Merge pull request bids-standard#499 from effigies/volume_timing

Sparse BOLD acquisitions

Author: effigies

.github/workflows/validate_datasets.yml

@@ -95,7 +95,7 @@ jobs:
         fi
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pheno004 volume_timing; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features

README.md

@@ -290,6 +290,7 @@ DO NOT EDIT DIRECTLY.
 | [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)                   | multiple tasks, T1w, DTI, BOLD, genetic info                                                | anat, dwi, func                 | FLAIR, T1w, bold, dwi, events, info                                                                            | n/a                                                            | [@cpernet](https://github.com/cpernet)     |
 | [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a                                                                                         | anat, fmap, func, ieeg          | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref                                         | n/a                                                            | [@irisgroen](https://github.com/irisgroen) |
 | [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic)                           | A synthetic dataset                                                                         | anat, beh, func                 | T1w, beh, bold, events, physio, scans, sessions, stim                                                          | n/a                                                            | [@effigies](https://github.com/effigies)   |
+| [volume_timing](https://github.com/bids-standard/bids-examples/tree/master/volume_timing)                   | Sparse BOLD acquisitions                                                                    | func                            | bold                                                                                                           | n/a                                                            | [@effigies](https://github.com/effigies)   |
 
 ### MRS
 

dataset_listing.tsv

@@ -33,6 +33,7 @@ ds116	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds0001
 ds210	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000210/versions/00002)		func	bold, physio
 hcp_example_bids		[link](https://bit.ly/2H0Z6Qt)	[@robertoostenveld](https://github.com/robertoostenveld)	anat, fmap	T1w, T2w, magnitude1, magnitude2, phasediff
 synthetic	A synthetic dataset		[@effigies](https://github.com/effigies)	anat, beh, func	T1w, beh, bold, events, physio, scans, sessions, stim
+volume_timing	Sparse BOLD acquisitions		[@effigies](https://github.com/effigies)	func	bold
 ds000001-fmriprep	Common derivatives example	[link](https://openneuro.org/datasets/ds000001/versions/1.0.0)	[@effigies](https://github.com/effigies)	n/a	n/a
 ds004332	Anat dataset with task entity	[link](https://openneuro.org/datasets/ds004332/versions/1.0.2)	[@Remi-Gau](https://github.com/Remi-Gau)	anat	FLAIR, T1w, T2starw, T2w
 asl001	T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries	[link](https://osf.io/yru2q/)	[@patsycle](https://github.com/patsycle)	anat, perf	T1w, asl, aslcontext, asllabeling

volume_timing/README.md

@@ -0,0 +1,20 @@
+# 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

@@ -0,0 +1,9 @@
+{
+  "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

@@ -0,0 +1,4 @@
+{
+  "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

@@ -0,0 +1,4 @@
+{
+  "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

@@ -0,0 +1,4 @@
+{
+  "RepetitionTime": 2,
+  "DelayTime": 1.0
+}