bids-standard · bclenet · May 23, 2025 · May 23, 2025 · May 28, 2025 · May 28, 2025
diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml
@@ -107,7 +107,7 @@ jobs:
         fi
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing; do touch $DS/.SKIP_VALIDATION; done
+      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
@@ -119,7 +119,7 @@ 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 dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in dwi_deriv pheno004 provenance_*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -128,7 +128,7 @@ 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: Validate all BIDS datasets using bids-validator
       run: |

diff --git 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_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             |
diff --git 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_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
diff --git a/provenance_spm/.bidsignore b/provenance_spm/.bidsignore
@@ -0,0 +1 @@
+sub-01/*
diff --git a/provenance_spm/README.md b/provenance_spm/README.md
@@ -0,0 +1,77 @@
+# Provenance of fMRI preprocessing with SPM
+
+This example aims at showing provenance metadata for a functional MRI preprocessing performed with [`SPM`](https://www.fil.ion.ucl.ac.uk/spm/). Provenance metadata was created manually ; it acts as a guideline for further machine-generated provenance by `SPM`. 
+
+> [!WARNING]
+> Validation of the `sub-01/` directory is ignored through a `.bidsignore` file, as the aim of the example is to focus on provenance metadata.
+
+## Original dataset
+
+This is a derivative dataset, based upon `sub-01` data from OpenfMRI DS000011 classification learning and tone counting experiment (cf. https://openfmri.org/dataset/ds000011/).
+
+## Code
+
+The Matlab batch file `code/spm_preprocessing.m` allows to perform the preprocessing.
+
+## Directory tree
+
+The directory tree is as follows. Files marked with a ✍️ were generated manually, other files were generated by the preprocessing step.
+
+> [!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.
+
+```
+.
+├── ✍️ code
+│   └── ✍️ spm_preprocessing.m
+├── ✍️ dataset_description.json
+├── ✍️ docs
+│   ├── ✍️ prov-spm.jsonld
+│   └── ✍️ prov-spm.png
+├── ✍️ prov
+│   ├── ✍️ prov-spm_act.json
+│   ├── ✍️ prov-spm_ent.json
+│   └── ✍️ prov-spm_soft.json
+├── ✍️ README.md
+└── sub-01
+    ├── anat
+    │   ├── ✍️ c1sub-01_T1w.json
+    │   ├── c1sub-01_T1w.nii
+    │   ├── ✍️ c2sub-01_T1w.json
+    │   ├── c2sub-01_T1w.nii
+    │   ├── ✍️ c3sub-01_T1w.json
+    │   ├── c3sub-01_T1w.nii
+    │   ├── ✍️ c4sub-01_T1w.json
+    │   ├── c4sub-01_T1w.nii
+    │   ├── ✍️ c5sub-01_T1w.json
+    │   ├── c5sub-01_T1w.nii
+    │   ├── ✍️ msub-01_T1w.json
+    │   ├── msub-01_T1w.nii
+    │   ├── ✍️ sub-01_T1w.json
+    │   ├── sub-01_T1w.nii
+    │   ├── ✍️ sub-01_T1w_seg8.json
+    │   ├── sub-01_T1w_seg8.mat
+    │   ├── ✍️ wmsub-01_T1w.json
+    │   ├── wmsub-01_T1w.nii
+    │   ├── ✍️ y_sub-01_T1w.json
+    │   └── y_sub-01_T1w.nii
+    └── func
+        ├── ✍️ meansub-01_task-tonecounting_bold.json
+        ├── meansub-01_task-tonecounting_bold.nii
+        ├── ✍️ rp_sub-01_task-tonecounting_bold.json
+        ├── rp_sub-01_task-tonecounting_bold.txt
+        ├── ✍️ rsub-01_task-tonecounting_bold.json
+        ├── rsub-01_task-tonecounting_bold.nii
+        ├── sub-01_task-tonecounting_bold.mat
+        ├── sub-01_task-tonecounting_bold.nii
+        ├── ✍️ swrsub-01_task-tonecounting_bold.json
+        ├── swrsub-01_task-tonecounting_bold.nii
+        ├── ✍️ wrsub-01_task-tonecounting_bold.json
+        └── wrsub-01_task-tonecounting_bold.nii
+```
+
+## Provenance as a RDF graph
+
+Provenance metadata can be aggregated as a JSON-LD RDF graph, which is available in [`docs/prov-spm.jsonld`](docs/prov-spm.jsonld). This is a rendered version of the graph, also available in docs/prov-spm.png.
+
+![Rendered version of the RDF graph](docs/prov-spm.png)
diff --git a/provenance_spm/code/spm_preprocessing.m b/provenance_spm/code/spm_preprocessing.m
@@ -0,0 +1,89 @@
+%-----------------------------------------------------------------------
+% Job saved on 06-Jun-2025 15:40:49 by cfg_util (rev $Rev: 7345 $)
+% spm SPM - SPM12 (7771)
+% cfg_basicio BasicIO - Unknown
+%-----------------------------------------------------------------------
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'data/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'sub-01/func'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'data/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'sub-01/anat'};
+matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
+matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.outdir = {''};
+matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.keep = false;
+matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
+matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.outdir = {''};
+matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.keep = false;
+matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('Gunzip Files: Gunzipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
+matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
+matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;
+matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
+matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
+matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;
+matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
+matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';
+matlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [2 1];
+matlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;
+matlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
+matlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;
+matlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';
+matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
+matlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('Gunzip Files: Gunzipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
+matlabbatch{6}.spm.spatial.coreg.estimate.other = {''};
+matlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
+matlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
+matlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
+matlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
+matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('Gunzip Files: Gunzipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
+matlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;
+matlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;
+matlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];
+matlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii,1'};
+matlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;
+matlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii,2'};
+matlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;
+matlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii,3'};
+matlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;
+matlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii,4'};
+matlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;
+matlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii,5'};
+matlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;
+matlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii,6'};
+matlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;
+matlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];
+matlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];
+matlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;
+matlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;
+matlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
+matlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';
+matlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;
+matlabbatch{7}.spm.spatial.preproc.warp.samp = 3;
+matlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];
+matlabbatch{7}.spm.spatial.preproc.warp.vox = NaN;
+matlabbatch{7}.spm.spatial.preproc.warp.bb = [NaN NaN NaN NaN NaN NaN];
+matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
+matlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Resliced Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','rfiles'));
+matlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];
+matlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];
+matlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;
+matlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';
+matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
+matlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));
+matlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];
+matlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];
+matlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;
+matlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';
+matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
+matlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];
+matlabbatch{10}.spm.spatial.smooth.dtype = 0;
+matlabbatch{10}.spm.spatial.smooth.im = 0;
+matlabbatch{10}.spm.spatial.smooth.prefix = 's';
diff --git a/provenance_spm/dataset_description.json b/provenance_spm/dataset_description.json
@@ -0,0 +1,29 @@
+{
+    "Name": "Provenance records for SPM-based fMRI statistical analysis",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "derivative",
+    "License": "CC0",
+    "Authors": [
+        "Boris Clénet",
+        "Thomas Betton",
+        "Hermann Courteille",
+        "Cyril Regan"
+    ],
+    "GeneratedBy": [
+        {
+            "Name": "SPM preprocessing"
+        }
+    ],
+    "SourceDatasets": [
+        {
+            "URL": "ds000011",
+            "Version": "1.0.0"
+        },
+        {
+            "URL": "https://github.com/incf-nidash/nidmresults-examples/"
+        }
+    ],
+    "DatasetLinks": {
+        "ds000011": "https://doi.org/10.18112/openneuro.ds000011.v1.0.0"
+    }
+}