feat: Add example with all ways of calculating TotalReadoutTime

.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 fmaps; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features
@@ -107,7 +107,7 @@ jobs:
     - name: Skip main validation for datasets with unreleased spec features
       # Replace ${EMPTY} with dataset patterns, when this is needed
       # Reset to "for DS in ${EMPTY}; ..." after a spec release
-      run: for DS in dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in dwi_deriv pheno004 fmaps; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -116,7 +116,7 @@ jobs:
       # Update this URL to the schema.json from PRs to the spec, when needed.
       # If this variable is unset, dev will generally track the latest development
       # release of https://jsr.io/@bids/schema
-      run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV
+      run: echo BIDS_SCHEMA=https://bids-specification--2116.org.readthedocs.build/en/2116/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |

README.md

@@ -287,6 +287,7 @@ DO NOT EDIT DIRECTLY.
 | [ds116](https://github.com/bids-standard/bids-examples/tree/master/ds116)                                   | multiple tasks, multiple runs                                                               | anat, func                      | T1w, bold, events, inplaneT2                                                                                   | [link](https://openneuro.org/datasets/ds000116/versions/00003) | n/a                                        |
 | [ds210](https://github.com/bids-standard/bids-examples/tree/master/ds210)                                   | multiple tasks, multiple runs                                                               | func                            | bold, physio                                                                                                   | [link](https://openneuro.org/datasets/ds000210/versions/00002) | n/a                                        |
 | [eeg_rest_fmri](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri)                   | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk)          | anat, dwi, eeg, func            | T1w, bold, dwi, eeg                                                                                            | n/a                                                            | [@cpernet](https://github.com/cpernet)     |
+| [fmap](https://github.com/bids-standard/bids-examples/tree/master/fmap)                                     | A synthetic fieldmap-only dataset                                                           | fmap, func                      | epi                                                                                                            | n/a                                                            | [@effigies](https://github.com/effigies)   |
 | [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)   |

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
+fmap	A synthetic fieldmap-only dataset		[@effigies](https://github.com/effigies)	fmap, func	epi
 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

fmaps/README.md

@@ -0,0 +1,8 @@
+# EPI fieldmap metadata test
+
+The total readout time is necessary to translate between deflections
+in the magnetic field and displacements induced by susceptibility artifacts.
+
+There are several ways to calculate the total readout time, given a BIDS
+dataset, and this example exists to demonstrate them.
+In particular this dataset SHOULD NOT emit `TOTAL_READOUT_TIME_MUST_DEFINE` errors.

fmaps/dataset_description.json

@@ -0,0 +1,4 @@
+{
+  "BIDSVersion": "1.10.0",
+  "Name": "EPI fieldmap metadata test"
+}

fmaps/sub-01/fmap/sub-01_acq-EES_dir-AP_epi.json

@@ -0,0 +1,4 @@
+{
+  "PhaseEncodingDirection": "j",
+  "EffectiveEchoSpacing": 0.00059
+}

fmaps/sub-01/fmap/sub-01_acq-ES_dir-AP_epi.json

@@ -0,0 +1,5 @@
+{
+  "PhaseEncodingDirection": "j",
+  "EchoSpacing": 0.00059,
+  "ParallelReductionFactorInPlane": 2
+}

fmaps/sub-01/fmap/sub-01_acq-Freq_dir-AP_epi.json

@@ -0,0 +1,6 @@
+{
+  "PhaseEncodingDirection": "j",
+  "WaterFatShift": 9.227266,
+  "EPIFactor": 35,
+  "ImagingFrequency": 127.7325
+}

fmaps/sub-01/fmap/sub-01_acq-Strength_dir-AP_epi.json

@@ -0,0 +1,6 @@
+{
+  "PhaseEncodingDirection": "j",
+  "WaterFatShift": 9.227266,
+  "EPIFactor": 35,
+  "MagneticFieldStrength": 3
+}

fmaps/sub-01/fmap/sub-01_acq-TRT_dir-AP_epi.json

@@ -0,0 +1,4 @@
+{
+  "PhaseEncodingDirection": "j",
+  "TotalReadoutTime": 0.05
+}

fmaps/sub-01/func/sub-01_task-rest_bold.json

@@ -0,0 +1,6 @@
+{
+  "TaskName": "rest",
+  "PhaseEncodingDirection": "j",
+  "TotalReadoutTime": 0.05,
+  "RepetitionTime": 2
+}