diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index bee7d711ca..c98be49603 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -6,7 +6,7 @@ MR Data described in the following sections share the following RECOMMENDED meta fields (stored in sidecar JSON files). MRI acquisition parameters are divided into several categories based on ["A checklist for fMRI acquisition methods reporting in the literature"](https://thewinnower.com/papers/977-a-checklist-for-fmri-acquisition-methods-reporting-in-the-literature) -by Ben Inglis: +by Ben Inglis. ### Scanner Hardware @@ -558,6 +558,15 @@ participant, task and run takes precedence. ## Diffusion imaging data +Several [example datasets](https://github.com/bids-standard/bids-examples) +contain diffusion imaging data formatted using this specification +and that can be used for practical guidance when curating a new dataset: + +- [`genetics_ukbb`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) +- [`eeg_rest_fmri`](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri) +- [`ds114`](https://github.com/bids-standard/bids-examples/tree/master/ds114) +- [`ds000117`](https://github.com/bids-standard/bids-examples/tree/master/ds000117) + Diffusion-weighted imaging data acquired for a participant. Currently supported image types include: @@ -744,6 +753,10 @@ JSON example: ## Arterial Spin Labeling perfusion data +Several [example ASL datasets](https://github.com/bids-standard/bids-examples#asl-datasets) +have been formatted using this specification +and can be used for practical guidance when curating a new dataset. + {{ MACROS___make_filename_template(datatypes=["perf"]) }} The complete ASL time series should be stored as a 4D NIfTI file in the original acquisition order, @@ -974,6 +987,13 @@ For example: #### Case 1: Phase-difference map and at least one magnitude image +[Example datasets](https://github.com/bids-standard/bids-examples) +containing that type of fieldmap can be found here: + +- [`7t_trt`](https://github.com/bids-standard/bids-examples/tree/master/7t_trt) +- [`genetics_ukbb`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) +- [`ds000117`](https://github.com/bids-standard/bids-examples/tree/master/ds000117) + {{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["phasediff", "magnitude1", "magnitude2"]) }} where @@ -1063,6 +1083,11 @@ for details on the `IntendedFor` field. #### Case 4: Multiple phase encoded directions ("pepolar") +An [example dataset](https://github.com/bids-standard/bids-examples) +containing that type of fieldmap can be found here: + +- [`ieeg_visual_multimodal`](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) + The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo EPI scans with different phase encoding directions to estimate the distortion map corresponding to the nonuniformities of the *B0* field. diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md index cb0bec11f6..2d6908b523 100644 --- a/src/04-modality-specific-files/02-magnetoencephalography.md +++ b/src/04-modality-specific-files/02-magnetoencephalography.md @@ -6,6 +6,14 @@ Please see [Citing BIDS](../01-introduction.md#citing-bids) on how to appropriately credit this extension when referring to it in the context of the academic literature. +The following example MEG datasets have been formatted using this specification +and can be used for practical guidance when curating a new dataset. + +- [`multimodal MEG and MRI`](https://github.com/bids-standard/bids-examples/tree/master/ds000117) + +Further datasets are available from +the [BIDS examples repository](https://github.com/bids-standard/bids-examples). + ## MEG recording data {{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["meg", "markers", "events"]) }} diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md index 1222db4453..f2a4192029 100644 --- a/src/04-modality-specific-files/03-electroencephalography.md +++ b/src/04-modality-specific-files/03-electroencephalography.md @@ -6,15 +6,10 @@ Please see [Citing BIDS](../01-introduction.md#citing-bids) on how to appropriately credit this extension when referring to it in the context of the academic literature. -The following example EEG datasets have been formatted using this specification +Several [example EEG datasets](https://github.com/bids-standard/bids-examples#eeg-datasets) +have been formatted using this specification and can be used for practical guidance when curating a new dataset. -- Single session per subject: [`eeg_matchingpennies`](https://doi.org/10.17605/OSF.IO/CJ2DR) -- Multiple sessions per subject: [`eeg_rishikesh`](https://doi.org/10.5281/zenodo.1490922) -- Combined with fMRI: [`eeg_rest_fmri`](https://osf.io/94c5t/files/) - -Further datasets are available from the [BIDS examples repository](https://github.com/bids-standard/bids-examples). - ## EEG recording data {{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["eeg", "events"]) }} diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md index a577e048c7..68087f83e6 100644 --- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md +++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md @@ -6,6 +6,10 @@ Please see [Citing BIDS](../01-introduction.md#citing-bids) on how to appropriately credit this extension when referring to it in the context of the academic literature. +Several [example iEEG datasets](https://github.com/bids-standard/bids-examples#ieeg-datasets) +have been formatted using this specification +and can be used for practical guidance when curating a new dataset. + ## iEEG recording data {{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["ieeg", "events"]) }} diff --git a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md index 8892618cf9..79f84a03f8 100644 --- a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md +++ b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md @@ -1,5 +1,12 @@ # Physiological and other continuous recordings +[Example datasets](https://github.com/bids-standard/bids-examples) +with physiological data have been formatted using this specification +and can be used for practical guidance when curating a new dataset: + +- [`7t_trt`](https://github.com/bids-standard/bids-examples/tree/master/7t_trt) +- [`ds210`](https://github.com/bids-standard/bids-examples/tree/master/ds210) + Template: ```Text diff --git a/src/04-modality-specific-files/08-genetic-descriptor.md b/src/04-modality-specific-files/08-genetic-descriptor.md index ad36f2e8b4..bdd7d3fa08 100644 --- a/src/04-modality-specific-files/08-genetic-descriptor.md +++ b/src/04-modality-specific-files/08-genetic-descriptor.md @@ -12,6 +12,11 @@ A genetic descriptor links a BIDS dataset to associated genetic data, potentially in a separate repository, with details of where to find the genetic data and the type of data available. +The following example dataset with genetics data have been formatted using this specification +and can be used for practical guidance when curating a new dataset. + +- [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) + ## Dataset Description Genetic descriptors are encoded as an additional, OPTIONAL entry in the diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md index c4312117ea..44a1943322 100644 --- a/src/04-modality-specific-files/09-positron-emission-tomography.md +++ b/src/04-modality-specific-files/09-positron-emission-tomography.md @@ -6,7 +6,8 @@ Please see [Citing BIDS](../01-introduction.md#citing-bids) on how to appropriately credit this extension when referring to it in the context of the academic literature. -Several [example PET datasets](https://github.com/bids-standard/bids-examples) have been formatted using this specification +Several [example PET datasets](https://github.com/bids-standard/bids-examples#pet-datasets) +have been formatted using this specification and can be used for practical guidance when curating a new dataset. Further PET datasets are available from [OpenNeuro](https://openneuro.org). diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md index ab9dadb5f3..5cd48cbfce 100644 --- a/src/99-appendices/11-qmri.md +++ b/src/99-appendices/11-qmri.md @@ -113,7 +113,8 @@ It is RECOMMENDED to share them along with the vendor outputs, whenever possible ### Example datasets -You can find example file collections and qMRI maps organized according to BIDS at [https://osf.io/k4bs5/](https://osf.io/k4bs5/). +You can find example file collections and qMRI maps organized according to BIDS +in the [BIDS examples](https://github.com/bids-standard/bids-examples#qmri-datasets). ## Metadata requirements for qMRI data