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

Merged
merged 15 commits into from
Nov 11, 2021
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Expand Up @@ -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

Expand Down Expand Up @@ -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:

Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 *B<sub>0</sub>* field.
Expand Down
9 changes: 9 additions & 0 deletions src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -6,6 +6,15 @@ 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"]) }}
Expand Down
9 changes: 2 additions & 7 deletions src/04-modality-specific-files/03-electroencephalography.md
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Expand Up @@ -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"]) }}
Expand Down
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Expand Up @@ -6,6 +6,11 @@ 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"]) }}
Expand Down
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@@ -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
Expand Down
5 changes: 5 additions & 0 deletions src/04-modality-specific-files/08-genetic-descriptor.md
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Expand Up @@ -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
Expand Down
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Expand Up @@ -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).
Expand Down
3 changes: 2 additions & 1 deletion src/99-appendices/11-qmri.md
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Expand Up @@ -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

Expand Down