Merge branch 'bids-standard:master' into master

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+        args: [--unsafe]
       - id: check-json
       - id: check-toml
       - id: check-ast

README.md

@@ -1,5 +1,7 @@
 [![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml)
 [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification)
+[![Bluesky Follow](https://img.shields.io/badge/bluesky-Follow_bidsstandard-blue?logo=bluesky)](https://bsky.app/profile/bidsstandard.bsky.social)
+![YouTube Channel Subscribers](https://img.shields.io/youtube/channel/subscribers/UCxZUcYfd_nvIVWAbzRB1tlw)
 [![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard)
 [![@BIDSstandard](https://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://x.com/BIDSstandard)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061)

mkdocs.yml

@@ -104,7 +104,12 @@ extra_javascript:
 markdown_extensions:
   - toc:
       anchorlink: true
-  - pymdownx.superfences
+  - pymdownx.superfences:
+      preserve_tabs: true
+      custom_fences:
+        - name: tsv
+          class: tsv
+          format: !!python/name:bidsschematools.render.tsv.fence
   - admonition
   - pymdownx.details
 plugins:
@@ -116,6 +121,7 @@ plugins:
             - css/watermark.css
   - macros:
       module_name: tools/mkdocs_macros_bids/main
+      on_error_fail: true
   - redirects:
       redirect_maps:
         "01-introduction.md": "introduction.md"

pdf_build_src/pandoc_script.py

@@ -39,7 +39,7 @@ def _flatten_values(lst):
     fname_mkdocs_yml = _find(HERE, "mkdocs.yml")
 
     with open(fname_mkdocs_yml, "r") as stream:
-        mkdocs_yml = yaml.safe_load(stream)
+        mkdocs_yml = yaml.load(stream, yaml.Loader)
 
     sections = mkdocs_yml["nav"][0]["The BIDS Specification"]
 

src/appendices/arterial-spin-labeling.md

@@ -26,7 +26,7 @@ and the exact volume_type series should be specified in the `*_aslcontext.tsv`.
 
 Example of `*_aslcontext.tsv`:
 
-```Text
+```tsv
 volume_type
 control
 label
@@ -44,7 +44,7 @@ In this case, the `deltam` should be included in the `*_asl.nii[.gz]` and specif
 
 Example of `*_aslcontext.tsv`:
 
-```Text
+```tsv
 volume_type
 deltam
 m0scan
@@ -58,7 +58,7 @@ the `cbf` should be included in the `*_asl.nii[.gz]` and specified in the `*_asl
 
 Example of `*_aslcontext.tsv`:
 
-```Text
+```tsv
 volume_type
 cbf
 m0scan

src/appendices/hed.md

@@ -44,10 +44,10 @@ meanings in associated JSON sidecar files (`events.json`).
 (`trial_type`, `response_time`, and `stim_file`) in addition to
 the required `onset` and `duration` columns.
 
-```Text
-onset  duration  trial_type  response_time stim_file
-1.2    0.6       go          1.435         images/red_square.jpg
-5.6    0.6       stop        n/a           images/blue_square.jpg
+```tsv
+onset	duration	trial_type	response_time	stim_file
+1.2	0.6	go	1.435	images/red_square.jpg
+5.6	0.6	stop	n/a	images/blue_square.jpg
 ```
 
 The `trial_type` column in the above example contains a limited number of distinct

src/common-principles.md

@@ -202,6 +202,11 @@ as the labels would collide on a case-insensitive filesystem.
 Additionally, because the suffix `eeg` is defined,
 then the suffix `EEG` will not be added to future versions of the standard.
 
+### Dotfiles
+
+Files and directories starting with a dot (`.`) are reserved for system use and no valid recognized BIDS file or directory can start with a `.`.
+Any file or directory starting with a `.` present in a BIDS dataset is considered hidden and not subject to BIDS validation.
+
 ## Uniqueness of data files
 
 Data files MUST be uniquely identified by BIDS path components
@@ -489,8 +494,8 @@ first letter in lower case (for example, `variable_name`, not `Variable_name`).
 Column names defined in the header MUST be separated with tabs as for the data contents.
 Furthermore, column names MUST NOT be blank (that is, an empty string) and MUST NOT
 be duplicated within a single TSV file.
-String values containing tabs MUST be escaped using double quotes.
 Missing and non-applicable values MUST be coded as `n/a`.
+String values containing tabs MUST be escaped using double quotes.
 Numerical values MUST employ the dot (`.`) as decimal separator and MAY be specified
 in scientific notation, using `e` or `E` to separate the significand from the
 exponent.

src/derivatives/common-data-types.md

@@ -328,11 +328,12 @@ A guide for using macros can be found at
 
 Contents of the `descriptions.tsv` file:
 
-| desc_id | description                                                                                     |
-| ------- | ----------------------------------------------------------------------------------------------- |
-| Filt    | low-pass filtered at 30Hz                                                                       |
-| FiltDs  | low-pass filtered at 30Hz, downsampled to 250Hz                                                 |
-| preproc | low-pass filtered at 30Hz, downsampled to 250Hz, and rereferenced to a common average reference |
+```tsv
+desc_id	description
+Filt	low-pass filtered at 30Hz
+FiltDs	low-pass filtered at 30Hz, downsampled to 250Hz
+preproc	low-pass filtered at 30Hz, downsampled to 250Hz, and rereferenced to a common average reference
+```
 
 <!-- Link Definitions -->
 

src/longitudinal-and-multi-site-studies.md

@@ -65,7 +65,7 @@ A guide for using macros can be found at
 
 `sub-control01_sessions.tsv` content:
 
-```Text
+```tsv
 session_id	acq_time	systolic_blood_pressure
 ses-predrug	2009-06-15T13:45:30	120
 ses-postdrug	2009-06-16T13:45:30	100

src/modality-agnostic-files.md

@@ -246,11 +246,11 @@ available").
 
 `participants.tsv` example:
 
-```Text
-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
+```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
@@ -320,13 +320,13 @@ and a guide for using macros can be found at
 
 `samples.tsv` example:
 
-```Text
-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
+```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
@@ -486,7 +486,7 @@ All such included additional fields SHOULD be documented in an accompanying
 
 Example `_scans.tsv`:
 
-```Text
+```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
@@ -522,7 +522,7 @@ and a guide for using macros can be found at
 
 `_sessions.tsv` example:
 
-```Text
+```tsv
 session_id	acq_time	systolic_blood_pressure
 ses-predrug	2009-06-15T13:45:30	120
 ses-postdrug	2009-06-16T13:45:30	100

src/modality-specific-files/behavioral-experiments.md

@@ -78,7 +78,7 @@ A guide for using macros can be found at
 
 ## Example `_beh.tsv`
 
-```Text
+```tsv
 trial	response	response_time	stim_file
 congruent	red	1.435	images/word-red_color-red.jpg
 incongruent	red	1.739	images/word-red_color-blue.jpg

src/modality-specific-files/electroencephalography.md

@@ -274,12 +274,12 @@ Examples of free-form text for field `description`
 
 See also the corresponding [`electrodes.tsv` example](#example-_electrodestsv).
 
-```Text
-name     type  units  description                     reference     status  status_description
-VEOG     VEOG  uV     left eye                        VEOG-, VEOG+  good    n/a
-FDI      EMG   uV     left first dorsal interosseous  FDI-, FDI+    good    n/a
-Cz       EEG   uV     n/a                             REF           bad     high frequency noise
-UADC001  MISC  n/a    envelope of audio signal        n/a           good    n/a
+```tsv
+name	type	units	description	reference	status	status_description
+VEOG	VEOG	uV	left eye	VEOG-, VEOG+	good	n/a
+FDI	EMG	uV	left first dorsal interosseous	FDI-, FDI+	good	n/a
+Cz	EEG	uV	n/a	REF	bad	high frequency noise
+UADC001	MISC	n/a	envelope of audio signal	n/a	good	n/a
 ```
 
 ## Electrodes description (`*_electrodes.tsv`)
@@ -318,15 +318,15 @@ If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to in
 
 See also the corresponding [`channels.tsv` example](#example-_channelstsv).
 
-```Text
-name   x        y	       z        type     material
-VEOG+  n/a      n/a      n/a      cup      Ag/AgCl
-VEOG-  n/a      n/a      n/a      cup      Ag/AgCl
-FDI+   n/a      n/a      n/a      cup      Ag/AgCl
-FDI-   n/a      n/a      n/a      cup      Ag/AgCl
-GND    -0.0707  0.0000   -0.0707  clip-on  Ag/AgCl
-Cz     0.0000   0.0714   0.0699   cup      Ag/AgCl
-REF    -0.0742  -0.0200  -0.0100  cup      Ag/AgCl
+```tsv
+name	x	y	z	type	material
+VEOG+	n/a	n/a	n/a	cup	Ag/AgCl
+VEOG-	n/a	n/a	n/a	cup	Ag/AgCl
+FDI+	n/a	n/a	n/a	cup	Ag/AgCl
+FDI-	n/a	n/a	n/a	cup	Ag/AgCl
+GND	-0.0707	0.0000	-0.0707	clip-on	Ag/AgCl
+Cz	0.0000	0.0714	0.0699	cup	Ag/AgCl
+REF	-0.0742	-0.0200	-0.0100	cup	Ag/AgCl
 ```
 
 The [`acq-<label>`](../appendices/entities.md#acq) entity can be used to

src/modality-specific-files/genetic-descriptor.md

@@ -70,7 +70,7 @@ Note that optional columns MUST be further described in an accompanying
 
 `participants.tsv` example:
 
-```Text
+```tsv
 participant_id	age	sex	group	genetic_id	idh_mutation
 sub-control01	34	M	control	124587	yes
 sub-control02	12	F	control	548936	yes

src/modality-specific-files/intracranial-electroencephalography.md

@@ -276,13 +276,13 @@ Examples of free-form text for field `description`:
 
 ### Example `*_channels.tsv`
 
-```Text
-name  type  units low_cutoff  high_cutoff status  status_description
-LT01  ECOG  uV    300         0.11        good    n/a
-LT02  ECOG  uV    300         0.11        bad     broken
-H01   SEEG  uV    300         0.11        bad     line_noise
-ECG1  ECG   uV    n/a         0.11        good    n/a
-TR1   TRIG  n/a   n/a         n/a         good    n/a
+```tsv
+name	type	units	low_cutoff	high_cutoff	status	status_description
+LT01	ECOG	uV	300	0.11	good	n/a
+LT02	ECOG	uV	300	0.11	bad	broken
+H01	SEEG	uV	300	0.11	bad	line_noise
+ECG1	ECG	uV	n/a	0.11	good	n/a
+TR1	TRIG	n/a	n/a	n/a	good	n/a
 ```
 
 ## Electrode description (`*_electrodes.tsv`)
@@ -304,7 +304,7 @@ that coordinates are expected in cartesian coordinates according to the
 
 The optional [`space-<label>`](../appendices/entities.md#space) entity (`*[_space-<label>]_electrodes.tsv`) can be used to
 indicate the way in which electrode positions are interpreted.
-The space `<label>` MUST be taken from one of the modality specific lists in
+The space `<label>` MUST be taken from one of the modality-specific lists in
 the [Coordinate Systems Appendix](../appendices/coordinate-systems.md).
 For example for iEEG data, the restricted keywords listed under
 [iEEG Specific Coordinate Systems](../appendices/coordinate-systems.md#ieeg-specific-coordinate-systems)
@@ -358,11 +358,11 @@ If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to in
 
 ### Example `*_electrodes.tsv`
 
-```Text
-name  x   y    z    size   manufacturer
-LT01  19  -39  -16  2.3    Integra
-LT02  23  -40  -19  2.3    Integra
-H01   27  -42  -21  5      AdTech
+```tsv
+name	x	y	z	size	manufacturer
+LT01	19	-39	-16	2.3	Integra
+LT02	23	-40	-19	2.3	Integra
+H01	27	-42	-21	5	AdTech
 ```
 
 ## Coordinate System JSON (`*_coordsystem.json`)
@@ -534,13 +534,13 @@ For example: `/stimuli/electrical_stimulation_functions/biphasic.tsv`
 
 ### Example `*_events.tsv`
 
-```Text
-onset duration trial_type             electrical_stimulation_type electrical_stimulation_site electrical_stimulation_current
-1.2   0.001    electrical_stimulation biphasic                    LT01-LT02                   0.005
-1.3   0.001    electrical_stimulation biphasic                    LT01-LT02                   0.005
-2.2   0.001    electrical_stimulation biphasic                    LT02-LT03                   0.005
-4.2   1        electrical_stimulation complex                     LT02-LT03                   n/a
-15.2  3        auditory_stimulus      n/a                         n/a                         n/a
+```tsv
+onset	duration	trial_type	electrical_stimulation_type	electrical_stimulation_site	electrical_stimulation_current
+1.2	0.001	electrical_stimulation	biphasic	LT01-LT02	0.005
+1.3	0.001	electrical_stimulation	biphasic	LT01-LT02	0.005
+2.2	0.001	electrical_stimulation	biphasic	LT02-LT03	0.005
+4.2	1	electrical_stimulation	complex	LT02-LT03	n/a
+15.2	3	auditory_stimulus	n/a	n/a	n/a
 ```
 
 <!-- Link Definitions -->

src/modality-specific-files/magnetoencephalography.md

@@ -311,12 +311,12 @@ Examples of free text for field `description`:
 
 ### Example `*_channels.tsv`
 
-```Text
-name type units description
-VEOG VEOG V vertical EOG
-FDI EMG V left first dorsal interosseous
-UDIO001 TRIG V analog trigger signal
-UADC001 AUDIO V envelope of audio signal presented to participant
+```tsv
+name	type	units	description
+VEOG	VEOG	V	vertical EOG
+FDI	EMG	V	left first dorsal interosseous
+UDIO001	TRIG	V	analog trigger signal
+UADC001	AUDIO	V	envelope of audio signal presented to participant
 ```
 
 ## Coordinate System JSON (`*_coordsystem.json`)

src/modality-specific-files/motion.md

@@ -185,21 +185,21 @@ Note that upper-case is REQUIRED:
 
 ### Example `*_channels.tsv`
 
-```Text
-name        component   type   tracked_point   units    reference_frame
-t1_acc_x    x           ACCEL  LeftFoot        m/s^2    global
-t1_acc_y    y           ACCEL  LeftFoot        m/s^2    global
-t1_acc_z    z           ACCEL  LeftFoot        m/s^2    global
-t1_gyro_x   x           GYRO   LeftFoot        rad/s    global
-t1_gyro_y   y           GYRO   LeftFoot        rad/s    global
-t1_gyro_z   z           GYRO   LeftFoot        rad/s    global
+```tsv
+name	component	type	tracked_point	units	reference_frame
+t1_acc_x	x	ACCEL	LeftFoot	m/s^2	global
+t1_acc_y	y	ACCEL	LeftFoot	m/s^2	global
+t1_acc_z	z	ACCEL	LeftFoot	m/s^2	global
+t1_gyro_x	x	GYRO	LeftFoot	rad/s	global
+t1_gyro_y	y	GYRO	LeftFoot	rad/s	global
+t1_gyro_z	z	GYRO	LeftFoot	rad/s	global
 …
-t2_acc_x    x           ACCEL  RightWrist      m/s^2    global
-t2_acc_y    y           ACCEL  RightWrist      m/s^2    global
-t2_acc_z    z           ACCEL  RightWrist      m/s^2    global
-t2_gyro_x   x           GYRO   RightWrist      rad/s    global
-t2_gyro_y   y           GYRO   RightWrist      rad/s    global
-t2_gyro_z   z           GYRO   RightWrist      rad/s    global
+t2_acc_x	x	ACCEL	RightWrist	m/s^2	global
+t2_acc_y	y	ACCEL	RightWrist	m/s^2	global
+t2_acc_z	z	ACCEL	RightWrist	m/s^2	global
+t2_gyro_x	x	GYRO	RightWrist	rad/s	global
+t2_gyro_y	y	GYRO	RightWrist	rad/s	global
+t2_gyro_z	z	GYRO	RightWrist	rad/s	global
 ```
 
 ## Reference frame description (`*_channels.json`)