AFQ.tractography.gputractography#
Module Contents#
Functions#
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Perform GPU tractography on DWI data. |
Attributes#
- AFQ.tractography.gputractography.gpu_track(data, gtab, seed_img, stop_img, odf_model, seed_threshold, stop_threshold, thresholds_as_percentages, max_angle, step_size, n_seeds, random_seeds, rng_seed, ngpus, chunk_size)[source]#
Perform GPU tractography on DWI data.
- Parameters
- datandarray
DWI data.
- gtabGradientTable
The gradient table.
- seed_imgNifti1Image
Float or binary mask describing the ROI within which we seed for tracking.
- stop_imgNifti1Image
A float or binary mask that determines a stopping criterion (e.g. FA).
- odf_modelstr, optional
One of {“OPDT”, “CSA”}
- seed_thresholdfloat
The value of the seed_img above which tracking is seeded.
- stop_thresholdfloat
The value of the stop_img below which tracking is terminated.
- thresholds_as_percentagesbool
Interpret seed_threshold and stop_threshold as percentages of the total non-nan voxels in the seed and stop mask to include (between 0 and 100), instead of as a threshold on the values themselves.
- max_anglefloat
The maximum turning angle in each step.
- step_sizefloat
The size of a step (in mm) of tractography.
- n_seedsint
The seeding density: if this is an int, it is is how many seeds in each voxel on each dimension (for example, 2 => [2, 2, 2]). If this is a 2D array, these are the coordinates of the seeds. Unless random_seeds is set to True, in which case this is the total number of random seeds to generate within the mask. Default: 1
- random_seedsbool
If True, n_seeds is total number of random seeds to generate. If False, n_seeds encodes the density of seeds to generate.
- rng_seedint
random seed used to generate random seeds if random_seeds is set to True. Default: None ngpus : int Number of GPUs to use.
- chunk_sizeint
Chunk size for GPU tracking.
- Returns
- ——-