`AFQ.tasks.tractography`¶

Module Contents¶

`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)

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.segmentation

AFQ.tasks.utils