bids-standard · rwblair · May 23, 2025 · May 23, 2025 · May 23, 2025 · May 23, 2025
diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml
@@ -95,6 +95,7 @@ jobs:
       run: |
         git clone -b dev https://github.com/bids-standard/bids-validator/ ../bids-validator
         cd ../bids-validator
+        git checkout bep028
         deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts
 
     - name: Install BIDS validator (dev-prs with VAL_PR)
@@ -139,6 +140,10 @@ jobs:
             exit 1;
         fi
 
+    - name: Skip legacy validation for post-legacy datasets
+      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing provenance_*; do touch $DS/.SKIP_VALIDATION; done
+      if: matrix.bids-validator == 'legacy'
+
     - name: Skip stable validation for datasets with unreleased validator features
       # Replace ${EMPTY} with dataset patterns, when this is needed
       # Reset to "for DS in ${EMPTY}; ..." after a validator release
@@ -148,7 +153,7 @@ jobs:
     - name: Skip main validation for datasets with unreleased spec features
       # Replace ${EMPTY} with dataset patterns, when this is needed
       # Reset to "for DS in ${EMPTY}; ..." after a spec release
-      run: for DS in ${EMPTY}; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in dwi_deriv pheno004 provenance_* eyetracking_* atlas-* emg_*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -157,7 +162,7 @@ jobs:
       # Update this URL to the schema.json from PRs to the spec, when needed.
       # If this variable is unset, dev will generally track the latest development
       # release of https://jsr.io/@bids/schema
-      run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV
+      run: echo BIDS_SCHEMA=https://bids-specification--2099.org.readthedocs.build/en/2099/schema.json >> $GITHUB_ENV
 
     - name: Set BIDS_SCHEMA variable for dev-prs version
       if: matrix.bids-validator == 'dev-prs' && env.SPEC_PR != ''

diff --git a/README.md b/README.md
@@ -418,3 +418,38 @@ DO NOT EDIT DIRECTLY.
 | [qmri_sa2rage](https://github.com/bids-standard/bids-examples/tree/master/qmri_sa2rage)     | Fast B1+ mapping using SA2RAGE                                                           | fmap        | TB1SRGE                                                | `not publicly available`      | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
 | [qmri_tb1tfl](https://github.com/bids-standard/bids-examples/tree/master/qmri_tb1tfl)       | B1+ mapping with TurboFLASH readout.                                                     | fmap        | TB1TFL                                                 | `not publicly available`      | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
 | [qmri_vfa](https://github.com/bids-standard/bids-examples/tree/master/qmri_vfa)             | Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example. | anat, fmap  | TB1AFI, VFA                                            | [link](https://osf.io/k4bs5/) | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
+=======
+
+### Phenotype
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                            | description                                                      | datatypes       | suffixes   | link to full data   | maintained by                            |
+|:--------------------------------------------------------------------------------|:-----------------------------------------------------------------|:----------------|:-----------|:--------------------|:-----------------------------------------|
+| [pheno004](https://github.com/bids-standard/bids-examples/tree/master/pheno004) | Minimal dataset with subjects with imaging and/or phenotype data | phenotype, anat | T1w        | n/a                 | [@ericearl](https://github.com/ericearl) |
+
+### Provenance
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                                                  | description                                                                                                                           | datatypes   | suffixes                 | link to full data                                                                                | maintained by                          |
+|:------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------|:------------|:-------------------------|:-------------------------------------------------------------------------------------------------|:---------------------------------------|
+| [provenance_dcm2niix](https://github.com/bids-standard/bids-examples/tree/master/provenance_dcm2niix) | Shows minimal example of provenance metadata for a DICOM to Nifti conversion with [`dcm2niix`](https://github.com/rordenlab/dcm2niix) | anat        | T1w, act, ent, env, soft | This example is based upon [hirni-demo](https://github.com/psychoinformatics-de/hirni-demo) data | [@bclenet](https://github.com/bclenet) |
+=======
+| name                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | description   | datatypes   | suffixes   | link to full data   | maintained by   |
+|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------|:------------|:-----------|:--------------------|:----------------|
+| [provenance_heudiconv Shows minimal example of provenance metadata for a DICOM to Nifti conversion with [`heudiconv`](https://heudiconv.readthedocs.io/en/latest/) This example is based upon [hirni-demo](https://github.com/psychoinformatics-de/hirni-demo) data [@bclenet](https://github.com/bclenet) anat T1w, act, ent, env, soft](https://github.com/bids-standard/bids-examples/tree/master/provenance_heudiconv Shows minimal example of provenance metadata for a DICOM to Nifti conversion with [`heudiconv`](https://heudiconv.readthedocs.io/en/latest/) This example is based upon [hirni-demo](https://github.com/psychoinformatics-de/hirni-demo) data [@bclenet](https://github.com/bclenet) anat T1w, act, ent, env, soft) | n/a           | n/a         | n/a        | n/a                 | n/a             |
+=======
+| name                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | description   | datatypes   | suffixes   | link to full data   | maintained by   |
+|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------|:------------|:-----------|:--------------------|:----------------|
+| [provenance_spm_default Provenance metadata for a derivative dataset after functional MRI preprocessing performed with [`SPM`](https://www.fil.ion.ucl.ac.uk/spm/). This example is based upon [ds000011](cf. https://openfmri.org/dataset/ds000011/) data. [@bclenet](https://github.com/bclenet) anat, func T1w, bold, seg8, act, ent, soft](https://github.com/bids-standard/bids-examples/tree/master/provenance_spm_default Provenance metadata for a derivative dataset after functional MRI preprocessing performed with [`SPM`](https://www.fil.ion.ucl.ac.uk/spm/). This example is based upon [ds000011](cf. https://openfmri.org/dataset/ds000011/) data. [@bclenet](https://github.com/bclenet) anat, func T1w, bold, seg8, act, ent, soft) | n/a           | n/a         | n/a        | n/a                 | n/a             |
+=======
+| name                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | description                    | datatypes   | suffixes   | link to full data   | maintained by   |
+|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------|:------------|:-----------|:--------------------|:----------------|
+| [provenance_fmriprep Provenance metadata for a derivative dataset after functional MRI preprocessing performed with [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). This example is based 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 metadata for a derivative dataset after functional MRI preprocessing performed with [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). This example is based 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
@@ -106,3 +106,8 @@ atlas-DiFuMo				n/a	n/a
 eyetracking_fmri				anat, fmap, func	T1w, T2w, bold, epi, events, fieldmap, magnitude, physio
 atlas-suit				n/a	T1w
 atlas-Juelich				n/a	n/a
+provenance_dcm2niix	Shows minimal example of provenance metadata for a DICOM to Nifti conversion with [`dcm2niix`](https://github.com/rordenlab/dcm2niix)	This example is based upon [hirni-demo](https://github.com/psychoinformatics-de/hirni-demo) data	[@bclenet](https://github.com/bclenet)	anat	T1w, act, ent, env, soft
+provenance_heudiconv Shows minimal example of provenance metadata for a DICOM to Nifti conversion with [`heudiconv`](https://heudiconv.readthedocs.io/en/latest/) This example is based upon [hirni-demo](https://github.com/psychoinformatics-de/hirni-demo) data [@bclenet](https://github.com/bclenet) anat T1w, act, ent, env, soft
+provenance_spm_default Provenance metadata for a derivative dataset after functional MRI preprocessing performed with [`SPM`](https://www.fil.ion.ucl.ac.uk/spm/). This example is based upon [ds000011](cf. https://openfmri.org/dataset/ds000011/) data. [@bclenet](https://github.com/bclenet) anat, func T1w, bold, seg8, act, ent, soft
+provenance_fmriprep Provenance metadata for a derivative dataset after functional MRI preprocessing performed with [`fMRIPrep`](https://fmriprep.org/en/23.1.3/index.html). This example is based 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_nilearn	Provenance metadata for the GLM Analysis of an fMRI dataset with Nilearn.		[@bclenet](https://github.com/bclenet)		act, ent, env, soft
diff --git a/provenance_dcm2niix/README.md b/provenance_dcm2niix/README.md
@@ -0,0 +1,45 @@
+# Provenance of DICOM to NIfTI conversion with `dcm2niix`
+
+## Goal
+
+This example aims at showing provenance metadata for a DICOM to NIfTI conversion with [`dcm2niix`](https://github.com/rordenlab/dcm2niix
+). Provenance metadata was created manually ; its acts as a guideline for further machine-generated provenance by `dcm2niix`. 
+
+## Source data
+
+That the `sourcedata/` directory contains the source dataset (DICOM files) known as [hirni-demo](https://github.com/psychoinformatics-de/hirni-demo).
+
+## Directory tree
+
+After conversion, and adding provenance traces, the directory tree is as follows.
+
+Legend:
+* files with a ⭐ were generated by `dcm2niix`;
+* files marked with a ✍️ were generated manually;
+* files marked with a 🤖 were computed from the manually generated provenance metadata;
+* the ⭐✍️ marked `sub-02/anat/sub-02_T1w.json` file was generated by `dcm2niix`, then the `GeneratedBy` and `SidecarGeneratedBy` provenance-related fields were added manually.
+
+> [!NOTE]
+> 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.
+
+```
+✍️ docs/
+├── 🤖 prov-dcm2niix.jsonld
+└── 🤖 prov-dcm2niix.png
+✍️ prov/
+├── ✍️ prov-dcm2niix_act.json
+├── ✍️ prov-dcm2niix_ent.json
+├── ✍️ prov-dcm2niix_env.json
+└── ✍️ prov-dcm2niix_soft.json
+sourcedata/
+⭐ sub-02/
+└── ⭐ anat
+    ├── ⭐✍️ sub-02_T1w.json
+    └── ⭐ sub-02_T1w.nii
+```
+
+## Provenance as a RDF graph
+
+Provenance metadata can be aggregated as a JSON-LD RDF graph, which is available in [`docs/prov-dcm2niix.jsonld`](docs/prov-dcm2niix.jsonld). This is a rendered version of the graph, also available in [`docs/prov-dcm2niix.png`](docs/prov-dcm2niix.png).
+
+![Rendered version of the RDF graph](docs/prov-dcm2niix.png)
diff --git a/provenance_dcm2niix/dataset_description.json b/provenance_dcm2niix/dataset_description.json
@@ -0,0 +1,14 @@
+{
+    "Name": "Provenance metadata for DICOM to NIfTI conversion with dcm2niix",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "raw",
+    "License": "CC0",
+    "Authors": [
+        "Boris Clénet"
+    ],
+    "SourceDatasets": [
+        {
+            "URL": "https://github.com/psychoinformatics-de/hirni-demo"
+        }
+    ]
+}
diff --git a/provenance_dcm2niix/docs/prov-dcm2niix.jsonld b/provenance_dcm2niix/docs/prov-dcm2niix.jsonld
@@ -0,0 +1,60 @@
+{
+  "@context": "https://bids-specification--2099.org.readthedocs.build/en/2099/provenance-context.json",
+  "Records": {
+    "Software": [
+      {
+        "Id": "bids::prov#dcm2niix-khhkm7u1",
+        "Label": "dcm2niix",
+        "AlternativeIdentifier": [
+          "RRID:SCR_023517"
+        ],
+        "Version": "v1.0.20220720"
+      }
+    ],
+    "Activities": [
+      {
+        "Id": "bids::prov#conversion-00f3a18f",
+        "Label": "Conversion",
+        "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+        "AssociatedWith": [
+          "bids::prov#dcm2niix-khhkm7u1"
+        ],
+        "Used": [
+          "bids::prov#fedora-uldfv058",
+          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms"
+        ]
+      }
+    ],
+    "Files": [
+      {
+        "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+        "Label": "dicoms"
+      },
+      {
+        "Id": "bids::sub-02/anat/sub-02_T1w.nii",
+        "Label": "sub-02_T1w.nii",
+        "AtLocation": "sub-02/anat/sub-02_T1w.nii",
+        "GeneratedBy": [
+          "bids::prov#conversion-00f3a18f"
+        ]
+      },
+      {
+        "Id": "bids::sub-02/anat/sub-02_T1w.json",
+        "Label": "sub-02_T1w.json",
+        "AtLocation": "sub-02/anat/sub-02_T1w.json",
+        "GeneratedBy": [
+          "bids::prov#conversion-00f3a18f"
+        ]
+      }
+    ],
+    "Datasets": [],
+    "prov:Entity": [],
+    "Environments": [
+      {
+        "Id": "bids::prov#fedora-uldfv058",
+        "Label": "Fedora release 36 (Thirty Six)",
+        "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64"
+      }
+    ]
+  }
+}
diff --git a/provenance_dcm2niix/docs/prov-dcm2niix.png b/provenance_dcm2niix/docs/prov-dcm2niix.png
diff --git a/provenance_dcm2niix/prov/prov-dcm2niix_act.json b/provenance_dcm2niix/prov/prov-dcm2niix_act.json
@@ -0,0 +1,16 @@
+{
+  "Activities": [
+    {
+      "Id": "bids::prov#conversion-00f3a18f",
+      "Label": "Conversion",
+      "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+      "AssociatedWith": [
+        "bids::prov#dcm2niix-khhkm7u1"
+      ],
+      "Used": [
+        "bids::prov#fedora-uldfv058",
+        "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms"
+      ]
+    }
+  ]
+}
diff --git a/provenance_dcm2niix/prov/prov-dcm2niix_ent.json b/provenance_dcm2niix/prov/prov-dcm2niix_ent.json
@@ -0,0 +1,8 @@
+{
+  "Files": [
+    {
+      "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+      "Label": "dicoms"
+    }
+  ]
+}
diff --git a/provenance_dcm2niix/prov/prov-dcm2niix_env.json b/provenance_dcm2niix/prov/prov-dcm2niix_env.json
@@ -0,0 +1,9 @@
+{
+  "Environments": [
+    {
+      "Id": "bids::prov#fedora-uldfv058",
+      "Label": "Fedora release 36 (Thirty Six)",
+      "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64"
+    }
+  ]
+}
diff --git a/provenance_dcm2niix/prov/prov-dcm2niix_soft.json b/provenance_dcm2niix/prov/prov-dcm2niix_soft.json
@@ -0,0 +1,12 @@
+{
+  "Software": [
+    {
+      "Id": "bids::prov#dcm2niix-khhkm7u1",
+      "Label": "dcm2niix",
+      "AlternativeIdentifier": [
+        "RRID:SCR_023517"
+      ],
+      "Version": "v1.0.20220720"
+    }
+  ]
+}