AFQ.tasks.tractography

Module Contents

Functions

_meta_from_tracking_params(tracking_params, ...)
export_seed_mask(data_imap, tracking_params)	full path to a nifti file containing the
export_stop_mask(data_imap, 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([import_tract])	full path to the complete, unsegmented tractography file
gpu_tractography(data_imap, tracking_params, seed, stop)	full path to the complete, unsegmented tractography file
get_tractography_plan(kwargs)
_gen_seeds(n_seeds, params_file[, seed_mask, ...])

Attributes

has_ray
has_trx
has_gputrack
logger

AFQ.tasks.tractography.has_ray = True

AFQ.tasks.tractography.has_trx = True

AFQ.tasks.tractography.has_gputrack = True

AFQ.tasks.tractography.logger

AFQ.tasks.tractography._meta_from_tracking_params(tracking_params, start_time, n_streamlines, seed, stop)

AFQ.tasks.tractography.export_seed_mask(data_imap, tracking_params)

full path to a nifti file containing the tractography seed mask

AFQ.tasks.tractography.export_stop_mask(data_imap, tracking_params)

full path to a nifti file containing the tractography stop mask

AFQ.tasks.tractography.export_stop_mask_pft(pve_wm, pve_gm, pve_csf)

full path to a nifti file containing the tractography stop mask

AFQ.tasks.tractography.streamlines(data_imap, seed, stop, tracking_params)

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(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.gpu_tractography(data_imap, tracking_params, seed, stop, tractography_ngpus=0, chunk_size=100000)

full path to the complete, unsegmented tractography file

Parameters

tractography_ngpusint, optional

Number of GPUs to use in tractography. If non-0, this algorithm is used for tractography, dipy/GPUStreamlines Default: 0

chunk_sizeint, optional

Chunk size for GPU tracking. Default: 100000

AFQ.tasks.tractography.get_tractography_plan(kwargs)

AFQ.tasks.tractography._gen_seeds(n_seeds, params_file, seed_mask=None, seed_threshold=0, thresholds_as_percentages=False, random_seeds=False, rng_seed=None)