pyhrf package

pyhrf package

pyhrf package – PyHRF is a set of tools for within-subject fMRI data analysis, which focuses on the characterization of the hemodynamics.

Within the chain of fMRI data processing, these tools provide alternatives to the classical within-subject GLM estimation step. The inputs are preprocessed within-subject data and the outputs are statistical maps and/or fitted HRFs.

The package is mainly written in Python and provides the implementation of the two following methods:

  • The joint-detection estimation (JDE) approach, which divides the brain into functionnaly homogeneous regions and provides one HRF estimate per region as well as response levels specific to each voxel and each experimental condition. This method embeds a temporal regularization on the estimated HRFs and an adaptive spatial regularization on the response levels.
  • The Regularized Finite Impulse Response (RFIR) approach, which provides HRF estimates for each voxel and experimental conditions. This method embeds a temporal regularization on the HRF shapes, but proceeds independently across voxels (no spatial model).
pyhrf package

Check website for details: www.pyhrf.orgclass pyhrf.Verbose(verbosity=0log=<open file ‘<stdout>’mode ‘w’>)

Bases: pyhrf._verbose.Verbose

This is a dummy class implementing the original Verbose class.

This is only to be able to raise a warning when one uses this old implementation.old_to_new_log_dict = {0: 30, 1: 20, 2: 20, 3: 20, 4: 20, 5: 10, 6: 10}

Subpackages

  • pyhrf.boldsynth package
    • Subpackages
      • pyhrf.boldsynth.pottsfield package
        • Submodules
          • pyhrf.boldsynth.pottsfield.swendsenwang module
    • Submodules
      • pyhrf.boldsynth.field module
      • pyhrf.boldsynth.hrf module
      • pyhrf.boldsynth.scenarios module
      • pyhrf.boldsynth.spatialconfig module
  • pyhrf.jde package
    • Subpackages
      • pyhrf.jde.nrl package
        • Submodules
          • pyhrf.jde.nrl.ar module
          • pyhrf.jde.nrl.base module
          • pyhrf.jde.nrl.bigaussian module
          • pyhrf.jde.nrl.bigaussian_drift module
          • pyhrf.jde.nrl.gammagaussian module
          • pyhrf.jde.nrl.habituation module
          • pyhrf.jde.nrl.trigaussian module
    • Submodules
      • pyhrf.jde.asl module
      • pyhrf.jde.asl_2steps module
      • pyhrf.jde.asl_physio module
      • pyhrf.jde.asl_physio_1step module
      • pyhrf.jde.asl_physio_1step_params module
      • pyhrf.jde.asl_physio_det_fwdm module
      • pyhrf.jde.asl_physio_hierarchical module
      • pyhrf.jde.asl_physio_joint module
      • pyhrf.jde.beta module
      • pyhrf.jde.drift module
      • pyhrf.jde.hrf module
      • pyhrf.jde.jde_multi_sess module
      • pyhrf.jde.jde_multi_sujets module
      • pyhrf.jde.jde_multi_sujets_alpha module
      • pyhrf.jde.models module
      • pyhrf.jde.noise module
      • pyhrf.jde.samplerbase module
      • pyhrf.jde.wsampler module
  • pyhrf.sandbox package
    • Submodules
      • pyhrf.sandbox.data_parser module
      • pyhrf.sandbox.func_BMA_consensus_clustering module
      • pyhrf.sandbox.make_parcellation module
      • pyhrf.sandbox.parcellation module
      • pyhrf.sandbox.physio module
      • pyhrf.sandbox.physio_params module
      • pyhrf.sandbox.stats module
  • pyhrf.stats package
    • Submodules
      • pyhrf.stats.misc module
      • pyhrf.stats.random module
  • pyhrf.tools package
    • Submodules
      • pyhrf.tools.aexpression module
      • pyhrf.tools.backports module
      • pyhrf.tools.cpus module
      • pyhrf.tools.message module
      • pyhrf.tools.misc module
  • pyhrf.ui package
    • Submodules
      • pyhrf.ui.analyser_ui module
      • pyhrf.ui.glm_analyser module
      • pyhrf.ui.glm_ui module
      • pyhrf.ui.jde module
      • pyhrf.ui.rfir_ui module
      • pyhrf.ui.treatment module
      • pyhrf.ui.vb_jde_analyser module
      • pyhrf.ui.vb_jde_analyser_asl_fast module
      • pyhrf.ui.vb_jde_analyser_bold_fast module
  • pyhrf.vbjde package
    • Submodules
      • pyhrf.vbjde.vem_asl_models_fast module
      • pyhrf.vbjde.vem_asl_models_fast_ms module
      • pyhrf.vbjde.vem_bold module
      • pyhrf.vbjde.vem_bold_constrained module
      • pyhrf.vbjde.vem_bold_models_fast module
      • pyhrf.vbjde.vem_bold_models_fast_ms module
      • pyhrf.vbjde.vem_tools module
  • pyhrf.xmliobak package
    • Submodules
      • pyhrf.xmliobak.xmlbase module
      • pyhrf.xmliobak.xmlmatlab module
      • pyhrf.xmliobak.xmlnumpy module
pyhrf package

Submodules

  • pyhrf.configuration module
  • pyhrf.core module
  • pyhrf.glm module
  • pyhrf.graph module
  • pyhrf.grid module
  • pyhrf.ndarray module
  • pyhrf.paradigm module
  • pyhrf.parallel module
  • pyhrf.parcellation module
  • pyhrf.plot module
  • pyhrf.rfir module
  • pyhrf.surface module
  • pyhrf.usemode module
  • pyhrf.version module
  • pyhrf.xmlio module