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mariehbourget authored Jul 7, 2021
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11 changes: 9 additions & 2 deletions README.md
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To organize your data in BIDS, all you need is neuro data, a computer, and the
[BIDS specification](https://bids-specification.readthedocs.io/en/stable/).

BIDS currently supports MRI, MEG, EEG, iEEG, behavioral, and physiological data
and more modalities will be added.
BIDS currently supports the following data modalities with more to come in the future:

- MRI
- MEG
- EEG
- iEEG
- behavioral
- physiological
- PET

# Formatting your data with BIDS

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1 change: 1 addition & 0 deletions mkdocs.yml
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site_name: Brain Imaging Data Structure v1.6.1-dev
site_url: https://bids-specification.readthedocs.io/en/stable/
theme:
name: material
custom_dir: theme_customizations/
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26 changes: 15 additions & 11 deletions src/02-common-principles.md
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Expand Up @@ -37,15 +37,19 @@ misunderstanding we clarify them here.
scanning sequence/protocol.

1. **Data type** - a functional group of different types of data.
BIDS defines eight data types:
`func` (task based and resting state functional MRI),
`dwi` (diffusion weighted imaging),
`fmap` (field inhomogeneity mapping data such as field maps),
`anat` (structural imaging such as T1, T2, PD, and so on),
`meg` (magnetoencephalography),
`eeg` (electroencephalography),
`ieeg` (intracranial electroencephalography),
`beh` (behavioral).
BIDS defines the following data types:

1. `func` (task based and resting state functional MRI)
1. `dwi` (diffusion weighted imaging)
1. `fmap` (field inhomogeneity mapping data such as field maps)
1. `anat` (structural imaging such as T1, T2, PD, and so on)
1. `perf` (perfusion)
1. `meg` (magnetoencephalography)
1. `eeg` (electroencephalography)
1. `ieeg` (intracranial electroencephalography)
1. `beh` (behavioral)
1. `pet` (positron emission tomography)

Data files are contained in a directory named for the data type.
In raw datasets, the data type directory is nested inside subject and
(optionally) session directories.
Expand Down Expand Up @@ -348,7 +352,7 @@ then Case 1 will be assumed for clarity in templates and examples, but removing
Case 2.
In both cases, every derivatives dataset is considered a BIDS dataset and must
include a `dataset_description.json` file at the root level (see
[Dataset description][dataset-description].
[Dataset description][dataset-description]).
Consequently, files should be organized to comply with BIDS to the full extent
possible (that is, unless explicitly contradicted for derivatives).
Any subject-specific derivatives should be housed within each subject’s directory;
Expand Down Expand Up @@ -709,6 +713,7 @@ individual files see descriptions in the next section:

```Text
sub-control01/
sub-control01_scans.tsv
anat/
sub-control01_T1w.nii.gz
sub-control01_T1w.json
Expand All @@ -729,7 +734,6 @@ sub-control01/
sub-control01_phasediff.nii.gz
sub-control01_phasediff.json
sub-control01_magnitude1.nii.gz
sub-control01_scans.tsv
code/
deface.py
derivatives/
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12 changes: 6 additions & 6 deletions src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -90,16 +90,16 @@ Whenever possible, please avoid using ad-hoc wording.

| **Key name** | **Requirement level** | **Data type** | **Description** |
| ---------------------- | --------------------- | ------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| InstitutionName | RECOMMENDED | [string][] | The name of the institution in charge of the equipment that produced the composite instances. |
| InstitutionAddress | RECOMMENDED | [string][] | The address of the institution in charge of the equipment that produced the composite instances. |
| InstitutionName | RECOMMENDED | [string][] | The name of the institution in charge of the equipment that produced the measurements. |
| InstitutionAddress | RECOMMENDED | [string][] | The address of the institution in charge of the equipment that produced the measurements. |
| Manufacturer | RECOMMENDED | [string][] | Manufacturer of the MEG system (`"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`, `"ITAB"`, `"KRISS"`, `"Other"`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names. |
| ManufacturersModelName | RECOMMENDED | [string][] | Manufacturer’s designation of the MEG scanner model (for example, `"CTF-275"`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names. |
| SoftwareVersions | RECOMMENDED | [string][] | Manufacturer’s designation of the acquisition software. |
| TaskDescription | RECOMMENDED | [string][] | Description of the task. |
| Instructions | RECOMMENDED | [string][] | Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (for example, to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [Cognitive Atlas](https://www.cognitiveatlas.org/) term that describes the task (for example, Resting State with eyes closed "<https://www.cognitiveatlas.org/task/id/trm_54e69c642d89b>"). |
| CogPOID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (for example, Rest "<http://wiki.cogpo.org/index.php?title=Rest>"). |
| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |
| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |

Specific MEG fields MUST be present:

Expand Down Expand Up @@ -197,7 +197,7 @@ Missing values MUST be indicated with `n/a`.

The columns of the Channels description table stored in `*_channels.tsv` are:

MUST be present:
MUST be present **in this specific order**:

| **Column name** | **Requirement level** | **Description** |
| --------------- | --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
Expand All @@ -221,8 +221,8 @@ SHOULD be present:
Example:

```Text
name type units description sampling_frequency low_cutoff high_cutoff notch software_filters status
UDIO001 TRIG V analogue trigger 1200 0.1 300 0 n/a good
name type units description sampling_frequency low_cutoff high_cutoff notch software_filters status
UDIO001 TRIG V analogue trigger 1200 0.1 300 0 n/a good
MLC11 MEGGRADAXIAL T sensor 1st-order grad 1200 0 n/a 50 SSS bad
```

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12 changes: 5 additions & 7 deletions src/04-modality-specific-files/03-electroencephalography.md
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Expand Up @@ -96,16 +96,16 @@ Whenever possible, please avoid using ad hoc wording.

| **Key name** | **Requirement level** | **Data type** | **Description** |
| ---------------------- | --------------------- | ------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| InstitutionName | RECOMMENDED | [string][] | The name of the institution in charge of the equipment that produced the composite instances. |
| InstitutionAddress | RECOMMENDED | [string][] | The address of the institution in charge of the equipment that produced the composite instances. |
| InstitutionName | RECOMMENDED | [string][] | The name of the institution in charge of the equipment that produced the measurements. |
| InstitutionAddress | RECOMMENDED | [string][] | The address of the institution in charge of the equipment that produced the measurements. |
| Manufacturer | RECOMMENDED | [string][] | Manufacturer of the EEG system (for example, `"Biosemi"`, `"Brain Products"`, `"Neuroscan"`). |
| ManufacturersModelName | RECOMMENDED | [string][] | Manufacturer's designation of the EEG system model (for example, `"BrainAmp DC"`). |
| SoftwareVersions | RECOMMENDED | [string][] | Manufacturer's designation of the acquisition software. |
| TaskDescription | RECOMMENDED | [string][] | Description of the task. |
| Instructions | RECOMMENDED | [string][] | Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (for example, to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [Cognitive Atlas](https://www.cognitiveatlas.org/) term that describes the task (for example, Resting State with eyes closed "<https://www.cognitiveatlas.org/task/id/trm_54e69c642d89b>"). |
| CogPOID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (for example, Rest "<http://wiki.cogpo.org/index.php?title=Rest>") . |
| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |
| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |

Specific EEG fields MUST be present:

Expand Down Expand Up @@ -188,8 +188,6 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri
This file is RECOMMENDED as it provides easily searchable information across
BIDS datasets for for example, general curation, response to queries or batch
analysis.
The required columns are channel `name`, `type` and `units` in this specific
order.
To avoid confusion, the channels SHOULD be listed in the order they
appear in the EEG data file.
Any number of additional columns may be added to provide additional information
Expand All @@ -205,7 +203,7 @@ See the examples for `*_channels.tsv` below, and for `*_electrodes.tsv` in

The columns of the Channels description table stored in `*_channels.tsv` are:

MUST be present:
MUST be present **in this specific order**:

| **Column name** | **Requirement level** | **Description** |
| --------------- | --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
Expand Down Expand Up @@ -277,7 +275,7 @@ expected in cartesian coordinates according to the `EEGCoordinateSystem` and
file MUST be specified as well**. The order of the required columns in the
`*_electrodes.tsv` file MUST be as listed below.

MUST be present:
MUST be present **in this specific order**:

| **Column name** | **Requirement level** | **Description** |
| --------------- | --------------------- | ----------------------------------- |
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