Welcome to pycorr’s documentation!

Pycorr allows you to produce quick, replicable pipelines for inter-subject correlation analyses. Oftentimes, analysis scripts become a tangled mess of experiment specific parameters and file paths. Sometimes you’re left with a dozen different folders with the data saved in slightly different ways, and names like “sub1_cropleft2_cropright4.nii”. We’ve all been there. No judgement. pycorr can help alleviate your research woes by doing a few things:

1. Seperating parameter configuration from analysis scripts
2. Modular structure, with functions for loading, analyzing, and saving data
3. Support for HDF5 using H5py. This allows you to store parameters in the data, rather than in it’s filename :).
4. Command-line tools for running analyses
5. Unit-tests and documentation

H5py: http://www.h5py.org/

General Workflow

The bulk of most pycorr analyses consist of two parts:

1. Configuration file
2. Analysis script

The configuration file has basic settings, such as filepaths to the data. The analysis scripts takes advantage of the two classes, Exp and Run. Exp loads the data using the config file, and Run wraps each functional run.

Contents:

• Setup
  • Installing Dependencies
  • Installing Pycorr
  • Using pycorr on Rondo
• Tutorial
  • Setting up Pipeline Directory
  • Example Data Structure
  • Config file
  • Running Pipeline
• API Reference
  • pycorr
  • cli
  • funcs_correlate
  • gen_corrmat
  • pietools
  • statistics
  • subject
  • workflows

Indices and tables

• Index
• Module Index
• Search Page