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
38 changes: 32 additions & 6 deletions src/02-common-principles.md
Original file line number Diff line number Diff line change
Expand Up @@ -264,8 +264,7 @@ additional meta information extracted from DICOM files in a sidecar JSON file
(with the same filename as the `.nii[.gz]` file, but with a `.json` extension).
Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix)
and [dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m)
DICOM to NIfTI converters. A provided
[validator](https://github.com/bids-standard/bids-validator)
DICOM to NIfTI converters. The [BIDS-validator](https://github.com/bids-standard/bids-validator)
will check for conflicts between the JSON file and the data recorded in the
NIfTI header.

Expand All @@ -274,9 +273,13 @@ NIfTI header.
Tabular data MUST be saved as tab delimited values (`.tsv`) files, i.e., CSV
files where commas are replaced by tabs. Tabs MUST be true tab characters and
MUST NOT be a series of space characters. Each TSV file MUST start with a header
line listing the names of all columns (with the exception of physiological and
other continuous acquisition data - see below for details). Names MUST be
separated with tabs. String values containing tabs MUST be escaped using double
line listing the names of all columns (with the exception of
[physiological and other continuous recordings](04-modality-specific-files/06-physiological-and-other-continuous-recordings.md)).
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`).
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
in scientific notation, using `e` or `E` to separate the significand from the
Expand Down Expand Up @@ -340,8 +343,14 @@ format can be found here: [http://json.org/](http://json.org/). Several editors
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
`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
as in the TSV file.

Example:
Example of a hypothetical `*_bold.json` file, accompanying a `*_bold.nii` file:

```JSON
{
Expand All @@ -350,6 +359,23 @@ Example:
}
```

Example of a hypothetical `*_events.json` file, accompanying an
`*_events.tsv` file. Note that the JSON file contains a key describing an
*arbitrary* column `stim_presentation_side` in the TSV file it accompanies.
See [task events section](04-modality-specific-files/05-task-events.md)
for more information.

```JSON
{
"stim_presentation_side": {
"Levels": {
"1": "stimulus presented on LEFT side",
"2": "stimulus presented on RIGHT side"
}
}
}
```

## Participant names and other labels

BIDS uses custom user-defined labels in several situations (naming of
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -102,9 +102,10 @@ Useful for multimodal co-registration with MEG, (S)EEG, TMS, etc.
| InstitutionAddress | RECOMMENDED. The address of the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`. |
| InstitutionalDepartmentName | RECOMMENDED. The department in the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`. |

When adding additional metadata please use the camelcase version of
When adding additional metadata please use the CamelCase version of
[DICOM ontology terms](https://scicrunch.org/scicrunch/interlex/dashboard)
whenever possible.
whenever possible. See also
[recommendations on JSON files](../02-common-principles.md#keyvalue-files-dictionaries).

### Anatomy imaging data

Expand Down
3 changes: 2 additions & 1 deletion src/04-modality-specific-files/05-task-events.md
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@ the first volume.

An arbitrary number of additional columns can be added. Those allow describing
other properties of events that could be later referred in modelling and
hypothesis extensions of BIDS.
hypothesis extensions of BIDS. Note that any additional columns in a TSV file
SHOULD be documented in an accompanying JSON sidecar file.

In case of multi-echo task run, a single `_events.tsv` file will suffice for all
echoes.
Expand Down