diff --git a/mkdocs.yml b/mkdocs.yml
index 1ec59b49f7..2e5c7b3576 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -5,7 +5,11 @@ nav:
   - The BIDS Specification:
       - Introduction: introduction.md
       - Common principles: common-principles.md
-      - Modality agnostic files: modality-agnostic-files.md
+      - Modality agnostic files:
+          - Dataset description: modality-agnostic-files/dataset-description.md
+          - Data summary files: modality-agnostic-files/data-summary-files.md
+          - Phenotypic and assessment data: modality-agnostic-files/phenotypic-and-assessment-data.md
+          - Code: modality-agnostic-files/code.md
       - Modality specific files:
           - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
           - Magnetoencephalography: modality-specific-files/magnetoencephalography.md
@@ -132,7 +136,8 @@ plugins:
       redirect_maps:
         "01-introduction.md": "introduction.md"
         "02-common-principles.md": "common-principles.md"
-        "03-modality-agnostic-files.md": "modality-agnostic-files.md"
+        "03-modality-agnostic-files.md": "modality-agnostic-files/dataset-description.md"
+        "modality-agnostic-files.md": "modality-agnostic-files/dataset-description.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"
diff --git a/src/CHANGES.md b/src/CHANGES.md
index 6350df47e8..8908abe800 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -625,7 +625,7 @@
 ## 1.0.1-rc1
 
 -   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 support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files/data-summary-files.md#participants-file).
 -   Added recommendations for multi site datasets.
 -   Added `SoftwareVersions`.
 -   Added `run-<run_index>` to the phase encoding maps. Improved the description.
diff --git a/src/appendices/meg-file-formats.md b/src/appendices/meg-file-formats.md
index 81b640b517..bd5d05be0c 100644
--- a/src/appendices/meg-file-formats.md
+++ b/src/appendices/meg-file-formats.md
@@ -212,7 +212,7 @@ entity to indicate each part.
 If there are multiple parts of a recording and the optional `scans.tsv` is provided,
 remember to list all files separately in `scans.tsv` and that the entries
 for the `acq_time` column in `scans.tsv` MUST all be identical, as described in
-[Scans file](../modality-agnostic-files.md#scans-file).
+[Scans file](../modality-agnostic-files/data-summary-files.md#scans-file).
 
 Example:
 
diff --git a/src/appendices/qmri.md b/src/appendices/qmri.md
index 83247c119b..3ca687e028 100644
--- a/src/appendices/qmri.md
+++ b/src/appendices/qmri.md
@@ -314,7 +314,7 @@ and a guide for using macros can be found at
 ### Metadata requirements for qMRI maps
 
 As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of
-[derived datasets](../modality-agnostic-files.md#derived-dataset-and-pipeline-description).
+[derived datasets](../modality-agnostic-files/dataset-description.md#derived-dataset-and-pipeline-description).
 
 An example `dataset_description.json` for a qMRI map derivatives directory:
 
diff --git a/src/common-principles.md b/src/common-principles.md
index 4503721165..dfdfd7dc3c 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -109,7 +109,7 @@ Data for each subject are placed in subdirectories named "`sub-<label>`",
 where string "`<label>`" is substituted with the unique identification
 label of each subject.
 Additional information on each participant MAY be provided in a
-[participants file](modality-agnostic-files.md#participants-file)
+[participants file](modality-agnostic-files/data-summary-files.md#participants-file)
 in the root directory of the dataset.
 
 If data for the subject were acquired across multiple sessions, then within
@@ -119,7 +119,7 @@ label for each session.
 In datasets where at least one subject has more than one session, this
 additional subdirectory later SHOULD be added for all subjects in the dataset.
 Additional information on each session MAY be provided in a
-[sessions file](modality-agnostic-files.md#sessions-file)
+[sessions file](modality-agnostic-files/data-summary-files.md#sessions-file)
 within the subject directory.
 
 Within the session subdirectory (or the subject subdirectory if no
@@ -1144,8 +1144,8 @@ to suppress warnings or provide interpretations of your filenames.
 
 <!-- Link Definitions -->
 
-[dataset-description]: modality-agnostic-files.md#dataset-description
-[dataset_description.json]: modality-agnostic-files.md#dataset_descriptionjson
-[derived-dataset-description]: modality-agnostic-files.md#derived-dataset-and-pipeline-description
+[dataset-description]: modality-agnostic-files/data-summary-files.md
+[dataset_description.json]: modality-agnostic-files/data-summary-files.md#dataset_descriptionjson
+[derived-dataset-description]: modality-agnostic-files/data-summary-files.md#derived-dataset-and-pipeline-description
 [deprecated]: #definitions
 [uris]: #uniform-resource-indicator
diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md
index af798f38bd..9878c239f9 100644
--- a/src/derivatives/introduction.md
+++ b/src/derivatives/introduction.md
@@ -129,7 +129,7 @@ for GIFTI files.
 
 [storage]: ../common-principles.md#storage-of-derived-datasets
 
-[derived-dataset-description]: ../modality-agnostic-files.md#derived-dataset-and-pipeline-description
+[derived-dataset-description]: ../modality-agnostic-files/dataset-description.md#derived-dataset-and-pipeline-description
 
 [gifti]: https://www.nitrc.org/projects/gifti/
 
diff --git a/src/longitudinal-and-multi-site-studies.md b/src/longitudinal-and-multi-site-studies.md
index 6fe102cb1a..5623bec305 100644
--- a/src/longitudinal-and-multi-site-studies.md
+++ b/src/longitudinal-and-multi-site-studies.md
@@ -3,7 +3,7 @@
 Multiple sessions (visits) are encoded by adding an extra layer of directories
 and [filenames](common-principles.md#filenames)
 in the form of a session (for example `ses-<label>`) and
-with a [`*_sessions.tsv` file](modality-agnostic-files.md#sessions-file).
+with a [`*_sessions.tsv` file](modality-agnostic-files/data-summary-files.md#sessions-file).
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
diff --git a/src/modality-agnostic-files.md b/src/modality-agnostic-files.md
deleted file mode 100644
index 84df1a2dca..0000000000
--- a/src/modality-agnostic-files.md
+++ /dev/null
@@ -1,547 +0,0 @@
-# Modality agnostic files
-
-## Dataset description
-
-Templates:
-
--   `dataset_description.json`
--   `README[.md|.rst|.txt]`
--   `CITATION.cff`
--   `CHANGES`
--   `LICENSE[.md|.rst|.txt]`
-
-### `dataset_description.json`
-
-<!-- This block generates a description.
-A guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___render_text("objects.files.dataset_description.description") }}
-
-Every dataset MUST include this file with the following fields:
-
-<!-- This block generates a metadata table.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_metadata_table(
-   {
-      "Name": "REQUIRED",
-      "BIDSVersion": "REQUIRED",
-      "HEDVersion": "RECOMMENDED",
-      "DatasetLinks": "REQUIRED if [BIDS URIs][] are used",
-      "DatasetType": "RECOMMENDED",
-      "License": "RECOMMENDED",
-      "Authors": "RECOMMENDED if CITATION.cff is not present",
-      "Acknowledgements": "OPTIONAL",
-      "HowToAcknowledge": "OPTIONAL",
-      "Funding": "OPTIONAL",
-      "EthicsApprovals": "OPTIONAL",
-      "ReferencesAndLinks": "OPTIONAL",
-      "DatasetDOI": "OPTIONAL",
-      "GeneratedBy": "RECOMMENDED",
-      "SourceDatasets": "RECOMMENDED",
-   }
-) }}
-
-Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
-and OPTIONAL keys:
-
-<!-- This block generates a table describing subfields within a metadata field.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_subobject_table("metadata.GeneratedBy.items") }}
-
-Example:
-
-```JSON
-{
-  "Name": "The mother of all experiments",
-  "BIDSVersion": "1.6.0",
-  "DatasetType": "raw",
-  "License": "CC0",
-  "Authors": [
-    "Paul Broca",
-    "Carl Wernicke"
-  ],
-  "Acknowledgements": "Special thanks to Korbinian Brodmann for help in formatting this dataset in BIDS. We thank Alan Lloyd Hodgkin and Andrew Huxley for helpful comments and discussions about the experiment and manuscript; Hermann Ludwig Helmholtz for administrative support; and Claudius Galenus for providing data for the medial-to-lateral index analysis.",
-  "HowToAcknowledge": "Please cite this paper: https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
-  "Funding": [
-    "National Institute of Neuroscience Grant F378236MFH1",
-    "National Institute of Neuroscience Grant 5RMZ0023106"
-  ],
-  "EthicsApprovals": [
-    "Army Human Research Protections Office (Protocol ARL-20098-10051, ARL 12-040, and ARL 12-041)"
-  ],
-  "ReferencesAndLinks": [
-    "https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
-    "Alzheimer A., & Kraepelin, E. (2015). Neural correlates of presenile dementia in humans. Journal of Neuroscientific Data, 2, 234001. doi:1920.8/jndata.2015.7"
-  ],
-  "DatasetDOI": "doi:10.0.2.3/dfjj.10",
-  "HEDVersion": "8.0.0",
-  "GeneratedBy": [
-    {
-      "Name": "reproin",
-      "Version": "0.6.0",
-      "Container": {
-        "Type": "docker",
-        "Tag": "repronim/reproin:0.6.0"
-      }
-    }
-  ],
-  "SourceDatasets": [
-    {
-      "URL": "s3://dicoms/studies/correlates",
-      "Version": "April 11 2011"
-    }
-  ]
-}
-```
-
-#### Derived dataset and pipeline description
-
-As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
-top level of every derived dataset:
-`<dataset>/derivatives/<pipeline_name>/dataset_description.json`.
-
-In contrast to raw BIDS datasets, derived BIDS datasets MUST include a
-`GeneratedBy` key:
-
-<!-- This block generates a metadata table.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_metadata_table(
-   {
-      "GeneratedBy": "REQUIRED"
-   }
-) }}
-
-If a derived dataset is stored as a subdirectory of the raw dataset, then the `Name` field
-of the first `GeneratedBy` object MUST be a substring of the derived dataset directory name.
-That is, in a directory `<dataset>/derivatives/<pipeline>[-<variant>]/`, the first
-`GeneratedBy` object should have a `Name` of `<pipeline>`.
-
-Example:
-
-```JSON
-{
-  "Name": "FMRIPREP Outputs",
-  "BIDSVersion": "1.6.0",
-  "DatasetType": "derivative",
-  "GeneratedBy": [
-    {
-      "Name": "fmriprep",
-      "Version": "1.4.1",
-      "Container": {
-        "Type": "docker",
-        "Tag": "poldracklab/fmriprep:1.4.1"
-        }
-    },
-    {
-      "Name": "Manual",
-      "Description": "Re-added RepetitionTime metadata to bold.json files"
-    }
-  ],
-  "SourceDatasets": [
-    {
-      "DOI": "doi:10.18112/openneuro.ds000114.v1.0.1",
-      "URL": "https://openneuro.org/datasets/ds000114/versions/1.0.1",
-      "Version": "1.0.1"
-    }
-  ]
-}
-```
-
-### `README`
-
-<!-- This block generates a file tree.
-A guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___render_text("objects.files.README.description") }}
-
-### `CITATION.cff`
-
-<!-- This block generates a file tree.
-A guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___render_text("objects.files.CITATION.description") }}
-
-For most redundant fields between `CITATION.cff` and `dataset_description.json`,
-the `CITATION.cff` SHOULD take precedence.
-To avoid inconsistency, metadata present in `CITATION.cff` SHOULD NOT be
-be included in `dataset_description.json`, with the exception of `Name` and
-`DatasetDOI`, to ensure that `CITATION.cff`-unaware tools can generate
-references to the dataset.
-In particular, if `CITATION.cff` is present,
-the `"Authors"` field of `dataset_description.json` MUST be omitted,
-and the `"HowToAcknowledge"`, `"License"` and `"ReferencesAndLinks"` SHOULD be omitted
-in favor of the `CITATION.cff` fields `message`/`preferred-citation`, `license` and
-`references`.
-
-### `CHANGES`
-
-<!-- This block generates a description.
-A guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___render_text("objects.files.CHANGES.description") }}
-
-Example:
-
-```Text
-1.0.1 2015-08-27
-  - Fixed slice timing information.
-
-1.0.0 2015-08-17
-  - Initial release.
-```
-
-### `LICENSE`
-
-<!-- This block generates a description.
-A guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___render_text("objects.files.LICENSE.description") }}
-
-## Participants file
-
-Template:
-
-```Text
-participants.tsv
-participants.json
-```
-
-<!-- This block generates a description.
-A guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___render_text("objects.files.participants.description") }}
-
-We RECOMMEND to make use of these columns, and
-in case that you do use them, we RECOMMEND to use the following values
-for them:
-
-<!-- This block generates a columns table.
-The definitions of these fields can be found in
-  src/schema/rules/tabular_data/*.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_columns_table("modality_agnostic.Participants") }}
-
-Throughout BIDS you can indicate missing values with `n/a` (for "not
-available").
-
-`participants.tsv` example:
-
-```tsv
-participant_id	age	sex	handedness	group
-sub-01	34	M	right	read
-sub-02	12	F	right	write
-sub-03	33	F	n/a	read
-```
-
-It is RECOMMENDED to accompany each `participants.tsv` file with a sidecar
-`participants.json` file to describe the TSV column names and properties of their values (see also
-the [section on tabular files](common-principles.md#tabular-files)).
-Such sidecar files are needed to interpret the data, especially so when
-optional columns are defined beyond `age`, `sex`, `handedness`, `species`, `strain`,
-and `strain_rrid`, such as `group` in this example, or when a different
-age unit is needed (for example, gestational weeks).
-If no `units` is provided for age, it will be assumed to be in years relative
-to date of birth.
-
-`participants.json` example:
-
-```JSON
-{
-    "age": {
-        "Description": "age of the participant",
-        "Units": "year"
-    },
-    "sex": {
-        "Description": "sex of the participant as reported by the participant",
-        "Levels": {
-            "M": "male",
-            "F": "female"
-        }
-    },
-    "handedness": {
-        "Description": "handedness of the participant as reported by the participant",
-        "Levels": {
-            "left": "left",
-            "right": "right"
-        }
-    },
-    "group": {
-        "Description": "experimental group the participant belonged to",
-        "Levels": {
-            "read": "participants who read an inspirational text before the experiment",
-            "write": "participants who wrote an inspirational text before the experiment"
-        }
-    }
-}
-```
-
-## Samples file
-
-Template:
-
-```Text
-samples.tsv
-samples.json
-```
-
-<!-- This block generates a description.
-A guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___render_text("objects.files.samples.description") }}
-
-<!-- This block generates a columns table.
-The definitions of these fields can be found in
-  src/schema/rules/tabular_data/*.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_columns_table("modality_agnostic.Samples") }}
-
-`samples.tsv` example:
-
-```tsv
-sample_id	participant_id	sample_type	derived_from
-sample-01	sub-01	tissue	n/a
-sample-02	sub-01	tissue	sample-01
-sample-03	sub-01	tissue	sample-01
-sample-04	sub-02	tissue	n/a
-sample-05	sub-02	tissue	n/a
-```
-
-It is RECOMMENDED to accompany each `samples.tsv` file with a sidecar
-`samples.json` file to describe the TSV column names and properties of their values
-(see also the [section on tabular files](common-principles.md#tabular-files)).
-
-`samples.json` example:
-
-```JSON
-{
-    "sample_type": {
-        "Description": "type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type)",
-    },
-    "derived_from": {
-        "Description": "sample_id from which the sample is derived"
-    }
-}
-```
-
-## Phenotypic and assessment data
-
-Template:
-
-```Text
-phenotype/
-    <measurement_tool_name>.tsv
-    <measurement_tool_name>.json
-```
-
-Optional: Yes
-
-If the dataset includes multiple sets of participant level measurements (for
-example responses from multiple questionnaires) they can be split into
-individual files separate from `participants.tsv`.
-
-Each of the measurement files MUST be kept in a `/phenotype` directory placed
-at the root of the BIDS dataset and MUST end with the `.tsv` extension.
-Filenames SHOULD be chosen to reflect the contents of the file.
-For example, the "Adult ADHD Clinical Diagnostic Scale" could be saved in a file
-called `/phenotype/acds_adult.tsv`.
-
-The files can include an arbitrary set of columns, but one of them MUST be
-`participant_id` and the entries of that column MUST correspond to the subjects
-in the BIDS dataset and `participants.tsv` file.
-
-As with all other tabular data, the additional phenotypic information files
-MAY be accompanied by a JSON file describing the columns in detail
-(see [Tabular files](common-principles.md#tabular-files)).
-
-In addition to the column descriptions, the JSON file MAY contain the following fields:
-
-<!-- This block generates a metadata table.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_metadata_table(
-   {
-      "MeasurementToolMetadata": "OPTIONAL",
-      "Derivative": "OPTIONAL",
-   }
-) }}
-
-As an example, consider the contents of a file called
-`phenotype/acds_adult.json`:
-
-```JSON
-{
-  "MeasurementToolMetadata": {
-    "Description": "Adult ADHD Clinical Diagnostic Scale V1.2",
-    "TermURL": "https://www.cognitiveatlas.org/task/id/trm_5586ff878155d"
-  },
-  "adhd_b": {
-    "Description": "B. CHILDHOOD ONSET OF ADHD (PRIOR TO AGE 7)",
-    "Levels": {
-      "1": "YES",
-      "2": "NO"
-    }
-  },
-  "adhd_c_dx": {
-    "Description": "As child met A, B, C, D, E and F diagnostic criteria",
-    "Levels": {
-      "1": "YES",
-      "2": "NO"
-    }
-  }
-}
-```
-
-Please note that in this example `MeasurementToolMetadata` includes information
-about the questionnaire and `adhd_b` and `adhd_c_dx` correspond to individual
-columns.
-
-In addition to the keys available to describe columns in all tabular files
-(`LongName`, `Description`, `Levels`, `Units`, and `TermURL`) the
-`participants.json` file as well as phenotypic files can also include column
-descriptions with a `Derivative` field that, when set to true, indicates that
-values in the corresponding column is a transformation of values from other
-columns (for example a summary score based on a subset of items in a
-questionnaire).
-
-## Scans file
-
-Template:
-
-```Text
-sub-<label>/
-    [ses-<label>/]
-        sub-<label>[_ses-<label>]_scans.tsv
-        sub-<label>[_ses-<label>]_scans.json
-```
-
-Optional: Yes
-
-The purpose of this file is to describe timing and other properties of each recording *file* within one session.
-In general, each of these files SHOULD be described by exactly one row.
-
-For *file formats* that are based on several files of different extensions,
-or a directory of files with different extensions (multi-file file formats),
-only that file SHOULD be listed that would also be passed to analysis software for reading the data.
-For example for BrainVision data (`.vhdr`, `.vmrk`, `.eeg`),
-only the `.vhdr` SHOULD be listed;
-for EEGLAB data (`.set`, `.fdt`),
-only the `.set` file SHOULD be listed;
-and for CTF data (`.ds`),
-the whole `.ds` directory SHOULD be listed,
-and not the individual files in that directory.
-
-Some neural recordings consist of multiple parts,
-that span several files,
-but that share the same extension.
-For example in [entity-linked file collections](./common-principles.md#entity-linked-file-collections),
-commonly used for qMRI,
-where recordings may be linked through entities such as `echo` and `part`
-(using `.nii` or `.nii.gz` extensions).
-For another example consider the case of large files in `.fif` format that are linked through the `split` entity
-(see [Split files](./appendices/meg-file-formats.md#split-files)).
-Such recordings MUST be documented with one row per file
-(unlike the case of multi-file file formats described above).
-
-<!-- This block generates a columns table.
-The definitions of these fields can be found in
-  src/schema/rules/tabular_data/*.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_columns_table("modality_agnostic.Scans") }}
-
-Additional fields can include external behavioral measures relevant to the
-scan.
-For example vigilance questionnaire score administered after a resting
-state scan.
-All such included additional fields SHOULD be documented in an accompanying
-`_scans.json` file that describes these fields in detail
-(see [Tabular files](common-principles.md#tabular-files)).
-
-Example `_scans.tsv`:
-
-```tsv
-filename	acq_time
-func/sub-control01_task-nback_bold.nii.gz	1877-06-15T13:45:30
-func/sub-control01_task-motor_bold.nii.gz	1877-06-15T13:55:33
-meg/sub-control01_task-rest_split-01_meg.nii.gz	1877-06-15T12:15:27
-meg/sub-control01_task-rest_split-02_meg.nii.gz	1877-06-15T12:15:27
-```
-
-## Sessions file
-
-Template:
-
-```Text
-sub-<label>/
-    sub-<label>_sessions.tsv
-```
-
-Optional: Yes
-
-In case of multiple sessions there is an option of adding additional
-`sessions.tsv` files describing variables changing between sessions.
-In such case one file per participant SHOULD be added.
-These files MUST include a `session_id` column and describe each session by one and only one row.
-Column names in `sessions.tsv` files MUST be different from group level participant key column names in the
-[`participants.tsv` file](./modality-agnostic-files.md#participants-file).
-
-<!-- This block generates a columns table.
-The definitions of these fields can be found in
-  src/schema/rules/tabular_data/*.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_columns_table("modality_agnostic.Sessions") }}
-
-`_sessions.tsv` example:
-
-```tsv
-session_id	acq_time	systolic_blood_pressure
-ses-predrug	2009-06-15T13:45:30	120
-ses-postdrug	2009-06-16T13:45:30	100
-ses-followup	2009-06-17T13:45:30	110
-```
-
-## Code
-
-Template: `code/*`
-
-Source code of scripts that were used to prepare the dataset MAY be stored here.
-Examples include deidentification or defacing of the data, or
-the conversion from the format of the source data to the BIDS format
-(see [source vs. raw vs. derived data](./common-principles.md#source-vs-raw-vs-derived-data)).
-Extra care should be taken to avoid including original IDs or
-any identifiable information with the source code.
-There are no limitations or recommendations on the language and/or
-code organization of these scripts at the moment.
-
-<!-- Link Definitions -->
-
-[bids uris]: ./common-principles.md#bids-uri
diff --git a/src/modality-agnostic-files/code.md b/src/modality-agnostic-files/code.md
new file mode 100644
index 0000000000..f005df6a22
--- /dev/null
+++ b/src/modality-agnostic-files/code.md
@@ -0,0 +1,12 @@
+# Code
+
+Template: `code/*`
+
+Source code of scripts that were used to prepare the dataset MAY be stored here.
+Examples include deidentification or defacing of the data, or
+the conversion from the format of the source data to the BIDS format
+(see [source vs. raw vs. derived data](../common-principles.md#source-vs-raw-vs-derived-data)).
+Extra care should be taken to avoid including original IDs or
+any identifiable information with the source code.
+There are no limitations or recommendations on the language and/or
+code organization of these scripts at the moment.
diff --git a/src/modality-agnostic-files/data-summary-files.md b/src/modality-agnostic-files/data-summary-files.md
new file mode 100644
index 0000000000..d6b5032c2b
--- /dev/null
+++ b/src/modality-agnostic-files/data-summary-files.md
@@ -0,0 +1,233 @@
+# Data summary files
+
+## Participants file
+
+Template:
+
+```Text
+participants.tsv
+participants.json
+```
+
+<!-- This block generates a description.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___render_text("objects.files.participants.description") }}
+
+We RECOMMEND to make use of these columns, and
+in case that you do use them, we RECOMMEND to use the following values
+for them:
+
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/rules/tabular_data/*.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_columns_table("modality_agnostic.Participants") }}
+
+Throughout BIDS you can indicate missing values with `n/a` (for "not
+available").
+
+`participants.tsv` example:
+
+```tsv
+participant_id	age	sex	handedness	group
+sub-01	34	M	right	read
+sub-02	12	F	right	write
+sub-03	33	F	n/a	read
+```
+
+It is RECOMMENDED to accompany each `participants.tsv` file with a sidecar
+`participants.json` file to describe the TSV column names and properties of their values (see also
+the [section on tabular files](../common-principles.md#tabular-files)).
+Such sidecar files are needed to interpret the data, especially so when
+optional columns are defined beyond `age`, `sex`, `handedness`, `species`, `strain`,
+and `strain_rrid`, such as `group` in this example, or when a different
+age unit is needed (for example, gestational weeks).
+If no `units` is provided for age, it will be assumed to be in years relative
+to date of birth.
+
+`participants.json` example:
+
+```JSON
+{
+    "age": {
+        "Description": "age of the participant",
+        "Units": "year"
+    },
+    "sex": {
+        "Description": "sex of the participant as reported by the participant",
+        "Levels": {
+            "M": "male",
+            "F": "female"
+        }
+    },
+    "handedness": {
+        "Description": "handedness of the participant as reported by the participant",
+        "Levels": {
+            "left": "left",
+            "right": "right"
+        }
+    },
+    "group": {
+        "Description": "experimental group the participant belonged to",
+        "Levels": {
+            "read": "participants who read an inspirational text before the experiment",
+            "write": "participants who wrote an inspirational text before the experiment"
+        }
+    }
+}
+```
+
+## Samples file
+
+Template:
+
+```Text
+samples.tsv
+samples.json
+```
+
+<!-- This block generates a description.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___render_text("objects.files.samples.description") }}
+
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/rules/tabular_data/*.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_columns_table("modality_agnostic.Samples") }}
+
+`samples.tsv` example:
+
+```tsv
+sample_id	participant_id	sample_type	derived_from
+sample-01	sub-01	tissue	n/a
+sample-02	sub-01	tissue	sample-01
+sample-03	sub-01	tissue	sample-01
+sample-04	sub-02	tissue	n/a
+sample-05	sub-02	tissue	n/a
+```
+
+It is RECOMMENDED to accompany each `samples.tsv` file with a sidecar
+`samples.json` file to describe the TSV column names and properties of their values
+(see also the [section on tabular files](../common-principles.md#tabular-files)).
+
+`samples.json` example:
+
+```JSON
+{
+    "sample_type": {
+        "Description": "type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type)",
+    },
+    "derived_from": {
+        "Description": "sample_id from which the sample is derived"
+    }
+}
+```
+
+## Scans file
+
+Template:
+
+```Text
+sub-<label>/
+    [ses-<label>/]
+        sub-<label>[_ses-<label>]_scans.tsv
+        sub-<label>[_ses-<label>]_scans.json
+```
+
+Optional: Yes
+
+The purpose of this file is to describe timing and other properties of each recording *file* within one session.
+In general, each of these files SHOULD be described by exactly one row.
+
+For *file formats* that are based on several files of different extensions,
+or a directory of files with different extensions (multi-file file formats),
+only that file SHOULD be listed that would also be passed to analysis software for reading the data.
+For example for BrainVision data (`.vhdr`, `.vmrk`, `.eeg`),
+only the `.vhdr` SHOULD be listed;
+for EEGLAB data (`.set`, `.fdt`),
+only the `.set` file SHOULD be listed;
+and for CTF data (`.ds`),
+the whole `.ds` directory SHOULD be listed,
+and not the individual files in that directory.
+
+Some neural recordings consist of multiple parts,
+that span several files,
+but that share the same extension.
+For example in [entity-linked file collections](../common-principles.md#entity-linked-file-collections),
+commonly used for qMRI,
+where recordings may be linked through entities such as `echo` and `part`
+(using `.nii` or `.nii.gz` extensions).
+For another example consider the case of large files in `.fif` format that are linked through the `split` entity
+(see [Split files](../appendices/meg-file-formats.md#split-files)).
+Such recordings MUST be documented with one row per file
+(unlike the case of multi-file file formats described above).
+
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/rules/tabular_data/*.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_columns_table("modality_agnostic.Scans") }}
+
+Additional fields can include external behavioral measures relevant to the
+scan.
+For example vigilance questionnaire score administered after a resting
+state scan.
+All such included additional fields SHOULD be documented in an accompanying
+`_scans.json` file that describes these fields in detail
+(see [Tabular files](../common-principles.md#tabular-files)).
+
+Example `_scans.tsv`:
+
+```tsv
+filename	acq_time
+func/sub-control01_task-nback_bold.nii.gz	1877-06-15T13:45:30
+func/sub-control01_task-motor_bold.nii.gz	1877-06-15T13:55:33
+meg/sub-control01_task-rest_split-01_meg.nii.gz	1877-06-15T12:15:27
+meg/sub-control01_task-rest_split-02_meg.nii.gz	1877-06-15T12:15:27
+```
+
+## Sessions file
+
+Template:
+
+```Text
+sub-<label>/
+    sub-<label>_sessions.tsv
+```
+
+Optional: Yes
+
+In case of multiple sessions there is an option of adding additional
+`sessions.tsv` files describing variables changing between sessions.
+In such case one file per participant SHOULD be added.
+These files MUST include a `session_id` column and describe each session by one and only one row.
+Column names in `sessions.tsv` files MUST be different from group level participant key column names in the
+[`participants.tsv` file](./data-summary-files.md#participants-file).
+
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/rules/tabular_data/*.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_columns_table("modality_agnostic.Sessions") }}
+
+`_sessions.tsv` example:
+
+```tsv
+session_id	acq_time	systolic_blood_pressure
+ses-predrug	2009-06-15T13:45:30	120
+ses-postdrug	2009-06-16T13:45:30	100
+ses-followup	2009-06-17T13:45:30	110
+```
diff --git a/src/modality-agnostic-files/dataset-description.md b/src/modality-agnostic-files/dataset-description.md
new file mode 100644
index 0000000000..10d61d6eab
--- /dev/null
+++ b/src/modality-agnostic-files/dataset-description.md
@@ -0,0 +1,217 @@
+# Dataset description
+
+Templates:
+
+-   `dataset_description.json`
+-   `README[.md|.rst|.txt]`
+-   `CITATION.cff`
+-   `CHANGES`
+-   `LICENSE[.md|.rst|.txt]`
+
+## `dataset_description.json`
+
+<!-- This block generates a description.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___render_text("objects.files.dataset_description.description") }}
+
+Every dataset MUST include this file with the following fields:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Name": "REQUIRED",
+      "BIDSVersion": "REQUIRED",
+      "HEDVersion": "RECOMMENDED",
+      "DatasetLinks": "REQUIRED if [BIDS URIs][] are used",
+      "DatasetType": "RECOMMENDED",
+      "License": "RECOMMENDED",
+      "Authors": "RECOMMENDED if CITATION.cff is not present",
+      "Acknowledgements": "OPTIONAL",
+      "HowToAcknowledge": "OPTIONAL",
+      "Funding": "OPTIONAL",
+      "EthicsApprovals": "OPTIONAL",
+      "ReferencesAndLinks": "OPTIONAL",
+      "DatasetDOI": "OPTIONAL",
+      "GeneratedBy": "RECOMMENDED",
+      "SourceDatasets": "RECOMMENDED",
+   }
+) }}
+
+Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
+and OPTIONAL keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.GeneratedBy.items") }}
+
+Example:
+
+```JSON
+{
+  "Name": "The mother of all experiments",
+  "BIDSVersion": "1.6.0",
+  "DatasetType": "raw",
+  "License": "CC0",
+  "Authors": [
+    "Paul Broca",
+    "Carl Wernicke"
+  ],
+  "Acknowledgements": "Special thanks to Korbinian Brodmann for help in formatting this dataset in BIDS. We thank Alan Lloyd Hodgkin and Andrew Huxley for helpful comments and discussions about the experiment and manuscript; Hermann Ludwig Helmholtz for administrative support; and Claudius Galenus for providing data for the medial-to-lateral index analysis.",
+  "HowToAcknowledge": "Please cite this paper: https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
+  "Funding": [
+    "National Institute of Neuroscience Grant F378236MFH1",
+    "National Institute of Neuroscience Grant 5RMZ0023106"
+  ],
+  "EthicsApprovals": [
+    "Army Human Research Protections Office (Protocol ARL-20098-10051, ARL 12-040, and ARL 12-041)"
+  ],
+  "ReferencesAndLinks": [
+    "https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
+    "Alzheimer A., & Kraepelin, E. (2015). Neural correlates of presenile dementia in humans. Journal of Neuroscientific Data, 2, 234001. doi:1920.8/jndata.2015.7"
+  ],
+  "DatasetDOI": "doi:10.0.2.3/dfjj.10",
+  "HEDVersion": "8.0.0",
+  "GeneratedBy": [
+    {
+      "Name": "reproin",
+      "Version": "0.6.0",
+      "Container": {
+        "Type": "docker",
+        "Tag": "repronim/reproin:0.6.0"
+      }
+    }
+  ],
+  "SourceDatasets": [
+    {
+      "URL": "s3://dicoms/studies/correlates",
+      "Version": "April 11 2011"
+    }
+  ]
+}
+```
+
+### Derived dataset and pipeline description
+
+As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
+top level of every derived dataset:
+`<dataset>/derivatives/<pipeline_name>/dataset_description.json`.
+
+In contrast to raw BIDS datasets, derived BIDS datasets MUST include a
+`GeneratedBy` key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "GeneratedBy": "REQUIRED"
+   }
+) }}
+
+If a derived dataset is stored as a subdirectory of the raw dataset, then the `Name` field
+of the first `GeneratedBy` object MUST be a substring of the derived dataset directory name.
+That is, in a directory `<dataset>/derivatives/<pipeline>[-<variant>]/`, the first
+`GeneratedBy` object should have a `Name` of `<pipeline>`.
+
+Example:
+
+```JSON
+{
+  "Name": "FMRIPREP Outputs",
+  "BIDSVersion": "1.6.0",
+  "DatasetType": "derivative",
+  "GeneratedBy": [
+    {
+      "Name": "fmriprep",
+      "Version": "1.4.1",
+      "Container": {
+        "Type": "docker",
+        "Tag": "poldracklab/fmriprep:1.4.1"
+        }
+    },
+    {
+      "Name": "Manual",
+      "Description": "Re-added RepetitionTime metadata to bold.json files"
+    }
+  ],
+  "SourceDatasets": [
+    {
+      "DOI": "doi:10.18112/openneuro.ds000114.v1.0.1",
+      "URL": "https://openneuro.org/datasets/ds000114/versions/1.0.1",
+      "Version": "1.0.1"
+    }
+  ]
+}
+```
+
+## `README`
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___render_text("objects.files.README.description") }}
+
+## `CITATION.cff`
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___render_text("objects.files.CITATION.description") }}
+
+For most redundant fields between `CITATION.cff` and `dataset_description.json`,
+the `CITATION.cff` SHOULD take precedence.
+To avoid inconsistency, metadata present in `CITATION.cff` SHOULD NOT be
+be included in `dataset_description.json`, with the exception of `Name` and
+`DatasetDOI`, to ensure that `CITATION.cff`-unaware tools can generate
+references to the dataset.
+In particular, if `CITATION.cff` is present,
+the `"Authors"` field of `dataset_description.json` MUST be omitted,
+and the `"HowToAcknowledge"`, `"License"` and `"ReferencesAndLinks"` SHOULD be omitted
+in favor of the `CITATION.cff` fields `message`/`preferred-citation`, `license` and
+`references`.
+
+## `CHANGES`
+
+<!-- This block generates a description.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___render_text("objects.files.CHANGES.description") }}
+
+Example:
+
+```Text
+1.0.1 2015-08-27
+  - Fixed slice timing information.
+
+1.0.0 2015-08-17
+  - Initial release.
+```
+
+## `LICENSE`
+
+<!-- This block generates a description.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___render_text("objects.files.LICENSE.description") }}
+
+<!-- Link Definitions -->
+
+[bids uris]: ../common-principles.md#bids-uri
diff --git a/src/modality-agnostic-files/phenotypic-and-assessment-data.md b/src/modality-agnostic-files/phenotypic-and-assessment-data.md
new file mode 100644
index 0000000000..d876a38ee7
--- /dev/null
+++ b/src/modality-agnostic-files/phenotypic-and-assessment-data.md
@@ -0,0 +1,82 @@
+# Phenotypic and assessment data
+
+Template:
+
+```Text
+phenotype/
+    <measurement_tool_name>.tsv
+    <measurement_tool_name>.json
+```
+
+Optional: Yes
+
+If the dataset includes multiple sets of participant level measurements (for
+example responses from multiple questionnaires) they can be split into
+individual files separate from `participants.tsv`.
+
+Each of the measurement files MUST be kept in a `/phenotype` directory placed
+at the root of the BIDS dataset and MUST end with the `.tsv` extension.
+Filenames SHOULD be chosen to reflect the contents of the file.
+For example, the "Adult ADHD Clinical Diagnostic Scale" could be saved in a file
+called `/phenotype/acds_adult.tsv`.
+
+The files can include an arbitrary set of columns, but one of them MUST be
+`participant_id` and the entries of that column MUST correspond to the subjects
+in the BIDS dataset and `participants.tsv` file.
+
+As with all other tabular data, the additional phenotypic information files
+MAY be accompanied by a JSON file describing the columns in detail
+(see [Tabular files](../common-principles.md#tabular-files)).
+
+In addition to the column descriptions, the JSON file MAY contain the following fields:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "MeasurementToolMetadata": "OPTIONAL",
+      "Derivative": "OPTIONAL",
+   }
+) }}
+
+As an example, consider the contents of a file called
+`phenotype/acds_adult.json`:
+
+```JSON
+{
+  "MeasurementToolMetadata": {
+    "Description": "Adult ADHD Clinical Diagnostic Scale V1.2",
+    "TermURL": "https://www.cognitiveatlas.org/task/id/trm_5586ff878155d"
+  },
+  "adhd_b": {
+    "Description": "B. CHILDHOOD ONSET OF ADHD (PRIOR TO AGE 7)",
+    "Levels": {
+      "1": "YES",
+      "2": "NO"
+    }
+  },
+  "adhd_c_dx": {
+    "Description": "As child met A, B, C, D, E and F diagnostic criteria",
+    "Levels": {
+      "1": "YES",
+      "2": "NO"
+    }
+  }
+}
+```
+
+Please note that in this example `MeasurementToolMetadata` includes information
+about the questionnaire and `adhd_b` and `adhd_c_dx` correspond to individual
+columns.
+
+In addition to the keys available to describe columns in all tabular files
+(`LongName`, `Description`, `Levels`, `Units`, and `TermURL`) the
+`participants.json` file as well as phenotypic files can also include column
+descriptions with a `Derivative` field that, when set to true, indicates that
+values in the corresponding column is a transformation of values from other
+columns (for example a summary score based on a subset of items in a
+questionnaire).
diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md
index cb765c9549..739a266aa3 100644
--- a/src/modality-specific-files/electroencephalography.md
+++ b/src/modality-specific-files/electroencephalography.md
@@ -200,7 +200,7 @@ A guide for using macros can be found at
 ```
 
 Note that the date and time information SHOULD be stored in the Study key file
-([`scans.tsv`](../modality-agnostic-files.md#scans-file)).
+([`scans.tsv`](../modality-agnostic-files/data-summary-files.md#scans-file)).
 Date time information MUST be expressed as indicated in [Units](../common-principles.md#units)
 
 ## Channels description (`*_channels.tsv`)
diff --git a/src/modality-specific-files/genetic-descriptor.md b/src/modality-specific-files/genetic-descriptor.md
index 07946da5fa..462aa7db99 100644
--- a/src/modality-specific-files/genetic-descriptor.md
+++ b/src/modality-specific-files/genetic-descriptor.md
@@ -23,7 +23,7 @@ with details of where to find the genetic data and the type of data available.
 
 If information on associated genetic data is supplied as part of a BIDS dataset,
 these "genetic descriptors" are encoded as an additional, REQUIRED entry in the
-[`dataset_description.json`](../modality-agnostic-files.md#dataset_descriptionjson)
+[`dataset_description.json`](../modality-agnostic-files/dataset-description.md#dataset_descriptionjson)
 file.
 
 Datasets linked to a genetic database entry include the following REQUIRED and OPTIONAL
diff --git a/src/modality-specific-files/intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md
index 1d5e146383..93533cda7e 100644
--- a/src/modality-specific-files/intracranial-electroencephalography.md
+++ b/src/modality-specific-files/intracranial-electroencephalography.md
@@ -134,7 +134,7 @@ A guide for using macros can be found at
 {{ MACROS___make_sidecar_table("ieeg.iEEGOptional") }}
 
 Note that the date and time information SHOULD be stored in the study key file
-([`scans.tsv`](../modality-agnostic-files.md#scans-file)).
+([`scans.tsv`](../modality-agnostic-files/data-summary-files.md#scans-file)).
 Date time information MUST be expressed as indicated in [Units](../common-principles.md#units)
 
 #### Hardware information
diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md
index cdfeef50b7..057ff3ad59 100644
--- a/src/modality-specific-files/magnetoencephalography.md
+++ b/src/modality-specific-files/magnetoencephalography.md
@@ -66,7 +66,7 @@ with split files.
 If there are multiple parts of a recording and the optional `scans.tsv` is provided,
 remember to list all files separately in `scans.tsv` and that the entries for the
 `acq_time` column in `scans.tsv` MUST all be identical, as described in
-[Scans file](../modality-agnostic-files.md#scans-file).
+[Scans file](../modality-agnostic-files/data-summary-files.md#scans-file).
 
 The Neuromag/Elekta/Megin system may also produce datasets that require a set of
 `crosstalk` and `calibration` files to be used properly (see also filename templates above).
@@ -234,7 +234,7 @@ A guide for using macros can be found at
 ```
 
 Note that the date and time information SHOULD be stored in the Study key file
-(`scans.tsv`), see [Scans file](../modality-agnostic-files.md#scans-file).
+(`scans.tsv`), see [Scans file](../modality-agnostic-files/data-summary-files.md#scans-file).
 Date time information MUST be expressed as indicated in [Units](../common-principles.md#units)
 
 ## Channels description (`*_channels.tsv`)
diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md
index 1053b2bdcc..617407cd0c 100644
--- a/src/modality-specific-files/microscopy.md
+++ b/src/modality-specific-files/microscopy.md
@@ -404,7 +404,7 @@ A guide for using macros can be found at
 
 ## Required Samples file
 
-For Microscopy data, the [Samples file](../modality-agnostic-files.md#samples-file)
+For Microscopy data, the [Samples file](../modality-agnostic-files/data-summary-files.md#samples-file)
 `samples.tsv` is REQUIRED and its associated sidecar `samples.json` file is RECOMMENDED.
 
 Additional optional columns MAY be used to describe other samples' attributes.
@@ -412,7 +412,7 @@ Additional optional columns MAY be used to describe other samples' attributes.
 ## Recommended Participants data
 
 For Microscopy data, we RECOMMEND to make use of the columns `species`, `strain` and
-`strain_rrid` in the [Participants file](../modality-agnostic-files.md#participants-file)
+`strain_rrid` in the [Participants file](../modality-agnostic-files/data-summary-files.md#participants-file)
 when applicable.
 
 Additional optional columns MAY be used to describe other subjects' attributes.
diff --git a/src/modality-specific-files/motion.md b/src/modality-specific-files/motion.md
index 109a55d198..4f4fb70ece 100644
--- a/src/modality-specific-files/motion.md
+++ b/src/modality-specific-files/motion.md
@@ -53,7 +53,7 @@ All relevant metadata about a tracking systems is stored in accompanying sidecar
 When multiple tracking systems are used to record motion or motion capture is used alongside the recording of other BIDS modalities and recordings should be interpreted together,
 it is advised to provide a possibility to synchronize recordings.
 The preferred way to do so is to use the acquisition time of the first data point of recordings and
-to store this information in the `acq_time` column of the [`*_scans.tsv`](../modality-agnostic-files.md#scans-file) file.
+to store this information in the `acq_time` column of the [`*_scans.tsv`](../modality-agnostic-files/data-summary-files.md#scans-file) file.
 Note that the [BIDS date time format](../common-principles.md#units) allows optional fractional seconds, which SHOULD be used to maximize the precision of the synchronization.
 Only if the precision of the synchronization is not high enough, the `*_events.tsv` file SHOULD be used to synchronize recordings.
 In this file, the start- and stop time of the recording of a system are specified in relation to a system to synchronize with.
@@ -122,9 +122,9 @@ If there are additional tracking systems (for example [optical motion capture](h
 data from these MUST be stored as separate files like `*_tracksys-omcA_motion.tsv` and `*_tracksys-omcB_motion.tsv`.
 All specified tracking systems MAY share `tracked_point` defined in `*_channels.tsv`, when tracking devices are placed on the same object or body part.
 
-Note that the onsets of the recordings SHOULD be stored in the study key file [(`scans.tsv`)](../modality-agnostic-files.md#scans-file).
+Note that the onsets of the recordings SHOULD be stored in the study key file [(`scans.tsv`)](../modality-agnostic-files/data-summary-files.md#scans-file).
 Here, date-time information MUST be expressed as indicated in [Units](../common-principles.md#units).
-The [`scans.tsv`](../modality-agnostic-files.md#scans-file) file contains the filename and the acquisition time of a recording,
+The [`scans.tsv`](../modality-agnostic-files/data-summary-files.md#scans-file) file contains the filename and the acquisition time of a recording,
 which MAY be used to synchronize multiple recordings.
 
 ## Channels description (`*_channels.tsv`)
diff --git a/src/modality-specific-files/positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md
index 0b992c7c25..a1ec4a4061 100644
--- a/src/modality-specific-files/positron-emission-tomography.md
+++ b/src/modality-specific-files/positron-emission-tomography.md
@@ -313,8 +313,8 @@ Knudsen et al. 2020
 ([doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433))
 recommends recording participant body weight.
 If recorded once per participant, these data SHOULD be included in the
-[Participants file](../modality-agnostic-files.md#participants-file) or as
-[Phenotypic and assessment data](../modality-agnostic-files.md#phenotypic-and-assessment-data).
+[Participants file](../modality-agnostic-files/data-summary-files.md#participants-file) or as
+[Phenotypic and assessment data](../modality-agnostic-files/data-summary-files.md#phenotypic-and-assessment-data).
 
 For example:
 
@@ -326,7 +326,7 @@ sub-03	72
 ```
 
 If multiple measurements are made, these data SHOULD be included in the
-[Sessions file](../modality-agnostic-files.md#sessions-file).
+[Sessions file](../modality-agnostic-files/data-summary-files.md#sessions-file).
 
 For example:
 
diff --git a/src/pregh-changes.md b/src/pregh-changes.md
index 2cba2a81df..7d9052b69d 100644
--- a/src/pregh-changes.md
+++ b/src/pregh-changes.md
@@ -32,7 +32,7 @@
 ## 1.0.1-rc1
 
 -   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 support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files/data-summary-files.md#participants-file).
 -   Added recommendations for multi site datasets.
 -   Added `SoftwareVersions`.
 -   Added `run-<run_index>` to the phase encoding maps. Improved the description.
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index df0edb09e0..885d54e91b 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -357,7 +357,7 @@ split:
     If there are multiple parts of a recording and the optional `scans.tsv` is provided,
     all files MUST be listed separately in `scans.tsv` and
     the entries for the `acq_time` column in `scans.tsv` MUST all be identical,
-    as described in [Scans file](SPEC_ROOT/modality-agnostic-files.md#scans-file).
+    as described in [Scans file](SPEC_ROOT/modality-agnostic-files/data-summary-files.md#scans-file).
   type: string
   format: index
 stain:
diff --git a/src/schema/objects/files.yaml b/src/schema/objects/files.yaml
index d2d8761410..b16a8c9c1d 100644
--- a/src/schema/objects/files.yaml
+++ b/src/schema/objects/files.yaml
@@ -100,7 +100,7 @@ code:
   description: |
     A directory in which to store any code
     (for example the one used to generate the derivatives from the raw data).
-    See the [Code section](SPEC_ROOT/modality-agnostic-files.md#code)
+    See the [Code section](SPEC_ROOT/modality-agnostic-files/code.md)
     for more information.
 derivatives:
   display_name: Derivative data
@@ -116,7 +116,7 @@ phenotype:
     A directory where to store participant level measurements (for
     example responses from multiple questionnaires) split into
     individual files separate from `participants.tsv`.
-    See the [relevant section](SPEC_ROOT/modality-agnostic-files.md#phenotypic-and-assessment-data)
+    See the [relevant section](SPEC_ROOT/modality-agnostic-files/phenotypic-and-assessment-data.md)
     for more information.
 sourcedata:
   display_name: Source data
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 09984125ad..8af01e23a4 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -3164,7 +3164,7 @@ ScanDate:
   description: |
     Date of scan in the format `"YYYY-MM-DD[Z]"`.
     This field is DEPRECATED, and this metadata SHOULD be recorded in the `acq_time` column of the
-    corresponding [Scans file](SPEC_ROOT/modality-agnostic-files.md#scans-file).
+    corresponding [Scans file](SPEC_ROOT/modality-agnostic-files/data-summary-files.md#scans-file).
   type: string
   format: date
 ScanOptions: