xcp_d.utils.atlas module

Functions for working with atlases.

xcp_d.utils.atlas.copy_atlas(name_source, in_file, output_dir, atlas)[source]

Copy atlas file to output directory.

I can’t use DerivativesDataSink because it has a problem with dlabel CIFTI files. It gives the following error: “AttributeError: ‘Cifti2Header’ object has no attribute ‘set_data_dtype’”

I can’t override the CIFTI atlas’s data dtype ahead of time because setting it to int8 or int16 somehow converts all of the values in the data array to weird floats. This could be a version-specific nibabel issue.

xcp_d.utils.atlas.get_atlas_cifti(atlas_name)[source]

Select atlas by name from xcp_d/data.

All atlases are in 91K space.

NOTE: This is a Node function.

Parameters:

atlas_name ({“4S156Parcels”, “4S256Parcels”, “4S356Parcels”, “4S456Parcels”, “4S556Parcels”, “4S656Parcels”, “4S756Parcels”, “4S856Parcels”, “4S956Parcels”, “4S1056Parcels”, “Glasser”, “Gordon”, “Tian”, “HCP”}) – The name of the CIFTI atlas to fetch.

Returns:

  • atlas_file (str) – Path to the atlas file.

  • atlas_labels_file (str) – The labels TSV file associated with the atlas.

  • atlas_metadata_file (str) – The metadata JSON file associated with the atlas.

xcp_d.utils.atlas.get_atlas_names(subset)[source]

Get a list of atlases to be used for parcellation and functional connectivity analyses.

The actual list of files for the atlases is loaded from a different function.

NOTE: This is a Node function.

Parameters:

subset = {“all”, “subcortical”, “cortical”} – Description of the subset of atlases to collect.

Returns:

List of atlases.

Return type:

list of str

xcp_d.utils.atlas.get_atlas_nifti(atlas_name)[source]

Select atlas by name from xcp_d/data using pkgrf.

All atlases are in MNI space.

NOTE: This is a Node function.

Parameters:

atlas_name ({“4S156Parcels”, “4S256Parcels”, “4S356Parcels”, “4S456Parcels”, “4S556Parcels”, “4S656Parcels”, “4S756Parcels”, “4S856Parcels”, “4S956Parcels”, “4S1056Parcels”, “Glasser”, “Gordon”, “Tian”, “HCP”}) – The name of the NIFTI atlas to fetch.

Returns:

  • atlas_file (str) – Path to the atlas file.

  • atlas_labels_file (str) – Path to the atlas labels file.

  • atlas_metadata_file (str) – Path to the atlas metadata file.