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sappelhoff committed Nov 29, 2021
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8 changes: 4 additions & 4 deletions src/05-derivatives/02-common-data-types.md
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Expand Up @@ -78,10 +78,10 @@ comparison of acquired data across runs, sessions, subjects or datasets.
A file may indicate the spatial reference to which it has been aligned using the
[`space` entity](../99-appendices/09-entities.md#space) and/or the `SpatialReference` metadata.

The [`space` entity]((../99-appendices/09-entities.md#space)) may take any value in
The [`space` entity](../99-appendices/09-entities.md#space) may take any value in
[Image-Based Coordinate Systems][coordsys].

If the [`space` entity]((../99-appendices/09-entities.md#space)) is omitted,
If the [`space` entity](../99-appendices/09-entities.md#space) is omitted,
or the space is not in the [Standard template identifiers][templates] table,
then the `SpatialReference` metadata is REQUIRED.

Expand Down Expand Up @@ -176,11 +176,11 @@ Examples of preprocessing:
- Time-domain filtered EEG data
- MaxFilter (for example, SSS) cleaned MEG data

The [`space` entity]((../99-appendices/09-entities.md#space))
The [`space` entity](../99-appendices/09-entities.md#space)
is recommended to distinguish files with different underlying
coordinate systems or registered to different reference maps.
See [Spatial references](#spatial-references) for details.
The [`desc` entity]((../99-appendices/09-entities.md#desc)) ("description")
The [`desc` entity](../99-appendices/09-entities.md#desc) ("description")
is a general purpose field with freeform values,
which SHOULD be used to distinguish between multiple different versions of
processing for the same input data.
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16 changes: 8 additions & 8 deletions src/05-derivatives/03-imaging.md
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Expand Up @@ -22,13 +22,13 @@ sufficiently similar in practice to treat them equivalently.

When two or more instances of a given derivative are provided with resolution
or surface sampling density being the only difference between them, then the
[`res`]((../99-appendices/09-entities.md#res)) (for *resolution* of regularly sampled N-D data) and/or
[`den`]((../99-appendices/09-entities.md#den)) (for *density* of non-parametric surfaces)
[`res`](../99-appendices/09-entities.md#res) (for *resolution* of regularly sampled N-D data) and/or
[`den`](../99-appendices/09-entities.md#den) (for *density* of non-parametric surfaces)
entities SHOULD be used to avoid name conflicts.
Note that only files combining both regularly sampled (for example, gridded)
and surface sampled data (and their downstream derivatives) are allowed
to present both [`res`](../99-appendices/09-entities.md#res) and
[`den`]((../99-appendices/09-entities.md#den)) entities simultaneously.
[`den`](../99-appendices/09-entities.md#den) entities simultaneously.

Examples:

Expand Down Expand Up @@ -92,7 +92,7 @@ And one corresponding to `res-hi`

Example of CIFTI-2 files (a format that combines regularly sampled data
and non-parametric surfaces) having both [`res`](../99-appendices/09-entities.md#res)
and [`den`]((../99-appendices/09-entities.md#den)) entities:
and [`den`](../99-appendices/09-entities.md#den) entities:

{{ MACROS___make_filetree_example(
{
Expand Down Expand Up @@ -139,7 +139,7 @@ Template:

A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../99-appendices/09-entities.md#space).
If no transformation has taken place, the value of `space` SHOULD be set to `orig`.
If the mask is an ROI mask derived from an atlas, then the [`label` entity]((../99-appendices/09-entities.md#label)) SHOULD
If the mask is an ROI mask derived from an atlas, then the [`label` entity](../99-appendices/09-entities.md#label)) SHOULD
be used to specify the masked structure
(see [Common image-derived labels](#common-image-derived-labels)),
and the `Atlas` metadata SHOULD be defined.
Expand Down Expand Up @@ -251,7 +251,7 @@ Example:
A segmentation can be used to generate a binary mask that functions as a
discrete "label" for a single structure.
In this case, the mask suffix MUST be used,
the [`label` entity]((../99-appendices/09-entities.md#label)) SHOULD be used
the [`label` entity](../99-appendices/09-entities.md#label)) SHOULD be used
to specify the masked structure
(see [Common image-derived labels](#common-image-derived-labels)),
and the `Atlas` metadata SHOULD be defined.
Expand All @@ -275,7 +275,7 @@ Probabilistic segmentations of brain tissue represent a single anatomical
structure with values ranging from 0 to 1 in individual 3D volumes or across
multiple frames.
If a single structure is included,
the [`label` entity]((../99-appendices/09-entities.md#label)) SHOULD be used to specify
the [`label` entity](../99-appendices/09-entities.md#label) SHOULD be used to specify
the structure.

Template:
Expand Down Expand Up @@ -303,7 +303,7 @@ Example:
) }}

See [Common image-derived labels](#common-image-derived-labels)
for reserved key values for [`label`]((../99-appendices/09-entities.md#label)).
for reserved key values for [`label`](../99-appendices/09-entities.md#label).

A 4D probabilistic segmentation, in which each frame corresponds to a different
tissue class, must provide a label mapping in its JSON sidecar. For example:
Expand Down

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