [ + "bids::prov#fmriprep-awf6cvk6" + ], + "Used": [ + "bids::prov#poldracklab/fmriprep-mHl7Dqa0", + "bids:ds001734" + ] + } + ] +} \ No newline at end of file diff --git a/provenance_fmriprep/prov/prov-fmriprep_ent.json b/provenance_fmriprep/prov/prov-fmriprep_ent.json new file mode 100644 index 000000000..205530df9 --- /dev/null +++ b/provenance_fmriprep/prov/prov-fmriprep_ent.json @@ -0,0 +1,8 @@ +{ + "Entities": [ + { + "Id": "bids:ds001734", + "Label": "NARPS" + } + ] +} \ No newline at end of file diff --git a/provenance_fmriprep/prov/prov-fmriprep_env.json b/provenance_fmriprep/prov/prov-fmriprep_env.json new file mode 100644 index 000000000..efa6c0c87 --- /dev/null +++ b/provenance_fmriprep/prov/prov-fmriprep_env.json @@ -0,0 +1,8 @@ +{ + "Environments": [ + { + "Id": "bids::prov#poldracklab/fmriprep-mHl7Dqa0", + "Label": "poldracklab/fmriprep:1.1.4" + } + ] +} \ No newline at end of file diff --git a/provenance_fmriprep/prov/prov-fmriprep_soft.json b/provenance_fmriprep/prov/prov-fmriprep_soft.json new file mode 100644 index 000000000..225daa63d --- /dev/null +++ b/provenance_fmriprep/prov/prov-fmriprep_soft.json @@ -0,0 +1,10 @@ +{ + "Software": [ + { + "Id": "bids::prov#fmriprep-awf6cvk6", + "Label": "fMRIPrep", + "Version": "1.1.4", + "AltIdentifier": "RRID:SCR_016216" + } + ] +} \ No newline at end of file diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_brainmask.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_brainmask.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_dtissue.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_dtissue.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_label-aparcaseg_roi.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_label-aparcaseg_roi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_label-aseg_roi.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_label-aseg_roi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz b/provenance_fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_confounds.tsv b/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_confounds.tsv new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz b/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git 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a/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz b/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz b/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz b/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-T1w_label-aseg_roi.nii.gz b/provenance_fmriprep/sub-001/func/sub-001_task-MGT_run-02_bold_space-T1w_label-aseg_roi.nii.gz new 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