bidsignore

Author: bclenet

provenance_spm/.bidsignore

@@ -0,0 +1 @@
+sub-01/*

provenance_spm/README.md

@@ -2,6 +2,9 @@
 
 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/).
@@ -12,40 +15,59 @@ The Matlab batch file `code/spm_preprocessing.m` allows to perform the preproces
 
 ## Directory tree
 
-The directory tree is as follows. Files marked with a ✍️ were generated manually.
+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
-│   ├── ✍️ merge_prov.py
 │   └── ✍️ 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
+├── ✍️ 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.nii.gz
+    │   ├── ✍️ 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
-        ├── sub-01_task-tonecounting_bold.nii.gz
-        ├── swsub-01_task-tonecounting_bold.nii
-        └── wsub-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