Add example with sparse BOLD acquisitions

Author: effigies

volume_timing/README.md

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+# BOLD volume timing test
+
+This example is intended to exercise BOLD volume timing options enumerated in
+https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#timing-parameters_1.
+
+All JSON files describe 1-second volume acquisitions, in various configurations.
+
+| Filename                                       | Acquisition type   | Metadata fields                            | Description                                                                      |
+| ---------------------------------------------- | ------------------ | ------------------------------------------ | -------------------------------------------------------------------------------- |
+| `sub-01_task-rest_acq-dense_bold.json`         | Dense              | `RepetitionTime`                           | No gaps in volume acquisitions.                                                  |
+| `sub-01_task-rest_acq-constantDelay_bold.json` | Constant-TR sparse | `RepetitionTime`, `DelayTime`              | Constant TR with a gap between volume acquisitions.                              |
+| `sub-01_task-rest_acq-constantST_bold.json`    | Constant-TR sparse | `RepetitionTime`, `SliceTiming`            | Constant TR, with acquisition duration calculable from `SliceTiming`.            |
+| `sub-01_task-rest_acq-clusteredTA_bold.json`   | Varying-TR sparse  | `VolumeTiming`, `FrameAcquisitionDuration` | Volume onsets and constant acquisition duration provided.                        |
+| `sub-01_task-rest_acq-clusteredST_bold.json`   | Varying-TR sparse  | `VolumeTiming`, `SliceTiming`              | Volume onsets provided, with acquisition duration calculable from `SliceTiming`. |
+| `sub-01_task-rest_acq-deprecated_bold.json`    | Varying-TR sparse  | `VolumeTiming`, `AcquisitionDuration`      | Volume onsets and constant acquisition duration provided.                        |
+
+Note the `acq-deprecated` option, which uses the `AcquisitionDuration` field.
+This field was identified with a DICOM field that has a distinct meaning from the meaning
+used in BIDS, which more closely aligns with `FrameAcquisitionDuration`.
+This form is still permitted by the validator, but should be migrated away from.

volume_timing/dataset_description.json

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+{
+  "BIDSVersion": "1.10.0",
+  "Name": "BOLD volume timing test",
+  "Authors": ["Christopher J. Markiewicz", "John Doe"],
+  "License": "CC0",
+  "DatasetType": "raw",
+  "GeneratedBy": [ { "Name": "manual" } ],
+  "SourceDatasets": []
+}

volume_timing/sub-01/func/sub-01_task-rest_acq-clusteredST_bold.json

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+{
+  "VolumeTiming": [0.0, 1.0, 2.0, 6.0, 7.0, 8.0, 12.0, 13.0, 14.0],
+  "SliceTiming": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
+}

volume_timing/sub-01/func/sub-01_task-rest_acq-clusteredST_bold.nii.gz

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+{
+  "VolumeTiming": [0.0, 1.0, 2.0, 6.0, 7.0, 8.0, 12.0, 13.0, 14.0],
+  "FrameAcquisitionDuration": 1.0
+}

volume_timing/sub-01/func/sub-01_task-rest_acq-clusteredTA_bold.json

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+{
+  "RepetitionTime": 2,
+  "DelayTime": 1.0
+}

volume_timing/sub-01/func/sub-01_task-rest_acq-clusteredTA_bold.nii.gz

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+{
+  "RepetitionTime": 2,
+  "SliceTiming": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
+}