Merge branch 'master' into enh_mkdocs

bids-standard · Sep 26, 2023 · b3f5331 · b3f5331
2 parents cf07618 + a340ef0
commit b3f5331
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diff --git a/mkdocs.yml b/mkdocs.yml
@@ -77,7 +77,7 @@ theme:
 
 edit_uri: https://github.com/bids-standard/bids-specification/edit/master/src/
 
-copyright: Copyright &copy; 2018-2022, BIDS Contributors - <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a>
+copyright: Copyright &copy; BIDS Contributors - <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a>
 
 extra:
     generator: false

diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md
@@ -86,7 +86,7 @@ of restricted keywords for MEG, EEG, or iEEG, please open a new issue on the
 
 Note that the short descriptions below may not capture all details.
 For detailed descriptions of the coordinate systems below, please see the
-[FieldTrip webpage](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined).
+[FieldTrip webpage](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined/).
 
 ### Commonly used anatomical landmarks in MEG, EEG, and iEEG research
 

diff --git a/src/appendices/meg-file-formats.md b/src/appendices/meg-file-formats.md
@@ -356,7 +356,7 @@ the two marker measurements occur before and after the raw data acquisition,
 `pre` and `post` are used to differentiate the two situations.
 
 More about the KIT/Yokogawa/Ricoh data organization at:
-[https://www.fieldtriptoolbox.org/getting_started/yokogawa](https://www.fieldtriptoolbox.org/getting_started/yokogawa)
+[https://www.fieldtriptoolbox.org/getting_started/yokogawa](https://www.fieldtriptoolbox.org/getting_started/yokogawa/)
 
 ## KRISS
 

diff --git a/src/appendices/meg-systems.md b/src/appendices/meg-systems.md
@@ -20,7 +20,7 @@ Restricted keywords for ManufacturersModelName field in the `*_meg.json` file:
 | CTF-275                   | CTF                   | CTF-275: OMEGA 2000                                                                          |
 | Neuromag-122              | Neuromag/Elekta/Megin |                                                                                              |
 | ElektaVectorview          | Neuromag/Elekta/Megin | 102 magnetometers + 204 planar gradiometers                                                  |
-| ElektaTRIUX               | Neuromag/Elekta/Megin | [https://www.elekta.com/diagnostic-solutions/](https://www.elekta.com/diagnostic-solutions/) |
+| ElektaTRIUX               | Neuromag/Elekta/Megin | [https://www.elekta.com/products/neurosurgery/](https://www.elekta.com/products/neurosurgery/) |
 | 4D-Magnes-WH2500          | BTi/4D                |                                                                                              |
 | 4D-Magnes-WH3600          | BTi/4D                |                                                                                              |
 | KIT-157                   | KIT/Yokogawa          |                                                                                              |

diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md
@@ -408,12 +408,12 @@ A guide for using macros can be found at
 {{ MACROS___make_sidecar_table("meg.MEGCoordsystemFiducialsInformation") }}
 
 For more information on the definition of anatomical landmarks, please visit:
-[http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
+[https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
 
 For more information on typical coordinate systems for MEG-MRI coregistration:
-[http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined),
+[https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined),
 or:
-[http://neuroimage.usc.edu/brainstorm/CoordinateSystems](http://neuroimage.usc.edu/brainstorm/CoordinateSystems)
+[https://neuroimage.usc.edu/brainstorm/CoordinateSystems](https://neuroimage.usc.edu/brainstorm/CoordinateSystems)
 
 ## Landmark photos (`*_photo.<extension>`)
 

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
@@ -41,9 +41,12 @@ chunk:
   name: chunk
   display_name: Chunk
   description: |
-    The `chunk-<index>` key/value pair is used to distinguish between different regions,
-    2D images or 3D volumes files,
-    of the same physical sample with different fields of view acquired in the same imaging experiment.
+    The `chunk-<index>` key/value pair is used to distinguish between images of
+    the same physical sample with different fields of view acquired in the same
+    imaging experiment.
+    This entity applies to collections of 2D images, 3D volumes or 4D volume series
+    (for example, diffusion weighted images), and may be used to indicate different
+    anatomical structures or regions of the same structure.
   type: string
   format: index
 density:

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
@@ -385,7 +385,7 @@ CellType:
   description: |
     Describes the type of cell analyzed.
     Values SHOULD come from the
-    [cell ontology](http://obofoundry.org/ontology/cl.html).
+    [cell ontology](https://obofoundry.org/ontology/cl.html).
   type: string
 ChunkTransformationMatrix:
   name: ChunkTransformationMatrix

diff --git a/src/schema/rules/files/raw/anat.yaml b/src/schema/rules/files/raw/anat.yaml
@@ -29,6 +29,7 @@ nonparametric:
     run: optional
     echo: optional
     part: optional
+    chunk: optional
 
 parametric:
   suffixes:
@@ -62,6 +63,7 @@ parametric:
     ceagent: optional
     reconstruction: optional
     run: optional
+    chunk: optional
 
 defacemask:
   suffixes:
@@ -81,6 +83,7 @@ defacemask:
     reconstruction: optional
     run: optional
     modality: optional
+    chunk: optional
 
 multiecho:
   suffixes:
@@ -102,6 +105,7 @@ multiecho:
     run: optional
     echo: required
     part: optional
+    chunk: optional
 
 multiflip:
   suffixes:
@@ -123,6 +127,7 @@ multiflip:
     echo: optional
     flip: required
     part: optional
+    chunk: optional
 
 multiinversion:
   suffixes:
@@ -143,6 +148,7 @@ multiinversion:
     run: optional
     inversion: required
     part: optional
+    chunk: optional
 
 mp2rage:
   suffixes:
@@ -165,6 +171,7 @@ mp2rage:
     flip: optional
     inversion: required
     part: optional
+    chunk: optional
 
 vfamt:
   suffixes:
@@ -188,6 +195,7 @@ vfamt:
     flip: required
     mtransfer: required
     part: optional
+    chunk: optional
 
 mtr:
   suffixes:
@@ -208,3 +216,4 @@ mtr:
     run: optional
     mtransfer: required
     part: optional
+    chunk: optional
diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
@@ -18,6 +18,7 @@ dwi:
     direction: optional
     run: optional
     part: optional
+    chunk: optional
 
 sbref:
   suffixes:
@@ -36,3 +37,4 @@ sbref:
     direction: optional
     run: optional
     part: optional
+    chunk: optional
diff --git a/src/schema/rules/files/raw/fmap.yaml b/src/schema/rules/files/raw/fmap.yaml
@@ -19,6 +19,7 @@ fieldmaps:
     session: optional
     acquisition: optional
     run: optional
+    chunk: optional
 
 pepolar:
   suffixes:
@@ -37,6 +38,7 @@ pepolar:
     ceagent: optional
     direction: required
     run: optional
+    chunk: optional
 
 TB1DAM:
   suffixes:
@@ -57,6 +59,7 @@ TB1DAM:
     flip: required
     inversion: optional
     part: optional
+    chunk: optional
 
 TB1EPI:
   suffixes:
@@ -78,6 +81,7 @@ TB1EPI:
     flip: required
     inversion: optional
     part: optional
+    chunk: optional
 
 RFFieldMaps:
   suffixes:
@@ -102,6 +106,7 @@ RFFieldMaps:
     flip: optional
     inversion: optional
     part: optional
+    chunk: optional
 
 TB1SRGE:
   suffixes:
@@ -123,6 +128,7 @@ TB1SRGE:
     flip: required
     inversion: required
     part: optional
+    chunk: optional
 
 parametric:
   suffixes:
@@ -141,3 +147,4 @@ parametric:
     ceagent: optional
     reconstruction: optional
     run: optional
+    chunk: optional
diff --git a/src/schema/rules/files/raw/func.yaml b/src/schema/rules/files/raw/func.yaml
@@ -21,6 +21,7 @@ func:
     run: optional
     echo: optional
     part: optional
+    chunk: optional
 
 phase:
   suffixes:
@@ -41,3 +42,4 @@ phase:
     direction: optional
     run: optional
     echo: optional
+    chunk: optional
diff --git a/src/schema/rules/sidecars/micr.yaml b/src/schema/rules/sidecars/micr.yaml
@@ -50,7 +50,7 @@ MicroscopySample:
       level: recommended
       description_addendum: |
         From [DICOM Body Part
-        Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L)
+        Examined](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L)
         (for example `"BRAIN"`).
     BodyPartDetails: recommended
     BodyPartDetailsOntology: optional