Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -239,7 +239,7 @@ Here is a list of the files and subfolders of the schema, roughly in order of im
Data types supported by the specification.
Each datatype may support many suffixes.
These suffixes are divided into groups based on what extensions and entities are allowed for each.
Data types correspond to subfolders (e.g., `anat`, `func`) in the BIDS structure.
Data types correspond to subfolders (for example, `anat`, `func`) in the BIDS structure.
- `auxdatatypes/*.yaml`:
Auxiliary (not directly imaging or data-containing) data types supported by the specification.
Each auxiliary data type is associated with a set of data types, and these auxiliary data types are grouped based on what data types, extensions, and entities are allowed for each.
Expand Down
2 changes: 1 addition & 1 deletion Release_Guideline.md
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ Patch releases will generally be more frequent, and indicate less significant ch
The following is a non-exhaustive set of justifications for a patch release:

- A modality field has changed and the [bids-validator](https://github.com/bids-standard/bids-validator) has been updated to reflect this change.
- Links or information in the specification are no longer accurate, *e.g.* if a BEP document is added or moved
- Links or information in the specification are no longer accurate, for example if a BEP document is added or moved
- The rendering of the [specification](https://bids-specification.readthedocs.io/en/stable/) has changed
- A metadata field or file type is added at the request of a curator attempting to release BIDS-compliant data

Expand Down
2 changes: 1 addition & 1 deletion Release_Protocol.md
Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ $ git push -u upstream rel/1.2.0
```

### 4. Open a pull request against the master branch
Important note: The pull request title **must** be named "REL: vX.Y.Z" (*e.g.*, "REL: v1.2.0").
Important note: The pull request title **must** be named "REL: vX.Y.Z" (for example, "REL: v1.2.0").

**This will open a period of discussion for 5 business days regarding if we are ready to release.**

Expand Down
43 changes: 23 additions & 20 deletions src/02-common-principles.md
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ misunderstanding we clarify them here.
by DWI the day after) those can be grouped in one session. Defining multiple
sessions is appropriate when several identical or similar data acquisitions
are planned and performed on all -or most- subjects, often in the case of
some intervention between sessions (e.g., training).
some intervention between sessions (for example, training).

1. **Data acquisition** - a continuous uninterrupted block of time during which
a brain scanning instrument was acquiring data according to particular
Expand Down Expand Up @@ -57,7 +57,7 @@ misunderstanding we clarify them here.

1. **Event** - a stimulus or subject response recorded during a task. Each
event has an onset time and duration. Note that not all tasks will have
recorded events (e.g., “resting state”).
recorded events (for example, “resting state”).

1. **Run** - an uninterrupted repetition of data acquisition that has the same
acquisition parameters and task (however events can change from run to run
Expand All @@ -75,15 +75,15 @@ misunderstanding we clarify them here.
the **data type**.

1. **`<index>`** - a nonnegative integer, possibly prefixed with arbitrary number of
0s for consistent indentation, e.g., it is `01` in `run-01` following
0s for consistent indentation, for example, it is `01` in `run-01` following
`run-<index>` specification.

1. **`<label>`** - an alphanumeric value, possibly prefixed with arbitrary
number of 0s for consistent indentation, e.g., it is `rest` in `task-rest`
number of 0s for consistent indentation, for example, it is `rest` in `task-rest`
following `task-<label>` specification.

1. **`suffix`** - an alphanumeric value, located after the `key-value_` pairs (thus after
the final `_`), right before the **File extension**, e.g., it is `eeg` in
the final `_`), right before the **File extension**, for example, it is `eeg` in
`sub-05_task-matchingpennies_eeg.vhdr`.

1. **File extension** - a portion of the the file name after the left-most
Expand Down Expand Up @@ -214,14 +214,17 @@ Derivatives can be stored/distributed in two ways:

1. Under a `derivatives/` subfolder in the root of the source BIDS dataset
folder to make a clear distinction between raw data and results of data
processing. A data processing pipeline will typically have a dedicated directory
under which it stores all of its outputs. Different components of a pipeline can,
however, also be stored under different subfolders. There are few restrictions on
the directory names; it is RECOMMENDED to use the format `<pipeline>-<variant>` in
cases where it is anticipated that the same pipeline will output more than one variant (e.g.,
`AFNI-blurring`, `AFNI-noblurring`, etc.). For the sake of consistency, the
subfolder name SHOULD be the `GeneratedBy.Name` field in
`data_description.json`, optionally followed by a hyphen and a suffix (see
processing.
A data processing pipeline will typically have a dedicated directory
under which it stores all of its outputs.
Different components of a pipeline can, however, also be stored under different
subfolders.
There are few restrictions on the directory names; it is RECOMMENDED to use
the format `<pipeline>-<variant>` in cases where it is anticipated that
the same pipeline will output more than one variant
(for example, `AFNI-blurring`, `AFNI-noblurring`, etc.).
For the sake of consistency, the subfolder name SHOULD be the `GeneratedBy.Name`
field in `data_description.json`, optionally followed by a hyphen and a suffix (see
[Derived dataset and pipeline description][derived-dataset-description]).

Example of derivatives with one directory per pipeline:
Expand Down Expand Up @@ -385,7 +388,7 @@ inherited by the `.json` file at the deeper level (but NOT vice versa!).

**Try to avoid excessive amount of overrides.** Do not specify a field
value in the upper levels if lower levels have more or less even
distribution of multiple possible values. E.g., if a field `X` has one
distribution of multiple possible values. For example, if a field `X` has one
value for all `ses-01/` and another for all `ses-02/` it better not to be
defined at all in the `.json` at the upper level.

Expand Down Expand Up @@ -417,7 +420,7 @@ line listing the names of all columns (with the exception of
Names MUST be separated with tabs.
It is RECOMMENDED that the column names in the header of the TSV file are
written in [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) with the
first letter in lower case (e.g., `variable_name`, not `Variable_name`).
first letter in lower case (for example, `variable_name`, not `Variable_name`).
String values containing tabs MUST be escaped using double
quotes. Missing and non-applicable values MUST be coded as `n/a`. Numerical
values MUST employ the dot (`.`) as decimal separator and MAY be specified
Expand Down Expand Up @@ -485,7 +488,7 @@ have built-in support for JSON syntax highlighting that aids manual creation of
such files. An online editor for JSON with built-in validation is available at:
[http://jsoneditoronline.org](http://jsoneditoronline.org).
It is RECOMMENDED that keys in a JSON file are written in [CamelCase](https://en.wikipedia.org/wiki/Camel_case)
with the first letter in upper case (e.g., `SamplingFrequency`, not
with the first letter in upper case (for example, `SamplingFrequency`, not
`samplingFrequency`). Note however, when a JSON file is used as an accompanying
sidecar file for a [TSV file](#tabular-files), the keys linking a TSV column
with their description in the JSON file need to follow the exact formatting
Expand Down Expand Up @@ -519,11 +522,11 @@ for more information.

## Participant names and other labels

BIDS allows for custom user-defined `<label>`s and `<index>`es e.g.,
BIDS allows for custom user-defined `<label>`s and `<index>`es for example,
for naming of participants, sessions, acquisition schemes, etc. Note
that they MUST consist only of allowed characters as described in
[Definitions](02-common-principles.md#definitions) above. In `<index>`es
we RECOMMEND using zero padding (e.g., `01` instead of `1` if you have more than
we RECOMMEND using zero padding (for example, `01` instead of `1` if you have more than
nine subjects) to make alphabetical sorting more intuitive. Note that
zero padding SHOULD NOT be used to merely maintain uniqueness
of `<index>`es.
Expand Down Expand Up @@ -599,7 +602,7 @@ Describing dates and timestamps:

- WARNING: The Neuromag/Elekta/MEGIN file format for MEG (`.fif`) does *not*
support recording dates earlier than `1902` roughly.
Some analysis software packages (e.g., MNE-Python) handle their data as `.fif`
Some analysis software packages (for example, MNE-Python) handle their data as `.fif`
internally and will break if recording dates are specified prior to `1902`,
even if the original data format is not `.fif`.
See [MEG-file-formats](./99-appendices/06-meg-file-formats.md#recording-dates-in-fif-files)
Expand All @@ -608,7 +611,7 @@ Describing dates and timestamps:
- Age SHOULD be given as the number of years since birth at the time of
scanning (or first scan in case of multi session datasets). Using higher
accuracy (weeks) should in general be avoided due to privacy protection,
unless when appropriate given the study goals, e.g., when scanning babies.
unless when appropriate given the study goals, for example, when scanning babies.

## Directory structure

Expand Down
6 changes: 4 additions & 2 deletions src/03-modality-agnostic-files.md
Original file line number Diff line number Diff line change
Expand Up @@ -213,8 +213,10 @@ It is RECOMMENDED to accompany each `participants.tsv` file with a sidecar
the [section on tabular files](02-common-principles.md#tabular-files)).
Such sidecar files are needed to interpret the data, especially so when
optional columns are defined beyond `age`, `sex`, and `handedness`, such as
`group` in this example, or when a different age unit is needed (e.g., gestational weeks).
If no `units` is provided for age, it will be assumed to be in years relative to date of birth.
`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:

Expand Down
Loading