[BEP028] provenance - fMRIPrep preprocessing

README.md

@@ -370,5 +370,6 @@ 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             |

dataset_listing.tsv

@@ -83,3 +83,4 @@ mrs_fmrs	Functional MRS data involving a pain stimulus task from 15 subjects	[li
 xeeg_hed_score	EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE 		[@dorahermes](https://github.com/dorahermes)	anat, eeg, ieeg	T1w, channels, coordsystem, eeg, electrodes, events, ieeg
 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
+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

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.

provenance_fmriprep/dataset_description.json

@@ -0,0 +1,24 @@
+{
+  "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": [
+    {
+      "Name": "fmriprep",
+      "Id": "bids::prov#preprocessing-xMpFqB5q"
+    }
+  ]
+}

provenance_fmriprep/prov/prov-fmriprep.jsonld

@@ -0,0 +1,41 @@
+{
+  "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"
+        ]
+      }
+    ]
+  }
+}

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"
+      ]
+    }    
+  ]
+}

provenance_fmriprep/prov/prov-fmriprep_ent.json

@@ -0,0 +1,8 @@
+{
+  "Entities": [
+    {
+      "Id": "bids:ds001734",
+      "Label": "NARPS"
+    }
+  ]
+}

provenance_fmriprep/prov/prov-fmriprep_env.json

@@ -0,0 +1,8 @@
+{
+  "Environments": [
+    {
+      "Id": "bids::prov#poldracklab/fmriprep-mHl7Dqa0",
+      "Label": "poldracklab/fmriprep:1.1.4"
+    }    
+  ]
+}

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"
+    } 
+  ]
+}