[INFRA] Drop numeric XX- from markdown file names (#1345)

* MNT: Move table of contents to top of mkdocs.yml

* MNT: Drop numeric prefixes from filenames

* MNT: Update all links to remove XX-

* make link single-line

* fix links in pre gh changelog

* fix CODEOWNERS

* remove 04-

Co-authored-by: Stefan Appelhoff <[email protected]>

CODEOWNERS

@@ -5,19 +5,15 @@
 # Request for Review) please add your GitHub username next to the file you want to
 # monitor below.
 
-# Add your GitHub name below to get notified about proposed releases
-/src/CHANGES.md @chrisgorgo @sappelhoff @CPernet
-
 # Individual sections
-/src/01-common-principles.md @chrisgorgo @DimitriPapadopoulos
-/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisgorgo
-/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff @ezemikulan
-/src/04-modality-specific-files/04-intracranial-electroencephalography.md @ezemikulan
-/src/05-derivatives/03-imaging.md @effigies
-/src/05-derivatives/04-structural-derivatives.md @edickie @ahoopes
-/src/05-derivatives/05-functional-derivatives.md @effigies
-/src/05-derivatives/06-diffusion-derivatives.md @francopestilli @oesteban @Lestropie
-/src/appendices/meg-file-formats.md @monkeyman192
+/src/common-principles.md @chrisgorgo @DimitriPapadopoulos
+/src/modality-specific-files/magnetic-resonance-imaging-data.md @chrisgorgo
+/src/modality-specific-files/electroencephalography.md @sappelhoff @ezemikulan
+/src/modality-specific-files/intracranial-electroencephalography.md @ezemikulan
+/src/derivatives/imaging.md @effigies
+/src/derivatives/structural-derivatives.md @edickie @ahoopes
+/src/derivatives/functional-derivatives.md @effigies
+/src/derivatives/diffusion-derivatives.md @francopestilli @oesteban @Lestropie
 
 # The schema
 /src/schema/ @tsalo @erdalkaraca

mkdocs.yml

@@ -1,5 +1,48 @@
 site_name: Brain Imaging Data Structure v1.8.1-dev
 site_url: https://bids-specification.readthedocs.io/en/stable/
+nav:
+    - The BIDS Specification:
+      - Introduction: introduction.md
+      - Common principles: common-principles.md
+      - Modality agnostic files: modality-agnostic-files.md
+      - Modality specific files:
+        - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
+        - Magnetoencephalography: modality-specific-files/magnetoencephalography.md
+        - Electroencephalography: modality-specific-files/electroencephalography.md
+        - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md
+        - Task events: modality-specific-files/task-events.md
+        - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md
+        - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md
+        - Genetic Descriptor: modality-specific-files/genetic-descriptor.md
+        - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md
+        - Microscopy: modality-specific-files/microscopy.md
+        - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md
+      - Derivatives:
+        - BIDS Derivatives: derivatives/introduction.md
+        - Common data types and metadata: derivatives/common-data-types.md
+        - Imaging data types: derivatives/imaging.md
+      - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
+      - Glossary: glossary.md
+      - BIDS Extension Proposals: extensions.md
+      - Appendix:
+        - Contributors: appendices/contributors.md
+        - Licenses: appendices/licenses.md
+        - Entity table: appendices/entity-table.md
+        - Entities: appendices/entities.md
+        - File collections: appendices/file-collections.md
+        - Units: appendices/units.md
+        - Hierarchical Event Descriptors: appendices/hed.md
+        - MEG file formats: appendices/meg-file-formats.md
+        - MEG systems: appendices/meg-systems.md
+        - Coordinate systems: appendices/coordinate-systems.md
+        - Quantitative MRI: appendices/qmri.md
+        - Arterial Spin Labeling: appendices/arterial-spin-labeling.md
+        - Cross modality correspondence: appendices/cross-modality-correspondence.md
+      - Changelog: CHANGES.md
+    - The BIDS Starter Kit:
+      - Website: https://bids-standard.github.io/bids-starter-kit
+      - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
+      - GitHub repository: https://github.com/bids-standard/bids-starter-kit
 theme:
     name: material
     favicon: images/favicon.png
@@ -33,6 +76,25 @@ plugins:
         module_name: tools/mkdocs_macros_bids/main
     - redirects:
         redirect_maps:
+            '01-introduction.md': 'introduction.md'
+            '02-common-principles.md': 'common-principles.md'
+            '03-modality-agnostic-files.md': 'modality-agnostic-files.md'
+            '04-modality-specific-files/01-magnetic-resonance-imaging-data.md': 'modality-specific-files/magnetic-resonance-imaging-data.md'
+            '04-modality-specific-files/02-magnetoencephalography.md': 'modality-specific-files/magnetoencephalography.md'
+            '04-modality-specific-files/03-electroencephalography.md': 'modality-specific-files/electroencephalography.md'
+            '04-modality-specific-files/04-intracranial-electroencephalography.md': 'modality-specific-files/intracranial-electroencephalography.md'
+            '04-modality-specific-files/05-task-events.md': 'modality-specific-files/task-events.md'
+            '04-modality-specific-files/06-physiological-and-other-continuous-recordings.md': 'modality-specific-files/physiological-and-other-continuous-recordings.md'
+            '04-modality-specific-files/07-behavioral-experiments.md': 'modality-specific-files/behavioral-experiments.md'
+            '04-modality-specific-files/08-genetic-descriptor.md': 'modality-specific-files/genetic-descriptor.md'
+            '04-modality-specific-files/09-positron-emission-tomography.md': 'modality-specific-files/positron-emission-tomography.md'
+            '04-modality-specific-files/10-microscopy.md': 'modality-specific-files/microscopy.md'
+            '04-modality-specific-files/11-near-infrared-spectroscopy.md': 'modality-specific-files/near-infrared-spectroscopy.md'
+            '05-derivatives/01-introduction.md': 'derivatives/introduction.md'
+            '05-derivatives/02-common-data-types.md': 'derivatives/common-data-types.md'
+            '05-derivatives/03-imaging.md': 'derivatives/imaging.md'
+            '06-longitudinal-and-multi-site-studies.md': 'longitudinal-and-multi-site-studies.md'
+            '07-extensions.md': 'extensions.md'
             '99-appendices/14-glossary.md': 'glossary.md'
             '99-appendices/01-contributors.md': 'appendices/contributors.md'
             '99-appendices/02-licenses.md': 'appendices/licenses.md'
@@ -49,46 +111,3 @@ plugins:
             '99-appendices/13-cross-modality-correspondence.md': 'appendices/cross-modality-correspondence.md'
 docs_dir: 'src'
 use_directory_urls: false
-nav:
-    - The BIDS Specification:
-      - Introduction: 01-introduction.md
-      - Common principles: 02-common-principles.md
-      - Modality agnostic files: 03-modality-agnostic-files.md
-      - Modality specific files:
-        - Magnetic Resonance Imaging: 04-modality-specific-files/01-magnetic-resonance-imaging-data.md
-        - Magnetoencephalography: 04-modality-specific-files/02-magnetoencephalography.md
-        - Electroencephalography: 04-modality-specific-files/03-electroencephalography.md
-        - Intracranial Electroencephalography: 04-modality-specific-files/04-intracranial-electroencephalography.md
-        - Task events: 04-modality-specific-files/05-task-events.md
-        - Physiological and other continuous recordings: 04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
-        - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
-        - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
-        - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
-        - Microscopy: 04-modality-specific-files/10-microscopy.md
-        - Near-Infrared Spectroscopy: 04-modality-specific-files/11-near-infrared-spectroscopy.md
-      - Derivatives:
-        - BIDS Derivatives: 05-derivatives/01-introduction.md
-        - Common data types and metadata: 05-derivatives/02-common-data-types.md
-        - Imaging data types: 05-derivatives/03-imaging.md
-      - Longitudinal and multi-site studies: 06-longitudinal-and-multi-site-studies.md
-      - Glossary: glossary.md
-      - BIDS Extension Proposals: 07-extensions.md
-      - Appendix:
-        - Contributors: appendices/contributors.md
-        - Licenses: appendices/licenses.md
-        - Entity table: appendices/entity-table.md
-        - Entities: appendices/entities.md
-        - File collections: appendices/file-collections.md
-        - Units: appendices/units.md
-        - Hierarchical Event Descriptors: appendices/hed.md
-        - MEG file formats: appendices/meg-file-formats.md
-        - MEG systems: appendices/meg-systems.md
-        - Coordinate systems: appendices/coordinate-systems.md
-        - Quantitative MRI: appendices/qmri.md
-        - Arterial Spin Labeling: appendices/arterial-spin-labeling.md
-        - Cross modality correspondence: appendices/cross-modality-correspondence.md
-      - Changelog: CHANGES.md
-    - The BIDS Starter Kit:
-      - Website: https://bids-standard.github.io/bids-starter-kit
-      - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
-      - GitHub repository: https://github.com/bids-standard/bids-starter-kit

src/CHANGES.md

@@ -466,30 +466,30 @@
 
 -   Added support for MEG data (merged BEP008).
 -   Added `SequenceName` field.
--   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](04-modality-specific-files/05-task-events.md).
--   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](modality-specific-files/task-events.md).
+-   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 -   Added `DwellTime` field.
 
 ## [1.0.2](https://doi.org/10.5281/zenodo.3759801) (2017-07-18)
 
--   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for multiple defacing masks: [4.1 Anatomy imaging data](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](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](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](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for multiple defacing masks: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](modality-specific-files/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](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## [1.0.1](https://doi.org/10.5281/zenodo.3759788) (2017-03-13)
 
--   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](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](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](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## 1.0.1-rc1
 
--   Added T1 Rho maps: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for phenotypic information split into multiple files: [3.2 Participant key file](03-modality-agnostic-files.md#participants-file).
+-   Added T1 Rho maps: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files.md#participants-file).
 -   Added recommendations for multi site datasets.
 -   Added `SoftwareVersions`.
 -   Added `run-<run_index>` to the phase encoding maps. Improved the description.

src/appendices/arterial-spin-labeling.md

@@ -73,7 +73,7 @@ Y. Suzuki and [OSIPI Task force 4.1: ASL lexicon milestone 1](https://osipi.gith
 
 ### (P)CASL sequence
 
-![PCASL](../04-modality-specific-files/images/asl_pcasl_sequence.png)
+![PCASL](../modality-specific-files/images/asl_pcasl_sequence.png)
 
 For (P)CASL, specifying the `LabelingDuration` and the `PostLabelingDelay` is required.
 The `LabelingDuration` is defined as the total duration of the labeling pulse train in seconds.
@@ -89,7 +89,7 @@ whereas in case of `CASL`,the recommended `CASLType` field describes if a separa
 
 ### (P)CASL Labeling Pulses
 
-![PCASL Labeling Pulses](../04-modality-specific-files/images/asl_pcasl_labeling_pulses.png)
+![PCASL Labeling Pulses](../modality-specific-files/images/asl_pcasl_labeling_pulses.png)
 
 Several recommended metadata fields describe the labeling pulses of the labeling pulse train in PCASL.
 The `LabelingPulseAverageGradient` and the `LabelingPulseMaximumGradient` are the average labeling gradient
@@ -101,23 +101,23 @@ and the delay between the peaks of the individual labeling pulses in millisecond
 
 ### PASL sequence
 
-![PASL without Bolus Cut-off](../04-modality-specific-files/images/asl_pasl_boluscutoff_false.png)
+![PASL without Bolus Cut-off](../modality-specific-files/images/asl_pasl_boluscutoff_false.png)
 
 For PASL, specifying the `PostLabelingDelay` is required.
 `PostLabelingDelay` is the time, in seconds, from the middle of the labeling pulse until the middle of
 the excitation pulse applied to the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
 Additionally, the `BolusCutOffFlag` field is required,
 which is a boolean indicating if a bolus cut-off technique has been applied.
 
-![PASL QUIPSSII](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png)
+![PASL QUIPSSII](../modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png)
 
 When `BolusCutOffFlag` is set true for `PASL`, two additional metadata fields are required:
 `BolusCutOffTechnique` and `BolusCutOffDelay`.
 In this example, the `BolusCutOffTechnique`, which is the name of the technique used for applying a bolus cut-off,
 is QUIPSS-II consisting of only one bolus cut-off pulse.
 The `BolusCutOffDelay` is therefore a number, representing the duration between the end of the labeling and the start of the bolus cut-off saturation pulse, in seconds.
 
-![PASL Q2TIPS](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png)
+![PASL Q2TIPS](../modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png)
 
 In this example, the `BolusCutOffTechnique` applied is Q2TIPS, consisting of multiple bolus cut-off pulses.
 In this case, only the duration of the first and last pulse should be specified in `BolusCutOffDelay`.
@@ -127,4 +127,4 @@ In this case, only the duration of the first and last pulse should be specified
 The specification includes a dependency table, describing metadata field dependencies for ASL.
 This flowchart is intended to further clarify that table.
 
-![ASL Flowchart](../04-modality-specific-files/images/asl_flowchart.png)
+![ASL Flowchart](../modality-specific-files/images/asl_flowchart.png)

src/appendices/coordinate-systems.md

@@ -249,6 +249,6 @@ Please note that `space-scanner` SHOULD NOT be used, it is mentioned in this spe
 
 <!-- Link Definitions -->
 
-[common file level metadata fields]: ../05-derivatives/02-common-data-types.md#common-file-level-metadata-fields
+[common file level metadata fields]: ../derivatives/common-data-types.md#common-file-level-metadata-fields
 
-[deprecated]: ../02-common-principles.md#definitions
+[deprecated]: ../common-principles.md#definitions

src/appendices/cross-modality-correspondence.md

@@ -7,7 +7,7 @@ please pay specific attention to the format the MR images are in.
 It is important to note whether the MR images have been unwarped
 in order to correct for gradient non-linearities,
 indicated by the `NonlinearGradientCorrection` metadata field
-(see [Magnetic Resonance Imaging Data - Sequence Specifics](../04-modality-specific-files/01-magnetic-resonance-imaging-data.md#sequence-specifics)).
+(see [Magnetic Resonance Imaging Data - Sequence Specifics](../modality-specific-files/magnetic-resonance-imaging-data.md#sequence-specifics)).
 The reason for this is that the MRI needs to be corrected for nonlinear gradients
 in order to fit the accompanying PET scans for co-registration
 (Knudsen et al. 2020, [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433);

src/appendices/entities.md

@@ -4,7 +4,7 @@ This section compiles the entities (key-value pairs within file names) described
 specification, and describes each.
 
 A general introduction to entities is given in the section on
-[filename structure](../02-common-principles.md#file-name-structure).
+[filename structure](../common-principles.md#file-name-structure).
 
 The ordering of entities, and whether each is OPTIONAL, REQUIRED, or MUST NOT
 be specified for a given file type, is specified in the [Entity Table](entity-table.md).