Note

This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the user guide for the big picture.

brainprep.datasets.ibc.IBCDataset

class brainprep.datasets.ibc.IBCDataset(datadir)

Bases: object

Individual Brain Charting (IBC) multi-modal dataset.

This dataset [1] contains Magnetic Resonance (MR) images of 13 healthy volunteers. The first session is considered and includes T1W, T2W, FLAIR, DWI, and task fMRI.

Parameters:

datadirDirectory

Directory where data will be stored.

Attributes:

_urlstr

Internal URL used to fetch data.

References

[1]

Ana Luísa Pinho, Alexis Amadon, Torsten Ruest, Murielle Fabre, Elvis Dohmatob, Isabelle Denghien, Chantal Ginisty, Séverine Becuwe-Desmidt, Séverine Roger, Laurence Laurier, Véronique Joly-Testault, Gaëlle Médiouni-Cloarec, Christine Doublé, Bernadette Martins, Philippe Pinel, Evelyn Eger, Gaël Varoquaux, Christophe Pallier, Stanislas Dehaene, Lucie Hertz-Pannier, and Bertrand Thirion. Individual brain charting, a high-resolution fMRI dataset for cognitive mapping. Sci. Data, 5(1):180105, June 2018.

Examples

>>> from brainprep.config import Config
>>> from pathlib import Path
>>> from brainprep.datasets import IBCDataset
>>>
>>> datadir = Path("/tmp/brainprep-data")
>>> datadir.mkdir(parents=True, exist_ok=True)
>>> dataset = IBCDataset(datadir)
>>> with Config(verbose=False):
...     data = dataset.fetch(
...         subject="01",
...         modality="anat",
...     )
>>> data
Bunch(
  description: PosixPath('...')
  anat: PosixPath('...')
)

__init__(datadir)

fetch(subject, modality)

Fetch data.

Parameters:

subjectstr

Subject identifier: [‘01’ - ‘13’].

modalitystr

Modality to be fetched: ‘anat’, ‘func’ or ‘dwi’. A combination of modalitites can be specified using the ‘|’ delimiter.

Returns:

dataset: Bunch

Fetched data path. A ‘description’ entry is also available.

sanity_check(subject, modality)

Check that the fetch parameters are correct.

Parameters:

subjectstr

the subject identifier.

modalitystr

the modality to be fetched.

Raises:

ValueError

If the fetch input parameters are not correct.