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[ENH] Introduce GIFTI formats in derivatives #1333

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[ENH] Introduce GIFTI formats in derivatives #1333

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ENH: Introduce GIFTI formats in derivatives
effigies Oct 20, 2022
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Merge branch 'master' into enh/cifti-and-gifti
sappelhoff Jun 2, 2023
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2 changes: 1 addition & 1 deletion src/common-principles.md
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Expand Up @@ -388,7 +388,7 @@ In particular, if a BIDS dataset contains a `derivatives/` subdirectory,
the contents of that directory may be a heterogeneous mix of BIDS Derivatives
datasets and non-compliant derivatives.

## File Formation specification
## File format specification

### Imaging files

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36 changes: 36 additions & 0 deletions src/derivatives/introduction.md
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Expand Up @@ -70,10 +70,46 @@ in [Derived dataset and pipeline description][derived-dataset-description].
For example, if a summary statistic is derived from a given task, the file
name SHOULD contain [`_task-<label>`](../appendices/entities.md#task).

## File format specification

Derived data may be resampled into structures that are not well-handled by the
raw data formats.
In this section, we describe standard formats that SHOULD be adhered to when
appropriate, and the extensions they should have.

### GIFTI Surface Data Format

The [GIFTI][gifti] format is an XML-based structure containing one or more data arrays,
and is well-suited to describing surface geometry and parcellations.

The following extension table is reproduced in part from Section 9.0 of the
[GIFTI specification][gifti-spec], indicating the expected extensions of different data arrays
or combinations of data arrays.

| Intent | Extension |
|-------------|---------------|
| Coordinates | `.coord.gii` |
| Functional | `.func.gii` |
| Labels | `.label.gii` |
| RGB or RGBA | `.rgba.gii` |
| Shape | `.shape.gii` |
| Surface | `.surf.gii` |
| Tensors | `.tensor.gii` |
| Time Series | `.time.gii` |
| Topology | `.topo.gii` |
| Vector | `.vector.gii` |

Unless otherwise stated, bare `.gii` extensions SHOULD NOT be used
for GIFTI files.

<!-- Link Definitions -->

[definitions]: ../common-principles.md#definitions

[storage]: ../common-principles.md#storage-of-derived-datasets

[derived-dataset-description]: ../modality-agnostic-files.md#derived-dataset-and-pipeline-description

[gifti]: https://www.nitrc.org/projects/gifti/

[gifti-spec]: https://www.nitrc.org/frs/download.php/2871/GIFTI_Surface_Format.pdf