AFQ.tasks.mapping#

Attributes#

logger

Functions#

`export_registered_b0`(base_fname, data_imap, mapping)	full path to a nifti file containing
`template_xform`(base_fname, dwi_data_file, data_imap, ...)	full path to a nifti file containing
`export_rois`(base_fname, output_dir, dwi_data_file, ...)	dictionary of full paths to Nifti1Image files of ROIs
`mapping`(base_fname, dwi_data_file, reg_subject, data_imap)	mapping from subject to template space.
`sls_mapping`(base_fname, dwi_data_file, reg_subject, ...)	mapping from subject to template space.
`get_reg_subject`(structural_imap, data_imap, tissue_imap)	Nifti1Image which represents this subject
`get_mapping_plan`(kwargs[, use_sls])

Module Contents#

AFQ.tasks.mapping.logger[source]#

AFQ.tasks.mapping.export_registered_b0(base_fname, data_imap, mapping)[source]#: full path to a nifti file containing b0 transformed to template space

AFQ.tasks.mapping.template_xform(base_fname, dwi_data_file, data_imap, mapping)[source]#: full path to a nifti file containing registration template transformed to subject space

AFQ.tasks.mapping.export_rois(base_fname, output_dir, dwi_data_file, data_imap, mapping)[source]#: dictionary of full paths to Nifti1Image files of ROIs transformed to subject space

AFQ.tasks.mapping.mapping(base_fname, dwi_data_file, reg_subject, data_imap, mapping_definition=None)[source]#

mapping from subject to template space.

Parameters:

mapping_definitioninstance of AFQ.definitions.mapping, optional: This defines how to either create a mapping from each subject space to template space or load a mapping from another software. If creating a map, will register reg_subject and reg_template. If None, use SynMap() Default: None

AFQ.tasks.mapping.sls_mapping(base_fname, dwi_data_file, reg_subject, data_imap, tractography_imap, citations, mapping_definition=None)[source]#

mapping from subject to template space.

Parameters:

mapping_definitioninstance of AFQ.definitions.mapping, optional: This defines how to either create a mapping from each subject space to template space or load a mapping from another software. If creating a map, will register reg_subject and reg_template. If None, use SynMap() Default: None

AFQ.tasks.mapping.get_reg_subject(structural_imap, data_imap, tissue_imap, reg_subject_spec='t1w')[source]#

Nifti1Image which represents this subject when registering the subject to the template

Parameters:

reg_subject_specstr, instance of AFQ.definitions.ImageDefinition, optional: The source image data to be registered. Can either be a Nifti1Image, an ImageFile, or str. if “b0”, “dti_fa_subject”, “subject_sls”, “t1w”, or “power_map,” image data will be loaded automatically. If “subject_sls” is used, slr registration will be used and reg_template should be “hcp_atlas”. Default: “t1w”

AFQ.tasks.mapping.get_mapping_plan(kwargs, use_sls=False)[source]#