cedalion.data package

Module contents

Cedalion datasets and utility functions.

cedalion.data.get(fname: str | Path) → Path[source]

Returns the absolute path to a file under cedalion/data/.

cedalion.data.get_ninja_cap_probe()[source]

Load the fullhead Ninja NIRS cap probe.

cedalion.data.get_ninja_uhd_cap_probe()[source]

Load the fullhead Ninja NIRS ultra HD cap probe.

cedalion.data.get_snirf_test_data()[source]
cedalion.data.get_colin27_segmentation(downsampled=False)[source]

Retrieves the Colin27 segmentation dataset, based on Holmes et al. [HHC+98].

cedalion.data.get_colin27_parcel_file()[source]

Retrieves the Colin27 headmodel, based on Holmes et al. [HHC+98].

cedalion.data.get_icbm152_segmentation()[source]
cedalion.data.get_icbm152_parcel_file()[source]

Retrieves the Colin27 headmodel, based on Holmes et al. [HHC+98].

cedalion.data.get_fingertapping() → Recording[source]

Retrieves a finger tapping recording in BIDS format.

Data is from Luke and McAlpine [LM21a]

cedalion.data.get_fingertappingDOT() → Recording[source]

Retrieves a finger tapping DOT example dataset from the IBS Lab.

cedalion.data.get_fingertapping_snirf_path() → Path[source]
cedalion.data.get_multisubject_fingertapping_snirf_paths()[source]
cedalion.data.get_multisubject_fingertapping_path() → Path[source]
cedalion.data.get_photogrammetry_example_scan()[source]
cedalion.data.get_precomputed_fluence(dataset: str, head_model: str) → Path[source]

Precomputed forward model results for examples and documentation.

Parameters:

  • dataset – “fingertapping” or “fingertappingDOT”

  • head_model – “colin27” or “icbm152”

Returns:

A Path object pointing to the fluence file.

cedalion.data.get_precomputed_sensitivity(
dataset: str,
head_model: str,
) → DataArray[source]

Precomputed sensitivities for examples and documentation.

Parameters:

  • dataset – “fingertapping”, “fingertappingDOT”, “nn22_resting”, “ninja_cap_56x144”, “ninja_uhd_cap_164x496”

  • head_model – “colin27” or “icbm152”

Returns:

The precomputed sensitivity (Adot) matrix

cedalion.data.get_nn22_resting_state() → Recording[source]
cedalion.data.get_snirf2bids_example_dataset() → tuple[Path, Path][source]

A dataset for demonstrating the snirf2bids notebook.

Returns:

The path to the downloaded dataset directory and the path to the mapping file with changes that the user would do manually.

cedalion.data.get_fieldtrip_colin27_landmarks() → Annotated[DataArray, DataArraySchema(dims='label', coords='label', 'label', 'type')][source]
cedalion.data.get_spa_fnirs() → Recording[source]
class cedalion.data.HeadModelFiles(
basedir: pathlib.Path,
mask_files: dict[str, str],
landmarks_ras_file: str,
brain_vertex_coordinates: str,
scalp_surface_obj: str,
brain_surface_obj: str,
freesurfer_surface_obj: str,
inflated_surface_obj: str,
parcel_colors: str,
voxel_to_vertex_mapping: str,
)[source]

Bases: object

basedir: Path[source]
mask_files: dict[str, str][source]
landmarks_ras_file: str[source]
brain_vertex_coordinates: str[source]
scalp_surface_obj: str[source]
brain_surface_obj: str[source]
freesurfer_surface_obj: str[source]
inflated_surface_obj: str[source]
parcel_colors: str[source]
voxel_to_vertex_mapping: str[source]
cedalion.data.get_colin27_headmodel_files() → HeadModelFiles[source]

Retrieves the Colin27 segmentation dataset, based on Holmes et al. [HHC+98].

cedalion.data.get_icbm152_headmodel_files() → HeadModelFiles[source]

Retrieves the ICBM-152 segmentation dataset.