fix: pacify codespell + links to entities (rather than glossary)

Author: oesteban

src/derivatives/atlas.md

@@ -20,16 +20,16 @@ or the integration of existing ones to define a stereotactic space.
 
 For derivatives of template-generating pipelines, which typically aggregate
 several sessions and/or subjects, the derivatives-specific
-[`tpl-<label>` entity](../glossary.md#template-entities) indicates that the
+[`tpl-<label>` entity](../appendices/entities.md#tpl) indicates that the
 spatial frame of analysis is not defined by a single brain image but an
 aggregation thereof.
-On that sense, the [`tpl-<label>` entity](../glossary.md#template-entities)
-would be dual in terms of usage to BIDS raw's [`sub-<label>`](../glossary.md#subject-entities).
+On that sense, the [`tpl-<label>` entity](../appendices/entities.md#tpl)
+would be dual in terms of usage to BIDS raw's [`sub-<label>`](../appendices/entities.md#sub).
 
 !!! tip "Recommendation"
 
-    The selected `<label>` in the [`tpl-<label>` entity](../glossary.md#template-entities)
-    is RECOMMENDED for the [`space-<label>` entity](../appendices/entities.md#space-entities)
+    The selected `<label>` in the [`tpl-<label>` entity](../appendices/entities.md#tpl)
+    is RECOMMENDED for the [`space-<label>` entity](../appendices/entities.md#space)
     in downstream derivatives from this particular template (see previous section
     [Derivatives from atlases](imaging.md#derivatives-from-atlases)).
 
@@ -51,17 +51,17 @@ such as `T1w` or `PET`; and
 Please note that the [`<datatype>/` directory](../glossary.md#data_type-common_principles) is RECOMMENDED.
 Like for the remainder of BIDS Derivatives,
 the [`<datatype>/` directory](../glossary.md#data_type-common_principles) MAY be omitted in the case
-only one data type (such as `anat/`) is stored under the `tpl-<label>` directory.
+only one data type (such as `anat/`) is stored under the `tpl-<label>/` directory.
 
-The [`cohort-<label>` directory and entity](../glossary.md#cohort-entities) MUST be specified for templates
+The [`cohort-<label>` directory and entity](../appendices/entities.md#cohort) MUST be specified for templates
 with several cohorts.
-The [`cohort-<label>` directory and entity](../glossary.md#cohort-entities) are dual in terms of usage to BIDS raw's
-[`session-<label>`](../glossary.md#session-entities).
+The [`cohort-<label>` directory and entity](../appendices/entities.md#cohort) are dual in terms of usage to BIDS raw's
+[`session-<label>`](../appendices/entities.md#ses).
 
 ### Example: the `MNI152NLin2009cAsym` template
 
-For the pipeline that generated the MNI152NLin2009cAsym, the outputs could look
-like the following example:
+For the pipeline that generated [`MNI152NLin2009cAsym`](../appendices/coordinate-systems.md#standard-template-identifiers),
+the outputs could look like the following example:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -99,7 +99,7 @@ A guide for using macros can be found at
 
 In the case that the template-generating pipeline derives
 several cohorts, the file structure must employ the
-[`cohort-<label>` directory and entity](../glossary.md#cohort-entities).
+[`cohort-<label>` directory and entity](../appendices/entities.md#cohort).
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -260,7 +260,7 @@ corresponding to the atlas or atlases in the structure.
 !!! tip "Recommendation"
 
     The selected `<label>` in the `atlas-<label>_description.json` file is RECOMMENDED
-    for the [`atlas-<label>` entity](../appendices/entities.md#atlas-entities)
+    for the [`atlas-<label>` entity](../appendices/entities.md#atlas)
     in downstream derivatives from this particular atlas (see previous section
     [Derivatives from atlases](imaging.md#derivatives-from-atlases)).
 
@@ -389,7 +389,7 @@ where `atlas-Dietrich2009_description.json` could contain:
 
 Finally, in 2011 a second atlas was developed integrating new segmentations.
 Now, to disambiguate between the two atlases,
-the [`atlas-<label>` entity](../appendices/entities.md#atlas-entities) MUST be used:
+the [`atlas-<label>` entity](../appendices/entities.md#atlas) MUST be used:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -682,7 +682,8 @@ A guide for using macros can be found at
 **A more comprehensive example.**
 For example, the [PS13 atlas](https://doi.org/10.18112/openneuro.ds004401.v1.3.0),
 a molecular imaging brain atlas of Cyclooxygenase-1 (PET),
-was generated in two standard spaces: `MNI152Lin` and `fsaverage`:
+was generated in [two standard spaces](../appendices/coordinate-systems.md#standard-template-identifiers)
+(`MNI152Lin` and `fsaverage`):
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -760,11 +761,12 @@ A guide for using macros can be found at
 }}
 
 If the pipeline generates two different atlases for at least one template space
-in the output, then [`atlas-<label>`](../glossary.md#atlas-entities) is REQUIRED
+in the output, then [`atlas-<label>`](../appendices/entities.md#atlas) is REQUIRED
 for disambiguation.
 For example, let's imagine the PS13 atlas is revised in 2034, and based on the
 original pipeline and data, it generates now a new manual segmentation
-in the `MNI152Lin` space with some new regions defined.
+in the [`MNI152Lin` space](../appendices/coordinate-systems.md#standard-template-identifiers)
+with some new regions defined.
 The new atlas can be structured as follows:
 
 <!-- This block generates a file tree.
@@ -808,10 +810,10 @@ A guide for using macros can be found at
 ### Deriving an atlas in a study-specific template space and generating conversions to pre-existing template references
 
 A usual scenario involves the generation of the atlas in a new, study-specific space
-and then provide resamplings of the template with reference to existing, widely used
-spaces such as MNI.
+and then provide resamplings of the template with reference to existing,
+[standard spaces](../appendices/coordinate-systems.md#standard-template-identifiers).
 
-In this case, all atlas' derivatives MUST be stored within a single `tpl-<label>/` folder
+In this case, all atlas' derivatives MUST be stored within a single `tpl-<label>/` directory
 For example, if the previous PS13 example had been generated that way, the previous
 example would be updated as follows:
 
@@ -891,7 +893,8 @@ A guide for using macros can be found at
 }}
 
 where `tpl-ps13_desc-nopvc_pet.nii.gz` and `tpl-ps13_desc-pvc_pet.nii.gz` SHOULD NOT define
-a `space-<label>` and therefore MUST be defined in the space defined by `tpl-<label>`,
+a [`space-<label>`](../appendices/entities.md#space) and therefore
+MUST be defined in the space defined by [`tpl-<label>` entity](../appendices/entities.md#tpl),
 that is, the study-specific template.
 This example can be further extended to the example in which a revision of the atlas
 is done later in time:

src/derivatives/imaging.md

@@ -559,15 +559,15 @@ Template:
             <source_entities>[_space-<space>][_atlas-<label>][seg-<label>][_scale-<label>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
 ```
 
--    [`space-<label>`](../glossary.md#space-entities) is REQUIRED to disambiguate derivatives defined with
+-    [`space-<label>`](../appendices/entities.md#space) is REQUIRED to disambiguate derivatives defined with
      respect to different [coordinate systems](../appendices/coordinate-systems.md), following the general
      BIDS-Derivatives specifications.
--    [`atlas-<label>`](../glossary.md#atlas-entities) is REQUIRED to encode files pertaining
+-    [`atlas-<label>`](../appendices/entities.md#atlas) is REQUIRED to encode files pertaining
      or derived from the atlas identified by the entity's label.
--    [`seg-<label>`](../glossary.md#segmentation-entities) is REQUIRED when a single atlas has several different
+-    [`seg-<label>`](../appendices/entities.md#seg) is REQUIRED when a single atlas has several different
      realizations (for instance, segmentations and parcellations created with different criteria) that
      need disambiguation.
--    [`scale-<label>`](../glossary.md#scale-entities) is REQUIRED to disambiguate different atlas 'scales',
+-    [`scale-<label>`](../appendices/entities.md#scale) is REQUIRED to disambiguate different atlas 'scales',
      when the atlas has more than one 'brain unit' or 'areal resolution', typically relating to the
      number of regions defined and the area they cover.