fitlins package

Subpackages

• fitlins.cli package
  • Submodules
    • fitlins.cli.run module
      • fMRI model-fitting
      • INIT_MSG()
      • default_path()
      • get_parser()
      • main()
      • run_fitlins()
  • Module contents
• fitlins.interfaces package
  • Submodules
    • fitlins.interfaces.abstract module
      • DesignMatrixInputSpec
      • DesignMatrixInterface
      • DesignMatrixOutputSpec
      • EstimatorOutputSpec
      • FirstLevelEstimatorInputSpec
      • FirstLevelEstimatorInterface
      • SecondLevelEstimatorInputSpec
      • SecondLevelEstimatorInterface
      • SecondLevelEstimatorOutputSpec
    • fitlins.interfaces.afni module
      • FirstLevelModel
      • Pval
      • PvalInputSpec
      • create_glt_test_info()
      • extract_volume()
      • get_afni_design_matrix()
      • get_afni_intent_info()
      • get_afni_intent_info_for_subvol()
      • get_glt_rows()
      • load_bucket_by_prefix()
      • parse_afni_ext()
      • set_intents()
    • fitlins.interfaces.bids module
      • BIDSDataSink
      • BIDSDataSinkInputSpec
      • BIDSDataSinkOutputSpec
      • BIDSSelect
      • BIDSSelectInputSpec
      • BIDSSelectOutputSpec
      • LoadBIDSModel
      • LoadBIDSModelInputSpec
      • LoadBIDSModelOutputSpec
      • ModelSpecLoader
      • ModelSpecLoaderInputSpec
      • ModelSpecLoaderOutputSpec
      • bids_split_filename()
    • fitlins.interfaces.nistats module
      • DesignMatrix
      • FirstLevelModel
      • NistatsBaseInterface
      • SecondLevelModel
      • dscalar_from_cifti()
      • prepare_contrasts()
    • fitlins.interfaces.pymare_extension module
      • pymare_model
      • remove_zero_var_voxels_()
    • fitlins.interfaces.utils module
      • CollateWithMetadata
      • CollateWithMetadataInputSpec
      • CollateWithMetadataOutputSpec
      • MergeAll
    • fitlins.interfaces.visualizations module
      • ContrastMatrixPlot
      • ContrastMatrixPlotInputSpec
      • DesignCorrelationPlot
      • DesignCorrelationPlotInputSpec
      • DesignPlot
      • GlassBrainPlot
      • GlassBrainPlotInputSpec
      • Visualization
      • VisualizationInputSpec
      • VisualizationOutputSpec
      • decompose_dscalar()
      • plot_dscalar()
  • Module contents
• fitlins.tests package
  • Submodules
    • fitlins.tests.conftest module
      • pytest_addoption()
      • pytest_generate_tests()
    • fitlins.tests.test_outputs module
      • get_json_diff()
      • get_nan_diff()
      • test_get_nan_diff()
      • test_outputs()
  • Module contents
• fitlins.utils package
  • Submodules
    • fitlins.utils.bids module
      • Utilities to handle BIDS inputs
      • BIDSError
      • BIDSWarning
      • collect_participants()
      • load_all_specs()
      • write_derivative_description()
    • fitlins.utils.collections module
      • dict_intersection()
    • fitlins.utils.config module
      • get_fitlins_config()
    • fitlins.utils.strings module
      • snake_to_camel()
      • to_alphanum()
  • Module contents
• fitlins.viz package
  • Submodules
    • fitlins.viz.contrasts module
      • plot_contrast_matrix()
    • fitlins.viz.corr module
      • plot_corr_matrix()
    • fitlins.viz.reports module
      • build_report_dict()
      • deroot()
      • displayify()
      • write_full_report()
  • Module contents
    • plot_and_save()
• fitlins.workflows package
  • Subpackages
    • fitlins.workflows.tests package
      • Submodules
      • Module contents
  • Submodules
    • fitlins.workflows.base module
      • init_fitlins_wf()
  • Module contents

Submodules

• fitlins.conftest module
• fitlins.generate_dset module
  • DerivFuncFileCreator
    • DerivFuncFileCreator.FILE_PARAMS
    • DerivFuncFileCreator.PATTERN
    • DerivFuncFileCreator.create_fname()
    • DerivFuncFileCreator.init_data()
    • DerivFuncFileCreator.write_file()
  • DerivMaskFileCreator
    • DerivMaskFileCreator.FILE_PARAMS
    • DerivMaskFileCreator.PATTERN
    • DerivMaskFileCreator.create_fname()
    • DerivMaskFileCreator.init_data()
    • DerivMaskFileCreator.write_file()
  • DummyDerivatives
    • DummyDerivatives.BIDS_DICT
    • DummyDerivatives.DERIVATIVES_DICT
    • DummyDerivatives.create_dataset_descriptions()
    • DummyDerivatives.create_layout()
    • DummyDerivatives.write_bids_derivatives_dataset()
  • EventsFileCreator
    • EventsFileCreator.FILE_PARAMS
    • EventsFileCreator.PATTERN
    • EventsFileCreator.create_fname()
    • EventsFileCreator.init_data()
    • EventsFileCreator.write_file()
  • FuncFileCreator
    • FuncFileCreator.FILE_PARAMS
    • FuncFileCreator.PATTERN
    • FuncFileCreator.create_fname()
    • FuncFileCreator.init_data()
    • FuncFileCreator.write_file()
  • RegressorFileCreator
    • RegressorFileCreator.FILE_PARAMS
    • RegressorFileCreator.PATTERN
    • RegressorFileCreator.create_fname()
    • RegressorFileCreator.init_data()
    • RegressorFileCreator.write_file()
  • write_metadata()

Module contents