AFQ.tasks.mapping

Module Contents

Functions

export_registered_b0(data_imap, mapping)	full path to a nifti file containing
template_xform(mapping, data_imap)	full path to a nifti file containing
export_rois(base_fname, output_dir, data_imap, mapping)	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(data_imap[, reg_subject_spec])	Nifti1Image which represents this subject
get_mapping_plan(kwargs[, use_sls])

Attributes

logger

AFQ.tasks.mapping.logger

AFQ.tasks.mapping.export_registered_b0(data_imap, mapping)

full path to a nifti file containing b0 transformed to template space

AFQ.tasks.mapping.template_xform(mapping, data_imap)

full path to a nifti file containing registration template transformed to subject space

AFQ.tasks.mapping.export_rois(base_fname, output_dir, data_imap, mapping)

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)

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, mapping_definition=None)

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(data_imap, reg_subject_spec='power_map')

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

Parameters

reg_subject_specstr, instance of AFQ.definitions.ImageDefinition, optional # noqa

The source image data to be registered. Can either be a Nifti1Image, an ImageFile, or str. if “b0”, “dti_fa_subject”, “subject_sls”, 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: “power_map”

AFQ.tasks.mapping.get_mapping_plan(kwargs, use_sls=False)