`AFQ.tasks.tractography`#

Module Contents#

`export_seed_mask`(tracking_params)	full path to a nifti file containing the
`export_stop_mask`(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`(data_imap, seed, stop, tracking_params)	full path to the complete, unsegmented tractography file
`custom_tractography`(bids_info[, import_tract])	full path to the complete, unsegmented tractography file
`get_tractography_plan`(kwargs)

AFQ.tasks.tractography.export_seed_mask(tracking_params)[source]#: full path to a nifti file containing the tractography seed mask

AFQ.tasks.tractography.export_stop_mask(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(data_imap, seed, stop, 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.image.ImageFile instances. If tracker is set to “pft” then stop_mask should be an instance of AFQ.definitions.image.PFTImage.

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

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