scilpy
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Scilpy
Modules
Scripts
scil_NODDI_maps.py
scil_NODDI_priors.py
scil_aodf_metrics.py
scil_bids_validate.py
scil_bingham_metrics.py
scil_btensor_metrics.py
scil_bundle_clean_qbx_clusters.py
scil_bundle_diameter.py
scil_bundle_filter_by_occurence.py
scil_bundle_generate_priors.py
scil_bundle_mean_fixel_afd.py
scil_bundle_mean_fixel_afd_from_hdf5.py
scil_bundle_mean_fixel_bingham_metric.py
scil_bundle_mean_std.py
scil_bundle_score_same_bundle_many_segmentations.py
scil_bundle_volume_per_label.py
scil_connectivity_compare_populations.py
scil_connectivity_compute_matrices.py
scil_connectivity_compute_pca.py
scil_connectivity_filter.py
scil_connectivity_graph_measures.py
scil_connectivity_hdf5_average_density_map.py
scil_connectivity_math.py
scil_connectivity_normalize.py
scil_connectivity_pairwise_agreement.py
scil_connectivity_print_filenames.py
scil_connectivity_reorder_rois.py
scil_denoising_nlmeans.py
scil_dki_metrics.py
scil_dti_convert_tensors.py
scil_dti_metrics.py
scil_dwi_apply_bias_field.py
scil_dwi_compute_snr.py
scil_dwi_concatenate.py
scil_dwi_convert_FDF.py
scil_dwi_detect_volume_outliers.py
scil_dwi_extract_b0.py
scil_dwi_extract_shell.py
scil_dwi_powder_average.py
scil_dwi_prepare_eddy_command.py
scil_dwi_prepare_topup_command.py
scil_dwi_reorder_philips.py
scil_dwi_split_by_indices.py
scil_dwi_to_sh.py
scil_fodf_max_in_ventricles.py
scil_fodf_memsmt.py
scil_fodf_metrics.py
scil_fodf_msmt.py
scil_fodf_ssst.py
scil_fodf_to_bingham.py
scil_freewater_maps.py
scil_freewater_priors.py
scil_frf_mean.py
scil_frf_memsmt.py
scil_frf_msmt.py
scil_frf_set_diffusivities.py
scil_frf_ssst.py
scil_get_version.py
scil_gradients_apply_transform.py
scil_gradients_convert.py
scil_gradients_generate_sampling.py
scil_gradients_modify_axes.py
scil_gradients_round_bvals.py
scil_gradients_validate_correct.py
scil_gradients_validate_correct_eddy.py
scil_header_print_info.py
scil_header_validate_compatibility.py
scil_json_convert_entries_to_xlsx.py
scil_json_harmonize_entries.py
scil_json_merge_entries.py
scil_labels_combine.py
scil_labels_dilate.py
scil_labels_remove.py
scil_labels_split_volume_by_ids.py
scil_labels_split_volume_from_lut.py
scil_lesions_info.py
scil_mti_adjust_B1_header.py
scil_mti_maps_MT.py
scil_mti_maps_ihMT.py
scil_plot_stats_per_point.py
scil_qball_metrics.py
scil_rgb_convert.py
scil_search_keywords.py
scil_sh_convert.py
scil_sh_fusion.py
scil_sh_to_aodf.py
scil_sh_to_rish.py
scil_sh_to_sf.py
scil_stats_group_comparison.py
scil_surface_apply_transform.py
scil_surface_convert.py
scil_surface_flip.py
scil_surface_smooth.py
scil_tracking_local.py
scil_tracking_local_dev.py
scil_tracking_pft.py
scil_tracking_pft_maps.py
scil_tracking_pft_maps_edit.py
scil_tractogram_apply_transform.py
scil_tractogram_apply_transform_to_hdf5.py
scil_tractogram_assign_custom_color.py
scil_tractogram_assign_uniform_color.py
scil_tractogram_commit.py
scil_tractogram_compress.py
scil_tractogram_compute_TODI.py
scil_tractogram_compute_density_map.py
scil_tractogram_convert.py
scil_tractogram_convert_hdf5_to_trk.py
scil_tractogram_count_streamlines.py
scil_tractogram_detect_loops.py
scil_tractogram_dpp_math.py
scil_tractogram_filter_by_anatomy.py
scil_tractogram_filter_by_length.py
scil_tractogram_filter_by_orientation.py
scil_tractogram_filter_by_roi.py
scil_tractogram_fix_trk.py
scil_tractogram_flip.py
scil_tractogram_math.py
scil_tractogram_pairwise_comparison.py
scil_tractogram_print_info.py
scil_tractogram_project_map_to_streamlines.py
scil_tractogram_project_streamlines_to_map.py
scil_tractogram_qbx.py
scil_tractogram_register.py
scil_tractogram_remove_invalid.py
scil_tractogram_resample.py
scil_tractogram_resample_nb_points.py
scil_tractogram_seed_density_map.py
scil_tractogram_segment_bundles.py
scil_tractogram_segment_one_bundle.py
scil_tractogram_shuffle.py
scil_tractogram_smooth.py
scil_tractogram_split.py
scil_viz_bingham_fit.py
scil_viz_bundle.py
scil_viz_bundle_screenshot_mni.py
scil_viz_bundle_screenshot_mosaic.py
scil_viz_connectivity.py
scil_viz_dti_screenshot.py
scil_viz_fodf.py
scil_viz_gradients_screenshot.py
scil_viz_tractogram_seeds.py
scil_viz_tractogram_seeds_3d.py
scil_viz_volume_histogram.py
scil_viz_volume_scatterplot.py
scil_viz_volume_screenshot.py
scil_viz_volume_screenshot_mosaic.py
scil_volume_apply_transform.py
scil_volume_b0_synthesis.py
scil_volume_count_non_zero_voxels.py
scil_volume_crop.py
scil_volume_flip.py
scil_volume_math.py
scil_volume_remove_outliers_ransac.py
scil_volume_resample.py
scil_volume_reshape_to_reference.py
scil_volume_stats_in_ROI.py
scil_volume_stats_in_labels.py
Documentation
Instructions for tensor-valued dMRI scripts (b-tensor)
Instructions for estimation of bundle diameter
Instructions to write the tsv files “participants.tsv” for the script scil_group_comparison.py
Create overlapping slice mosaics
Using development containers with Visual Studio Code
Instructions for streamlines registration/transformation
scilpy
Scripts
scil_freewater_priors.py
Edit on GitHub
scil_freewater_priors.py
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