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pyafq_tractometry.json
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pyafq_tractometry.json
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{
"description": "Use pyAFQ to perform the full Tractometry pipeline",
"space": "T1w",
"name": "pyafq_tractometry",
"atlases": [],
"nodes": [
{
"name": "pyafq_tractometry",
"software": "pyAFQ",
"action": "pyafq_tractometry",
"input": "qsiprep",
"output_suffix": "PYAFQ_TRACTOMETRY",
"parameters": {
"use_external_tracking": false,
"export": "all",
"directions": "prob",
"max_angle": 30.0,
"sphere": "",
"seed_mask": "",
"seed_threshold": 0,
"n_seeds": 1,
"random_seeds": false,
"rng_seed": "",
"stop_mask": "",
"stop_threshold": 0,
"step_size": 0.5,
"min_length": 50,
"max_length": 250,
"odf_model": "CSD",
"tracker": "local",
"nb_points": false,
"nb_streamlines": false,
"seg_algo": "AFQ",
"reg_algo": "",
"clip_edges": false,
"parallel_segmentation": "{'n_jobs': -1, 'engine': 'joblib', 'backend': 'loky'}",
"progressive": true,
"greater_than": 50,
"rm_small_clusters": 50,
"model_clust_thr": 1.25,
"reduction_thr": 25,
"refine": false,
"pruning_thr": 12,
"b0_threshold": 50,
"prob_threshold": 0,
"roi_dist_tie_break": false,
"dist_to_waypoint": "",
"rng": "",
"return_idx": false,
"presegment_bundle_dict": "",
"presegment_kwargs": "{}",
"filter_by_endpoints": true,
"dist_to_atlas": 4,
"save_intermediates": "",
"n_points": 100,
"clean_rounds": 5,
"distance_threshold": 3,
"length_threshold": 4,
"min_sl": 20,
"stat": "mean",
"min_bval": "",
"max_bval": "",
"filter_b": true,
"robust_tensor_fitting": false,
"csd_response": "",
"csd_sh_order": "",
"csd_lambda_": 1,
"csd_tau": 0.1,
"gtol": 0.01,
"brain_mask_definition": "",
"bundle_info": "",
"reg_template_spec": "mni_T1",
"mapping_definition": "",
"reg_subject_spec": "power_map",
"profile_weights": "gauss",
"scalars": "['dti_fa', 'dti_md']",
"import_tract": "",
"sbv_lims_bundles": "[None, None]",
"volume_opacity_bundles": 0.3,
"n_points_bundles": 40,
"sbv_lims_indiv": "[None, None]",
"volume_opacity_indiv": 0.3,
"n_points_indiv": 40,
"viz_backend_spec": "plotly_no_gif",
"virtual_frame_buffer": false
}
}
]
}