NeuroSpin tools

The package nipy.labs hosts some tools that where originally developed at NeuroSpin, France. The list below also includes routines for estimating the empirical null, moved from nipy.labs to nipy.algorithms.statistics.

• Mask-extraction utilities
  • nipy.labs.utils.mask.compute_mask
    • compute_mask()
  • nipy.labs.utils.mask.compute_mask_files
    • compute_mask_files()
  • nipy.labs.utils.mask.compute_mask_sessions
    • compute_mask_sessions()
• Empirical null
  • Example
  • Class documentation
    • NormalEmpiricalNull
      • NormalEmpiricalNull.__init__()
      • NormalEmpiricalNull.fdr()
      • NormalEmpiricalNull.fdrcurve()
      • NormalEmpiricalNull.learn()
      • NormalEmpiricalNull.plot()
      • NormalEmpiricalNull.threshold()
      • NormalEmpiricalNull.uncorrected_threshold()
• Plotting of activation maps
  • An example
  • nipy.labs.viz functions
    • nipy.labs.viz_tools.activation_maps.plot_map
      • plot_map()
  • 3D plotting utilities
    • nipy.labs.viz_tools.maps_3d.plot_map_3d
      • plot_map_3d()
    • nipy.labs.viz_tools.maps_3d.plot_anat_3d
      • plot_anat_3d()
    • nipy.labs.viz_tools.maps_3d.affine_img_src
      • affine_img_src()
• Generating simulated activation maps
  • Example
  • Function documentation
    • surrogate_2d_dataset()
    • surrogate_3d_dataset()
    • surrogate_4d_dataset()
• Volumetric data structures
  • The image structure: VolumeImg
  • Useful methods on volume structures
    • nipy.labs.datasets.volumes.volume_field.VolumeField.values_in_world
      • VolumeField.values_in_world()
    • nipy.labs.datasets.volumes.volume_field.VolumeField.composed_with_transform
      • VolumeField.composed_with_transform()
    • nipy.labs.datasets.volumes.volume_field.VolumeField.as_volume_img
      • VolumeField.as_volume_img()
    • nipy.labs.datasets.volumes.volume_field.VolumeField.resampled_to_img
      • VolumeField.resampled_to_img()
  • More general data structures
    • Implemented classes
    • Abstract classes