[ENH] Add links to example datasets for each modality (#845)

* update link to bids example for EEG

* add link to example data set: genetics

* add link to example data sets: iEEG

* add link to example data sets: MEG

* Apply suggestions from code review

* Apply suggestions from code review

* add example link for PET

* add links to ASL datasets

* add links to DWI datasets

* add links to fieldmap examples

* add links to physio examples

* add links to qmri examples

* replace link to specific examples with links to table in example README

* fix MD

* one more MD fix

Co-authored-by: Stefan Appelhoff <[email protected]>

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
 
@@ -576,6 +576,15 @@ 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:
 
@@ -778,6 +787,10 @@ 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,
@@ -1008,6 +1021,13 @@ 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
@@ -1097,6 +1117,11 @@ 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 *B<sub>0</sub>* field.

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"]) }}

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"]) }}

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"]) }}

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

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

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).

src/99-appendices/11-qmri.md

@@ -135,7 +135,8 @@ 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