AFQ.tasks.tractography

Module Contents

Functions

export_seed_mask(subses_dict, dwi_affine, tracking_params)

full path to a nifti file containing the

export_stop_mask(subses_dict, dwi_affine, tracking_params)

full path to a nifti file containing the

export_stop_mask_pft(pve_wm, pve_gm, pve_csf)

full path to a nifti file containing the

streamlines(subses_dict, data_imap, seed_file, stop_file, tracking_params)

full path to the complete, unsegmented tractography file

custom_tractography(bids_info, import_tract=None)

full path to the complete, unsegmented tractography file

get_tractography_plan(kwargs)

Attributes

logger

AFQ.tasks.tractography.logger[source]
AFQ.tasks.tractography.export_seed_mask(subses_dict, dwi_affine, tracking_params)[source]

full path to a nifti file containing the tractography seed mask

AFQ.tasks.tractography.export_stop_mask(subses_dict, dwi_affine, tracking_params)[source]

full path to a nifti file containing the tractography stop mask

AFQ.tasks.tractography.export_stop_mask_pft(pve_wm, pve_gm, pve_csf)[source]

full path to a nifti file containing the tractography stop mask

AFQ.tasks.tractography.streamlines(subses_dict, data_imap, seed_file, stop_file, tracking_params)[source]

full path to the complete, unsegmented tractography file

Parameters
tracking_paramsdict, optional

The parameters for tracking. Default: use 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 and stop_mask items of this dict may be AFQ.definitions.mask.MaskFile instances. If tracker is set to “pft” then stop_mask should be an instance of AFQ.definitions.mask.PFTMask.

AFQ.tasks.tractography.custom_tractography(bids_info, import_tract=None)[source]

full path to the complete, unsegmented tractography file

Parameters
import_tractdict, optional

BIDS filters for inputing a user made tractography file. If None, tractography will be performed automatically. Default: None

AFQ.tasks.tractography.get_tractography_plan(kwargs)[source]