AFQ.tasks.mapping#

Module Contents#

Functions#

export_registered_b0(data_imap, mapping)

full path to a nifti file containing

template_xform(dwi_affine, mapping, data_imap)

full path to a nifti file containing

export_rois(base_fname, results_dir, data_imap, mapping, dwi_affine)

dictionary of full paths to Nifti1Image files of ROIs

mapping(base_fname, dwi, reg_subject, data_imap, bids_info, mapping_definition=None)

mapping from subject to template space.

sls_mapping(base_fname, dwi, reg_subject, data_imap, bids_info, tractography_imap, mapping_definition=None)

mapping from subject to template space.

get_reg_subject(data_imap, bids_info, base_fname, dwi, reg_subject_spec='power_map')

Nifti1Image which represents this subject

get_mapping_plan(kwargs, use_sls=False)

Attributes#

logger

AFQ.tasks.mapping.logger[source]#
AFQ.tasks.mapping.export_registered_b0(data_imap, mapping)[source]#

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

AFQ.tasks.mapping.template_xform(dwi_affine, mapping, data_imap)[source]#

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

AFQ.tasks.mapping.export_rois(base_fname, results_dir, data_imap, mapping, dwi_affine)[source]#

dictionary of full paths to Nifti1Image files of ROIs transformed to subject space

AFQ.tasks.mapping.mapping(base_fname, dwi, reg_subject, data_imap, bids_info, 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, reg_subject, data_imap, bids_info, tractography_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.get_reg_subject(data_imap, bids_info, base_fname, dwi, reg_subject_spec='power_map')[source]#

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)[source]#