Welcome to Nighres!

Nighres is a Python package for processing of high-resolution neuroimaging data. It developed out of CBS High-Res Brain Processing Tools and aims to make those tools easier to install, use and extend. Nighres now includes new functions from the IMCN imaging toolkit.

Getting started

• Installing Nighres
• Nighres usage examples

Modules and Functions

• Brain
  • dots_segmentation
  • extract_brain_region
  • filter_stacking
  • intensity_based_skullstripping
  • mgdm_segmentation
  • mp2rage_dura_estimation
  • mp2rage_skullstripping
• Cortex
  • cruise_cortex_extraction
• Data
  • download_data
• Filtering
  • filter_ridge_structures
  • multiscale_vessel_filter
  • recursive_ridge_diffusion
  • total_variation_filtering
• Intensity
  • background_estimation
  • flash_t2s_fitting
  • intensity_propagation
  • lcat_denoising
  • lcpca_denoising
  • mp2rage_t1_mapping
  • mp2rageme_pd_mapping
  • phase_unwrapping
  • t2s_optimal_combination
• Input/Output
  • io_volume
  • io_mesh
• Laminar
  • laminar_iterative_smoothing
  • laminar_regional_approximation
  • profile_averaging
  • profile_meshing
  • profile_sampling
  • volumetric_layering
• Microscopy
  • mgdm_cells
  • stack_intensity_regularisation
• Registration
  • apply_coordinate_mappings
  • apply_coordinate_mappings_2d
  • embedded_antsreg
  • embedded_antsreg_2d
  • embedded_antsreg_multi
  • generate_coordinate_mapping
  • simple_align
• Segmentation
  • conditional_shape
  • fuzzy_cmeans
• Shape
  • levelset_fusion
  • simple_skeleton
  • topology_correction
• Statistics
  • segmentation_statistics
• Surface
  • levelset_to_mesh
  • levelset_to_probability
  • mesh_to_levelset
  • probability_to_levelset
  • surface_inflation
  • surface_mesh_mapping
  • surface_som_mapping
  • volume_som_mapping

Good to know

• Data handling and formats
• Saving outputs
• Levelsets

Developer's guide

• Overview
• Setting up
• Wrapping an existing CBS Tools class
• Adding a new Python function
• Writing examples
• Adapting the docs
• Making a Pull Request

Reference

Huntenburg, Steele & Bazin (2018). Nighres: processing tools for high-resolution neuroimaging. GigaScience, 7(7). https://doi.org/10.1093/gigascience/giy082

Make sure to also cite the references indicated for the particular functions you use!

Credit

Nighres is a community-developed project made possible by its contributors. The project was born and continues to evolve at brainhack. We thank the Google Summer of Code 2017 and INCF as a mentoring organization, for supporting the initial development phase of Nighres. See also the development blog.