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chrisgorgo committed Oct 7, 2018
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Expand Up @@ -151,83 +151,6 @@ these data are to be included:
1. We RECOMMEND including the PDF print-out with the actual sequence parameters
generated by the scanner in the `sourcedata` folder.

## The Inheritance Principle

Any metadata file (`.json`, `.bvec`, `.tsv`, etc.) may be defined at any
directory level, but no more than one applicable file may be defined at a given
level (Example 1). The values from the top level are inherited by all lower
levels unless they are overridden by a file at the lower level. For example,
`sub-*_task-rest_bold.json` may be specified at the participant level, setting
TR to a specific value. If one of the runs has a different TR than the one
specified in that file, another `sub-*_task-rest_bold.json` file can be placed
within that specific series directory specifying the TR for that specific run.
There is no notion of "unsetting" a key/value pair. For example if there is a
JSON file corresponding to particular participant/run defining a key/value and
there is a JSON file on the root level of the dataset that does not define this
key/value it will not be "unset" for all subjects/runs. Files for a particular
participant can exist only at participant level directory, i.e
`/dataset/sub-*[/ses-*]/sub-*_T1w.json`. Similarly, any file that is not
specific to a participant is to be declared only at top level of dataset for eg:
`task-sist_bold.json` must be placed under `/dataset/task-sist_bold.json`

Example 1: Two JSON files at same level that are applicable for NIfTI file.

```Text
sub-01/
ses-test/
sub-test_task-overtverbgeneration_bold.json
sub-test_task-overtverbgeneration_run-2_bold.json
anat/
sub-01_ses-test_T1w.nii.gz
func/
sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz
sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz
```

In the above example, two JSON files are listed under `sub-01/ses-test/`, which
are each applicable to
`sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz`, violating the
constraint that no more than one file may be defined at a given level of the
directory structure. Instead `task-overtverbgeneration_run-2_bold.json` should
have been under `sub-01/ses-test/func/`.

Example 2: Multiple run and rec with same acquisition (acq) parameters acq-test1

```Text
sub-01/
anat/
func/
sub-01_task-xyz_acq-test1_run-1_bold.nii.gz
sub-01_task-xyz_acq-test1_run-2_bold.nii.gz
sub-01_task-xyz_acq-test1_rec-recon1_bold.nii.gz
sub-01_task-xyz_acq-test1_rec-recon2_bold.nii.gz
sub-01_task-xyz_acq-test1_bold.json
```

For the above example, all NIfTI files are acquired with same scanning
parameters (`acq-test1`). Hence a JSON file describing the acq parameters will
apply to different runs and rec files. Also if the JSON file
(`task-xyz_acq-test1_bold.json`) is defined at dataset top level directory, it
will be applicable to all task runs with `test1` acquisition parameter.

Case 2: Multiple json files at different levels for same task and acquisition
parameters

```Text
sub-01/
sub-01_task-xyz_acq-test1_bold.json
anat/
func/
sub-01_task-xyz_acq-test1_run-1_bold.nii.gz
sub-01_task-xyz_acq-test1_rec-recon1_bold.nii.gz
sub-01_task-xyz_acq-test1_rec-recon2_bold.nii.gz
```

In the above example, the fields from `task-xyz_acq-test1_bold.json` file will
apply to all bold runs. However, if there is a key with different value in
`sub-01/func/sub-01_task-xyz_acq-test1_run-1_bold.json`, the new value will be
applicable for that particular run/task NIfTI file/s.

## Extensions

The BIDS specification can be extended in a backwards compatible way and will
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