[DRAFT][BEP][SCHEMA] BEP023

.gitignore

@@ -161,3 +161,7 @@ dmypy.json
 cython_debug/
 
 .*.swp
+
+
+# BEP ignores
+bep-23_schema.json

.remarkrc

@@ -4,7 +4,7 @@
     "preset-lint-recommended",
     "remark-gfm",
     ["lint-no-duplicate-headings", false],
-    ["lint-list-item-indent", "tab"],
+    ["lint-list-item-indent", "tab-size"],
     ["lint-emphasis-marker", "consistent"],
     ["lint-maximum-line-length", false],
     ["lint-maximum-heading-length", false],

Makefile

@@ -52,3 +52,12 @@ schemacodedocs_build: schemacodedocs_clean
 
 schemacodedocs_serve: schemacodedocs_build
 	uv run python -m http.server -d tools/schemacode/docs/_build
+
+validateschema:
+<<<<<<< HEAD
+	uv run bst export > bep-23_schema.json
+	../bep023/bids-validator/local-run --schema file://${PWD}/bep-23_schema.json ../bep023/bids-examples/petprep/ --config ${PWD}/bep023ValidatorConfig.json --ignoreWarnings --verbose --ignoreNiftiHeaders -r
+=======
+	uv run bst export > local_schema.json
+	../bids-validator/local-run  ../bids-examples/petprep/ --ignoreWarnings --verbose --ignoreNiftiHeaders -r --schema file://${PWD}/local_schema.json --config bep023ValidatorConfig.json
+>>>>>>> 363a844151710b0e2a5b2d7b6dcb9e24700698f6

bep023ValidatorConfig.json

@@ -0,0 +1,8 @@
+{
+  "ignore": [
+    { "code": "EMPTY_FILE" },
+    { "code": "HED_ERROR"},
+    { "code": "SIDECAR_KEY_REQUIRED"},
+    { "code": "ALL_FILENAME_RULES_HAVE_ISSUES"}
+  ]
+}

mkdocs.yml

@@ -29,6 +29,7 @@ nav:
           - BIDS Derivatives: derivatives/introduction.md
           - Common data types and metadata: derivatives/common-data-types.md
           - Imaging data types: derivatives/imaging.md
+          - Positron Emission Tomography: derivatives/positron-emmision-tomography.md
           - Templates and atlases: derivatives/atlas.md
       - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
       - Glossary: glossary.md

src/derivatives/imaging.md

@@ -453,13 +453,19 @@ A guide for using macros can be found at
         "sub-001": {
             "anat": {
                 "sub-001_dseg.dlabel.nii": "",
-                "sub-001_dseg.dlabel.nii": "",
+                "sub-001_dseg.dlabel.json": "",
                 },
             },
         }
    }
 ) }}
 
+## Spatial transformations
+
+Spatial transformations between coordinate spaces SHOULD be stored using the pattern `from-<space>_to-<space>_mode-image_xfm.<extension>`. The `from` and `to` entities identify the source and target spaces, such as `orig`. Allowed extensions are `.txt` and `.json`.
+
+For example: `sub-01_ses-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.txt`
+
 ### Common image-derived labels
 
 BIDS supplies a standard, generic label-index mapping, defined in the table