utilities package#

Subpackages#

Submodules#

utilities.wm_assess_cluster_location module#

utilities.wm_assess_cluster_location.main()#

utilities.wm_compute_FA_from_DWIs module#

utilities.wm_compute_FA_from_DWIs.list_nhdr_files(input_dir)#

utilities.wm_compute_FA_from_DWIs.main()#

utilities.wm_compute_TAP module#

utilities.wm_compute_TAP.main()#

utilities.wm_compute_bundle_feature_population_math module#

Compute bundle feature population math: computes the - difference - stats - sum

for each bundle feature across participants according to the values contained in the provided CSV files.

For the difference case, the first CSV file given is taken as the reference; for the sum case, only the streamline count addition is performed.

class utilities.wm_compute_bundle_feature_population_math.BundlePopulationMathOperation(value)#

Bases: Enum

An enumeration.

DIFFERENCE = 'difference'#

STATS = 'stats'#

SUM = 'sum'#

class utilities.wm_compute_bundle_feature_population_math.WMABundleFeatureDataMap(value)#

Bases: Enum

An enumeration.

BundleName = ('Name', <class 'str'>)#

ClusterIdxMean = ('cluster_idx.Mean', <class 'float'>)#

EstimatedUncertaintyMean = ('EstimatedUncertainty.Mean', <class 'float'>)#

FA1Mean = ('FA1.Mean', <class 'float'>)#

FA2Mean = ('FA2.Mean', <class 'float'>)#

FWMean = ('FreeWater.Mean', <class 'float'>)#

HemisphereLocationMean = ('HemisphereLocation.Mean', <class 'float'>)#

MeanLength = ('Mean_Length', <class 'float'>)#

PointCount = ('Num_Points', <class 'int'>)#

StreamlineCount = ('Num_Fibers', <class 'int'>)#

Trace1Mean = ('trace1.Mean', <class 'float'>)#

Trace2Mean = ('trace2.Mean', <class 'str'>)#

static get_name(name)#

static get_type(name)#

static get_type_map()#

utilities.wm_compute_bundle_feature_population_math.cast_feature_data(df)#

utilities.wm_compute_bundle_feature_population_math.clean_up_feature_data(df)#

utilities.wm_compute_bundle_feature_population_math.compute_bundle_population_feature_diff(df_list)#

utilities.wm_compute_bundle_feature_population_math.compute_bundle_population_feature_diff_relative(df_diff, def_ref)#

utilities.wm_compute_bundle_feature_population_math.compute_bundle_population_feature_stats(df_list)#

utilities.wm_compute_bundle_feature_population_math.compute_bundle_population_feature_sum(df_list)#

utilities.wm_compute_bundle_feature_population_math.main()#

utilities.wm_compute_bundle_feature_population_math.perform_bundle_population_operation(operation, df_list)#

utilities.wm_compute_bundle_feature_population_math.process_feature_data(df)#

utilities.wm_extract_cluster module#

utilities.wm_extract_cluster.main()#

utilities.wm_extract_clusters_by_endpoints module#

utilities.wm_extract_clusters_by_endpoints.main()#

utilities.wm_fix_UKF_trace module#

utilities.wm_fix_UKF_trace.fix_trace(inpd)#

utilities.wm_fix_UKF_trace.list_files(input_dir, regstr)#

utilities.wm_fix_UKF_trace.main()#

utilities.wm_fix_hemisphere_loc_name_in_tractogram module#

Fix hemisphere location property name in tractogram: older versions of WMA contain a typo in the hemisphere location VTK array scalar property. Change HemisphereLocataion to HemisphereLocation.

utilities.wm_fix_hemisphere_loc_name_in_tractogram.fix_hemisphere_location_property_name(polydata)#

utilities.wm_fix_hemisphere_loc_name_in_tractogram.main()#

utilities.wm_flatten_length_distribution module#

utilities.wm_flatten_length_distribution.main()#

utilities.wm_laterality_all module#

utilities.wm_laterality_all.main()#

utilities.wm_measure_all_clusters module#

utilities.wm_measure_all_clusters.main()#

utilities.wm_measure_endpoint_overlap module#

utilities.wm_measure_endpoint_overlap.main()#

utilities.wm_query_atlas_bundles_names module#

Query the atlas bundle names.

e.g. python wm_query_atlas_bundles.py /mnt/data/atlas/ORG-Atlas-1.4/ORG-800FC-100HCP/ /mnt/data/atlas/ORG-Atlas-1.4/bundle_names_default.txt DEFAULT

python wm_query_atlas_bundles.py /mnt/data/atlas/ORG-Atlas-1.4/ORG-800FC-100HCP-separated/AnatomicalTracts/ /mnt/data/atlas/ORG-Atlas-1.4/bundle_names_separated.txt SEPARATED

utilities.wm_query_atlas_bundles_names.main()#

utilities.wm_statistics module#

utilities.wm_statistics.main()#

utilities.wm_statistics_export_data module#

utilities.wm_statistics_export_data.main()#

utilities.wm_transform_polydata module#

utilities.wm_transform_polydata.main()#