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FIX: Apply suggestions from @sappelhoff review
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effigies committed May 28, 2019
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5 changes: 2 additions & 3 deletions CODEOWNERS
Validating CODEOWNERS rules …
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# Individual sections
/src/01-common-principles.md @chrisgorgo @DimitriPapadopoulos
/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisgorgo
/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff
/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff @ezemikulan
/src/04-modality-specific-files/04-intracranial-electroencephalography.md @ezemikulan
/src/05-derivatives/03-structural-derivatives.md @edickie @ahoopes
/src/05-derivatives/04-functional-derivatives.md @effigies
/src/05-derivatives/05-diffusion-derivatives.md @francopestilli @oesteban
/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff @ezemikulan
/src/04-modality-specific-files/04-intracranial-electroencephalography.md @ezemikulan
/src/99-appendices/06-meg-file-formats.md @monkeyman192
9 changes: 4 additions & 5 deletions src/02-common-principles.md
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Expand Up @@ -96,11 +96,10 @@ However, in the case that these data are to be included:
`sourcedata/sub-01/ses-pre/func/sub-01_ses-pre_task-rest_bold.dicom.tgz` or
`sourcedata/sub-01/ses-pre/func/MyEvent.sce`.

1. A README file SHOULD be found at the root of the `sourcedata` folder
(or both). This file should describe the nature of the
raw data or the derived data. We RECOMMEND including the PDF print-out with
the actual sequence parameters generated by the scanner in the `sourcedata`
folder.
1. A README file SHOULD be found at the root of the `sourcedata` folder.
This file should describe the nature of the raw data or the derived data.
We RECOMMEND including the PDF print-out with the actual sequence
parameters generated by the scanner in the `sourcedata` folder.

Alternatively one can organize their data in the following way

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34 changes: 18 additions & 16 deletions src/05-derivatives/01-introduction.md
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Expand Up @@ -17,8 +17,8 @@ Derivatives can be stored/distributed in two ways:
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 needs to be a substring of `PipelineDescription.Name` field
in the `dataset_description.json` (see below).
subfolder name MUST be a substring of `PipelineDescription.Name` field in
the `dataset_description.json` (see below).

For example:

Expand All @@ -32,17 +32,17 @@ Derivatives can be stored/distributed in two ways:
dataset. This way of specifying derivatives is particularly useful when the
source dataset is provided with read-only access, and for publishing
derivatives as independent bodies of work, or for describing derivatives
that were created from more than one source dataset. It is consistent with
BIDS principles for the `sourcedata/` subdirectory to be used to include or
reference the source dataset(s) as it existed when the derivatives were
generated. Likewise, any code used to generate the derivatives from the
source data may be included in the `code/` subdirectory.
that were created from more than one source dataset. The `sourcedata/`
subdirectory MAY be used to include the source dataset(s) that were used
to generate the derivatives.
Likewise, any code used to generate the derivatives from the source data
MAY be included in the `code/` subdirectory.
The rest of the Derivatives specification assumes Case 1, but Case 2 applies
after removing `/derivatives/<pipeline_name>` from template names. In both cases
every derivatives dataset is considered a BIDS dataset and must include a
`dataset_description.json` file at the root level. Consequently, files should be
organized to comply with the BIDS to the full extent possible (i.e., unless
organized to comply with BIDS to the full extent possible (i.e., unless
explicitly contradicted below). Any subject-specific derivatives should be
housed within each subject’s directory; if session-specific derivatives are
generated, they should be deposited under a session subdirectory within the
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## Coordinate systems

Coordinate system (a.k.a. space) a particular derivative is in should be denoted
using a filename keyword `space` whenever such keyword is present in the
filename template of a given derivative type. The allowed values for this
The coordinate system (a.k.a. space) a particular derivative is in SHOULD be
denoted using a filename keyword `space` whenever such keyword is present in
the filename template of a given derivative type. The allowed values for this
keyword depend on the file format:

| File format | Description | Allowed `CoordinateSystem` values |
Expand All @@ -116,10 +116,11 @@ sub-01/func/sub-01_task-rest_space-HCPMNIfsLR32k_bold.nii
## Common file level metadata fields

Each derivative file SHOULD be described by a JSON file provided as a sidecar or
higher up in the hierarchy of the derived dataset (according to Inheritance
Principle - section 3.5 of the main specification) unless a particular
derivative includes REQUIRED metadata fields in which case a JSON file is also
REQUIRED. Each derivative type defines their own set of fields, but all of them
higher up in the hierarchy of the derived dataset (according to
[The Inheritance Principle](../02-common-principles.md#the-inheritance-principle))
unless a particular derivative includes REQUIRED metadata fields in which case a
JSON file is also REQUIRED.
Each derivative type defines their own set of fields, but all of them
share the following (non-required) ones:

| **Key name** | **Description** |
Expand Down Expand Up @@ -174,7 +175,8 @@ sub-01/anat/sub-01_hemi-L_space-individual_thickness.json
pertinent fields is very valuable and thus encouraged. Moreover, for some
types of files, there may be one or more required metadata fields, in which
case at least one metadata file containing that field must be located
somewhere within the file’s hierarchy (per the Inheritance Principle).
somewhere within the file’s hierarchy (per [the Inheritance
Principle](../02-common-principles.md#the-inheritance-principle)).

- When chaining derivative pipelines, any JSON fields that were specified as
mandatory in the input files should be propagated forward in the output
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