[MISC] Added appendix to mkdocs and added some internal links

CHANGES.md

@@ -1,118 +1,164 @@
-1 Changelog <a id="h.17phlwhk50et"></a>
-===============
+1 Changelog
 
 1.1.1
 
 -   Improved the MEG landmark coordinates description.
--   Replaced ManufacturersCapModelName in meg.json with CapManufacturer
-   and CapManufacturersModelName.
+
+-   Replaced ManufacturersCapModelName in meg.json with CapManufacturer and
+CapManufacturersModelName.
+
 -   Remove EEGSamplingFrequency and ManufacturersAmplifierModelName
-   from the meg.json.
+from the meg.json.
+
 -   Improved the behavioural data description.
 
 1.1.0
 
--   Added support for MEG data (merged BEP008)
--   Added SequenceName field.
--   Added support for describing events with Hierarchical Event Descriptors [[8.5 Task events](#heading=h.daip42kp5ndz)].
--   Added VolumeTiming and AcquisitionDuration fields [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
--   Added DwellTime field.
+- Added support for MEG data (merged BEP008)
+- Added SequenceName field.
+- Added support for describing events with Hierarchical Event Descriptors [[4.3 Task events](src/04-modality-specific-files/03-task-events.md)].
+- Added VolumeTiming and AcquisitionDuration fields [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+- Added DwellTime field.
 
 1.0.2
 
--   Added support for high resolution (anatomical) T2star images [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)].
--   Added support for multiple defacing masks [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)].
--   Added optional key and metadata field for contrast enhanced structural scans [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)].
--   Added DelayTime field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
--   Added support for multi echo BOLD data [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
+-   Added support for high resolution (anatomical) T2star images [[4.1 Anatomy imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].
+
+-   Added support for multiple defacing masks [[4.1 Anatomy imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].
+
+-   Added optional key and metadata field for contrast enhanced structural scans
+[[4.1 Anatomy imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]
+
+-   Added DelayTime field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+-   Added support for multi echo BOLD data [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
 
 1.0.1
 
--   Added InstitutionName field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
--   Added InstitutionAddress field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
--   Added DeviceSerialNumber field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
+-   Added InstitutionName field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+-   Added InstitutionAddress field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+-   Added DeviceSerialNumber field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
 -   Added NumberOfVolumesDiscardedByUser and
-   NumberOfVolumesDiscardedByScanner field [[8.4 Task (including
-   resting state) imaging data](#heading=h.r8mrcau3kkcq)].
+   NumberOfVolumesDiscardedByScanner field [[4.1 Task (including
+   resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
 -   Added TotalReadoutTime to functional images metadata list
-    [[8.4 Task (including resting state) imaging
-   data](#heading=h.r8mrcau3kkcq)].
+    [[4.1 Task (including resting state) imaging
+   data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
 
 1.0.1-rc1
 
--   Added T1 Rho maps [[8.3 Anatomy imaging
-   data](#heading=h.fm6ipijipc08)].
+-   Added T1 Rho maps [[4.1 Anatomy imaging
+   data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].
+
 -   Added support for phenotypic information split into multiple files
-   [[8.11 Participant key file](#heading=h.pi5iigxxt8vy)].
+   [[3.2 Participant key file](src/03-modality-agnostic-files.md#participants-file)].
+
 -   Added recommendations for multi site datasets
+
 -   Added SoftwareVersions
+
 -   Added run-&lt;run_index&gt; to the phase encoding
    maps. Improved the description.
+
 -   Added InversionTime metadata key.
+
 -   Clarification on the source vs raw language.
+
 -   Added trial_type column to the event files.
+
 -   Added missing sub-&lt;participant_label&gt; in
    behavioural data file names
+
 -   Added ability to store stimuli files.
+
 -   Clarified the language describing allowed subject labels.
+
 -   Added quantitative proton density maps.
 
 1.0.0
 
 -   Added ability to specify fieldmaps acquired with multiple parameter
    sets.
+
 -   Added ability to have multiple runs of the same fieldmap.
+
 -   Added FLASH anatomical images.
 
 1.0.0-rc4
 
 -   Replaced links to neurolex with explicit DICOM Tags.
+
 -   Added sourcedata.
+
 -   Added data dictionaries.
+
 -   Be more explicit about contents of JSON files for structural
    (anatomical) scans.
 
 1.0.0-rc3
 
 -   Renamed PhaseEncodingDirection values from “x”, “y”,
    “z” to “i”, “j”, “k” to avoid confusion with FSL parameters
+
 -   Renamed SliceEncodingDirection values from “x”, “y”,
    “z” to “i”, “j”, “k”
 
 1.0.0-rc2
 
 -   Removed the requirement that TSV files cannot include more than two
    consecutive spaces.
+
 -   Refactor of the definitions sections (copied from the
    manuscript)
+
 -   Make support for uncompressed .nii files more explicit.
+
 -   Added BIDSVersion to dataset.json
+
 -   Remove the statement that SliceEncodingDirection is
    necessary for slice time correction
+
 -   Change dicom converter recommendation from dcmstack to dcm2nii and
    dicm2nii following interactions with the community (see
    [https://github.com/moloney/dcmstack/issues/39](https://github.com/moloney/dcmstack/issues/39) and
    [https://github.com/neurolabusc/dcm2niix/issues/4](https://github.com/neurolabusc/dcm2niix/issues/4)).
+
 -   Added section on behavioral experiments with no accompanying MRI
    acquisition
+
 -   Add \_magnitude.nii\[.gz\] image for GE type
    fieldmaps.
+
 -   Replaced EchoTimeDifference with
    EchoTime1 and EchoTime2 (SPM toolbox
    requires this input).
+
 -   Added support for single band reference image for DWI.
+
 -   Added DatasetDOI field in the dataset
    description.
+
 -   Added description of more metadata fields relevant to DWI fieldmap
    correction.
--   PhaseEncodingDirection is now expressed in “x”, “y” etc.
-   instead of “PA” “RL” for DWI scans (so it’s the same as BOLD
-   scans)
+
+-   PhaseEncodingDirection is now expressed in “x”, “y” etc. instead of “PA”
+“RL” for DWI scans
+(so it’s the same as BOLD scans)
+
 -   Added rec-&lt;label&gt; flag to BOLD files to
-   distinguish between different reconstruction algorithms (analogous
-   to anatomical scans).
--   Added recommendation to use \_physio suffix for continuous recordings of motion parameters obtained by the scanner side reconstruction algorithms.
+   distinguish
+   between different reconstruction algorithms
+   (analogous to anatomical scans).
+
+-   Added recommendation to use \_physio suffix for continuous recordings
+of motion
+parameters obtained by
+the scanner side reconstruction algorithms.
 
 1.0.0-rc1
 
--   Initial release
+- Initial release

mkdocs.yml

@@ -16,4 +16,13 @@ nav:
         - Physiological and other continous recordings: 04-modality-specific-files/04-physiological-and-other-continous-recordings.md
         - Behavioral experiments (with no MRI): 04-modality-specific-files/05-behavioural-experiments.md
       - Longitudinal and multi-site studies: 05-longitudinal-and-multi-site-studies.md
+      - Appendix:
+        - Contributors: 99-appendices/01-contributors.md
+        - Licenses: 99-appendices/02-licenses.md
+        - HED: 99-appendices/03-hed.md
+        - Entity-table: 99-appendices/04-entity-table.md
+        - Units: 99-appendices/05-units.md
+        - MEG file formats: 99-appendices/06-meg-file-formats.md
+        - MEG systems: 99-appendices/07-meg-systems.md
+        - Coordinate-systems: 99-appendices/08-coordinate-systems.md
     - The BIDS Starter Kit: https://github.com/bids-standard/bids-starter-kit

src/02-common-principles.md

@@ -298,7 +298,7 @@ SI derived units. In case there are valid reasons to deviate from SI units or SI
 derived units, the units MUST be specified in the sidecar JSON file. In case
 data is expressed in SI units or SI derived units, the units MAY be specified in
 the sidecar JSON file. In case prefixes are added to SI or non-SI units (e.g.
-mm), the prefixed units MUST be specified in the JSON file (see Appendix V:
+mm), the prefixed units MUST be specified in the JSON file (see [Appendix V](99-appendices/05-units.md):
 Units). In particular:
 
 -   Elapsed time SHOULD be expressed in seconds. Please note that some DICOM

src/03-modality-agnostic-files.md

@@ -104,7 +104,8 @@ kept in phenotype/ folder and end with the `.tsv` extension. They can include
 arbitrary set of columns, but one of them has to be participant_id with matching
 `sub-<participant_label>`. As with all other tabular data, those additional
 phenotypic information files can be accompanied by a JSON file describing the
-columns in detail (see Section 4.2). In addition to the column description, a
+columns in detail (see [here](02-common-principles.md#tabular-files)).
+In addition to the column description, a
 section describing the measurement tool (as a whole) can be added under the name
 `MeasurementToolMetadata`. This section consists of two keys: `Description` - a
 free text description of the tool, and `TermURL` a link to an entity in an