clinicaio.dataset.BIDSDataset

class clinicaio.dataset.BIDSDataset(bids_path: str | pathlib.Path, description: clinicaio.dataset_description.BIDSDatasetDescription)

A BIDS dataset. See the general organisation of the library.

Examples

• Assorted dataset queries

Creates a new BIDS dataset. Useful when you want to write a new dataset to the filesystem.

See also

• write_to_folder()

Parameters:

• bids_path (str | pathlib.Path)

• description (clinicaio.dataset_description.BIDSDatasetDescription)

bids_path: pathlib.Path

description: clinicaio.dataset_description.BIDSDatasetDescription

Methods

subject_by_id(→ Optional[clinicaio.subject.Subject])	Retrieves from this dataset the given subject by its ID.
all_subjects(→ Iterable[clinicaio.subject.Subject])	Retrieves all the subjects that are part of this dataset.
subjects_count(→ int)	Retrieves the number of subjects that are part of this dataset.
all_sessions(→ Iterable[clinicaio.session.Session])	Retrieves all the sessions that this dataset's subjects are part of.
all_images(→ Iterable[clinicaio.image.Image])	Retrieves all the images present in this dataset.
populate_subjects_info_from_df(→ None)	Populates the subjects information from the given dataframe.
populate_from_dir(→ BIDSDataset)	Read a BIDS dataset from the given BIDS directory.
add_subject(→ clinicaio.subject.Subject)	Adds a new subject to this dataset.
write_to_folder(→ None)	Creates the dataset folder, writes the dataset description JSON and readme, creates the subjects and sessions
write_root_file(→ IO[Any])	Creates and opens for writing the given file at the root of the dataset, eventually in "binary" mode
query_images(→ Iterable[clinicaio.image.Image])	Returns all the images matching the query.
query_images_nifti_paths(→ Iterable[pathlib.Path])	Convenience function that only returns the NIFTI image paths instead of the images themselves.
query_images_companions_paths(→ Iterable[pathlib.Path])	Convenience function that only returns the companion image paths with the given file extension