AFQ.tasks.tractography

Attributes

logger

Functions

_meta_from_tracking_params(tracking_params, ...[, ...])
_fiber_odf(data_imap, tissue_imap, tracking_params)
streamlines(structural_imap, data_imap, seed, ...)	full path to the complete, unsegmented tractography file
custom_tractography([import_tract])	full path to the complete, unsegmented tractography file
get_tractography_plan(kwargs)

Module Contents

AFQ.tasks.tractography.logger

AFQ.tasks.tractography._meta_from_tracking_params(tracking_params, start_time, seed, pve, n_streamlines=0)

AFQ.tasks.tractography._fiber_odf(data_imap, tissue_imap, tracking_params)

AFQ.tasks.tractography.streamlines(structural_imap, data_imap, seed, tissue_imap, citations, tracking_params)

full path to the complete, unsegmented tractography file

Parameters:

tracking_paramsdict, optional

The parameters for tracking. Defaults to using the default behavior of the aft.track function. Seed mask and seed threshold, if not specified, are replaced with scalar masks from scalar[0] thresholded to 0.2. The seed_mask items of this dict may be AFQ.definitions.image.ImageFile instances.

AFQ.tasks.tractography.custom_tractography(import_tract=None)

full path to the complete, unsegmented tractography file

Parameters:

import_tractdict or str or None, optional

BIDS filters for inputing a user made tractography file, or a path to the tractography file. If None, DIPY is used to generate the tractography. Default: None

AFQ.tasks.tractography.get_tractography_plan(kwargs)