User Guide

• Getting started with pyAFQ
  • Tutorials: getting started with the pyAFQ Python library
• How To
  • How to install pyAFQ
    • How to install the release version
    • How to install the development version
    • How to install using Docker
    • How to build an Apptainer (Singularity) image
  • How to get help using pyAFQ
  • How to cite our work
  • Organizing your data
    • Example data
    • Preprocessing
  • Re-running pyAFQ
    • Method Parameters
    • Examples
  • How to add custom tissue properties from another pipeline
  • Tractography from other pipelines
  • Matlab AFQ to Python AFQ conversion
  • The pyAFQ docker image
  • The pyAFQ singularity image
  • The pyAFQ Image API
  • Tractography Parameters
    • Example Usage
    • Tractography Parameter Reference
  • Segmentation Parameters
    • Example Usage
    • Segmentation Parameter Reference
  • Cleaning Parameters
    • Example Usage
    • Cleaning Parameter Reference
  • How to examples
• Explanations
  • Automated Fiber Quantification
    • AFQ Tractometry Pipeline
    • Bundle Orientation
    • Modeling White Matter
    • Profiling
    • Bundle Recognition
    • Tractography
• Reference Documentation
  • API Reference
    • AFQ
      • Subpackages
        • AFQ.api
          • Submodules
            • AFQ.api.bundle_dict
              • Module Contents
                • Classes
                • Functions
                  • default18_bd()
                  • baby_bd()
                  • callosal_bd()
                  • reco_bd()
                  • cerebellar_bd()
                  • BundleDict
                    • BundleDict.__print__()
                    • BundleDict.update_max_includes()
                    • BundleDict._use_bids_info()
                    • BundleDict._cond_load()
                    • BundleDict.get_b_info()
                    • BundleDict.__getitem__()
                    • BundleDict.__setitem__()
                    • BundleDict.__len__()
                    • BundleDict.__delitem__()
                    • BundleDict.__iter__()
                    • BundleDict.copy()
                    • BundleDict.apply_to_rois()
                    • BundleDict._cond_load_bundle()
                    • BundleDict.is_bundle_in_template()
                    • BundleDict._roi_transform_helper()
                    • BundleDict.transform_rois()
                    • BundleDict.__add__()
            • AFQ.api.group
              • Module Contents
                • Classes
                  • GroupAFQ
                    • GroupAFQ.clobber
                    • GroupAFQ.combine_profiles()
                    • GroupAFQ.get_streamlines_json()
                    • GroupAFQ.export()
                    • GroupAFQ.export_up_to()
                    • GroupAFQ.export_all()
                    • GroupAFQ.cmd_outputs()
                    • GroupAFQ.make_all_participant_montages()
                    • GroupAFQ.group_montage()
                    • GroupAFQ.combine_bundle()
                    • GroupAFQ.upload_to_s3()
                    • GroupAFQ.export_group_density()
                    • GroupAFQ.assemble_AFQ_browser()
            • AFQ.api.participant
              • Module Contents
                • Classes
                  • ParticipantAFQ
                    • ParticipantAFQ.clobber
                    • ParticipantAFQ.make_workflow()
                    • ParticipantAFQ.export()
                    • ParticipantAFQ.export_up_to()
                    • ParticipantAFQ.export_all()
                    • ParticipantAFQ.participant_montage()
                    • ParticipantAFQ.cmd_outputs()
            • AFQ.api.utils
              • Module Contents
                • methods_descriptors
                • kwargs_descriptors
                • AFQclass_doc
                • AFQclass_doc
        • AFQ.data
          • Submodules
            • AFQ.data.fetch
              • Module Contents
                • Functions
                • Attributes
                  • fetch_callosum_templates
                  • read_callosum_templates()
                  • fetch_templates
                  • read_templates()
                  • fetch_or_templates
                  • read_or_templates()
                  • fetch_stanford_hardi_tractography
                  • read_stanford_hardi_tractography()
                  • organize_stanford_data()
                  • fetch_stanford_hardi_lv1
            • AFQ.data.utils
              • Module Contents
                • Functions
                • Attributes
                  • BUNDLE_RECO_2_AFQ
                  • BUNDLE_MAT_2_PYTHON
                  • aws_import_msg_error()
        • AFQ.definitions
          • Submodules
            • AFQ.definitions.image
              • Module Contents
                • Classes
                  • ImageFile
                    • ImageFile.find_path()
                    • ImageFile.get_path_data_affine()
                    • ImageFile.apply_conditions()
                    • ImageFile.get_name()
                    • ImageFile.get_image_getter()
                  • FullImage
                    • FullImage.get_name()
                    • FullImage.get_image_getter()
                  • RoiImage
                    • RoiImage.get_name()
                    • RoiImage.get_image_getter()
                  • GQImage
                    • GQImage.get_name()
                    • GQImage.get_image_getter()
                  • B0Image
                    • B0Image.get_name()
                    • B0Image.get_image_getter()
                  • LabelledImageFile
                    • LabelledImageFile.apply_conditions()
                  • ThresholdedImageFile
                    • ThresholdedImageFile.apply_conditions()
                  • ScalarImage
                    • ScalarImage.get_name()
                    • ScalarImage.get_image_getter()
                  • ThresholdedScalarImage
                  • TemplateImage
                    • TemplateImage.get_name()
                    • TemplateImage.get_image_getter()
            • AFQ.definitions.mapping
              • Module Contents
                • Classes
                  • FnirtMap
                    • FnirtMap.find_path()
                    • FnirtMap.get_for_subses()
                  • IdentityMap
                    • IdentityMap.get_for_subses()
                  • SynMap
                    • SynMap.gen_mapping()
                  • SlrMap
                    • SlrMap.gen_mapping()
                  • AffMap
                    • AffMap.gen_mapping()
            • AFQ.definitions.utils
              • Module Contents
                • Classes
                • Functions
                  • Definition
                    • Definition.find_path()
                    • Definition.str_for_toml()
                  • name_from_path()
                  • find_file()
        • AFQ.models
          • Submodules
            • AFQ.models.QBallTP
              • Module Contents
                • Functions
                  • extract_odf()
                  • anisotropic_index()
            • AFQ.models.csd
              • Module Contents
                • Functions
                  • fit_csd()
            • AFQ.models.dki
              • Module Contents
                • Functions
                  • fit_dki()
                  • predict()
            • AFQ.models.dti
              • Module Contents
                • Functions
                  • fit_dti()
                  • predict()
            • AFQ.models.fwdti
              • Module Contents
                • Functions
                  • fit_fwdti()
        • AFQ.recognition
          • Submodules
            • AFQ.recognition.cleaning
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • clean_by_orientation()
                  • clean_bundle()
            • AFQ.recognition.criteria
              • Module Contents
                • Functions
                • Attributes
                  • bundle_criterion_order
                  • valid_noncriterion
                  • logger
                  • prob_map()
                  • cross_midline()
                  • start()
                  • end()
                  • length()
                  • primary_axis()
                  • include()
                  • curvature()
                  • exclude()
                  • recobundles()
                  • qb_thresh()
                  • clean_by_other_bundle()
                  • mahalanobis()
                  • run_bundle_rec_plan()
            • AFQ.recognition.curvature
              • Module Contents
                • Functions
                  • sl_curve()
                  • sl_curve_dist()
            • AFQ.recognition.other_bundles
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • clean_by_other_density_map()
                  • clean_relative_to_other_core()
            • AFQ.recognition.preprocess
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • tolerance_mm_to_vox()
                  • fgarray()
                  • crosses()
                  • get_preproc_plan()
            • AFQ.recognition.recognize
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • recognize()
                  • _return_empty()
                  • _add_bundle_to_fiber_group()
                  • _add_bundle_to_meta()
            • AFQ.recognition.roi
              • Module Contents
                • Functions
                  • _interp3d()
                  • check_sls_with_inclusion()
                  • check_sl_with_inclusion()
                  • check_sl_with_exclusion()
                  • clean_by_endpoints()
            • AFQ.recognition.utils
              • Module Contents
                • Classes
                • Functions
                • Attributes
                  • logger
                  • flip_sls()
                  • cut_sls_by_closest()
                  • read_tg()
                  • orient_by_streamline()
                  • move_streamlines()
                  • resample_tg()
                  • SlsBeingRecognized
                    • SlsBeingRecognized.initiate_selection()
                    • SlsBeingRecognized.select()
                    • SlsBeingRecognized.get_selected_sls()
                    • SlsBeingRecognized.reorient()
                    • SlsBeingRecognized.__bool__()
                    • SlsBeingRecognized.__len__()
        • AFQ.tasks
          • Submodules
            • AFQ.tasks.data
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • DIPY_GH
                  • get_data_gtab()
                  • b0()
                  • b0_mask()
                  • dti_fit()
                  • dti_params()
                  • fwdti_fit()
                  • fwdti_params()
                  • dki_fit()
                  • dki_params()
                  • msdki_fit()
                  • msdki_params()
                  • msdki_msd()
                  • msdki_msk()
                  • csd_params()
                  • anisotropic_power_map()
                  • csd_anisotropic_index()
                  • gq()
                  • gq_pmap()
                  • gq_ai()
                  • rumba_model()
                  • rumba_params()
                  • rumba_fit()
                  • rumba_f_csf()
                  • rumba_f_gm()
                  • rumba_f_wm()
                  • opdt_params()
                  • opdt_pmap()
                  • opdt_ai()
                  • csa_params()
                  • csa_pmap()
                  • csa_ai()
                  • fwdti_fa()
                  • fwdti_md()
                  • fwdti_fwf()
                  • dti_fa()
                  • dti_lt()
                  • dti_cfa()
                  • dti_pdd()
                  • dti_md()
                  • dti_ga()
                  • dti_rd()
                  • dti_ad()
                  • dki_kt()
                  • dki_lt()
                  • dki_fa()
                  • dki_md()
                  • dki_awf()
                  • dki_mk()
                  • dki_kfa()
                  • dki_ga()
                  • dki_rd()
                  • dki_ad()
                  • dki_rk()
                  • dki_ak()
                  • brain_mask()
                  • get_bundle_dict()
                  • get_data_plan()
            • AFQ.tasks.decorators
              • Module Contents
                • Functions
                  • as_file()
                  • as_fit_deriv()
                  • as_img()
            • AFQ.tasks.mapping
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • export_registered_b0()
                  • template_xform()
                  • export_rois()
                  • mapping()
                  • sls_mapping()
                  • get_reg_subject()
                  • get_mapping_plan()
            • AFQ.tasks.segmentation
              • Module Contents
                • Functions
                • Attributes
                  • has_trx
                  • logger
                  • segment()
                  • export_bundles()
                  • export_sl_counts()
                  • export_bundle_lengths()
                  • export_density_maps()
                  • tract_profiles()
                  • get_scalar_dict()
                  • get_segmentation_plan()
            • AFQ.tasks.tractography
              • Module Contents
                • Functions
                • Attributes
                  • has_ray
                  • has_gputrack
                  • logger
                  • _meta_from_tracking_params()
                  • export_seed_mask()
                  • export_seed_mask_thresholded()
                  • export_stop_mask()
                  • export_stop_mask_thresholded()
                  • export_stop_mask_pft()
                  • streamlines()
                  • fiber_odf()
                  • custom_tractography()
                  • gpu_tractography()
                  • get_tractography_plan()
            • AFQ.tasks.utils
              • Module Contents
                • Functions
                  • get_base_fname()
                  • get_fname()
                  • with_name()
            • AFQ.tasks.viz
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • _viz_prepare_vol()
                  • viz_bundles()
                  • viz_indivBundle()
                  • plot_tract_profiles()
                  • init_viz_backend()
                  • get_viz_plan()
        • AFQ.tractography
          • Submodules
            • AFQ.tractography.gputractography
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • gpu_track()
            • AFQ.tractography.tractography
              • Module Contents
                • Functions
                  • track()
                  • _tracking()
            • AFQ.tractography.utils
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • get_percentile_threshold()
                  • gen_seeds()
        • AFQ.utils
          • Submodules
            • AFQ.utils.bin
              • Module Contents
                • Functions
                • Attributes
                  • model_input_parser()
                  • model_predict_input_parser()
                  • toml_to_val()
                  • val_to_toml()
                  • dict_to_toml()
                  • qsi_prep_ignore_params
                  • dict_to_json()
                  • func_dict_to_arg_dict()
                  • parse_config_run_afq()
                  • generate_config()
                  • generate_json()
            • AFQ.utils.docs
              • Module Contents
                • Classes
                  • PNGScraper
                    • PNGScraper.__repr__()
                    • PNGScraper.__call__()
                  • GIFScraper
                    • GIFScraper.__repr__()
                    • GIFScraper.__call__()
            • AFQ.utils.docstring_parser
              • Module Contents
                • Functions
                  • parse_numpy_docstring()
            • AFQ.utils.models
              • Module Contents
                • Functions
                  • prepare_data()
            • AFQ.utils.path
              • Module Contents
                • Functions
                  • write_json()
                  • read_json()
                  • drop_extension()
                  • space_from_fname()
                  • apply_cmd_to_afq_derivs()
            • AFQ.utils.stats
              • Module Contents
                • Functions
                  • contrast_index()
            • AFQ.utils.streamlines
              • Module Contents
                • Classes
                • Functions
                • Attributes
                  • has_trx
                  • SegmentedSFT
                    • SegmentedSFT.get_sft_and_sidecar()
                    • SegmentedSFT.get_bundle()
                    • SegmentedSFT.get_bundle_param_info()
                    • SegmentedSFT.fromfile()
                  • split_streamline()
            • AFQ.utils.volume
              • Module Contents
                • Functions
                • Attributes
                  • logger
                  • transform_inverse_roi()
                  • patch_up_roi()
                  • density_map()
                  • dice_coeff()
        • AFQ.viz
          • Submodules
            • AFQ.viz.altair
              • Module Contents
                • Functions
                  • altair_color_dict()
                  • combined_profiles_df_to_altair_df()
                  • altair_df_to_chart()
            • AFQ.viz.fury_backend
              • Module Contents
                • Functions
                • Attributes
                  • viz_logger
                  • _inline_interact()
                  • visualize_bundles()
                  • scene_rotate_forward()
                  • create_gif()
                  • visualize_roi()
                  • visualize_volume()
                  • _draw_core()
                  • single_bundle_viz()
            • AFQ.viz.plot
              • Module Contents
                • Functions
                  • visualize_tract_profiles()
                  • visualize_gif_inline()
            • AFQ.viz.plotly_backend
              • Module Contents
                • Classes
                • Functions
                • Attributes
                  • scope
                  • viz_logger
                  • _inline_interact()
                  • _to_color_range()
                  • _color_arr2str()
                  • set_layout()
                  • _draw_streamlines()
                  • _plot_profiles()
                  • visualize_bundles()
                  • create_gif()
                  • _draw_roi()
                  • visualize_roi()
                  • Axes
                    • Axes.X
                    • Axes.Y
                    • Axes.Z
                  • _draw_slice()
                  • _name_from_enum()
                  • visualize_volume()
                  • _draw_core()
                  • single_bundle_viz()
            • AFQ.viz.utils
              • Module Contents
                • Classes
                  • Viz
      • Submodules
        • AFQ.registration
          • Module Contents
            • Functions
              • syn_register_dwi()
              • write_mapping()
              • read_mapping()
              • slr_registration()
      • Package Contents
        • _ga_id
  • Defining Custom Bundle Dictionaries
  • Major Fiber Tracts
  • Tissue Properties in pyAFQ
    • DTI Model Parameters
    • Free-water DTI (FWDTI) Parameters
    • DKI Model Parameters
    • Mean Signal DKI (MSDKI) Parameters
    • CSD Model Parameters
    • GQ (Generalized Q-Sampling) Parameters
    • OPDT (Orientation Probability Density Transform) Parameters
    • CSA (Constant Solid Angle) Parameters
    • RUMBA Model Parameters
  • The pyAFQ API methods
  • Visualization Backends
  • Fury Dockerfile for Cloudknot
  • The pyAFQ Mapping API
  • The pyAFQ configuration file