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pyretroicor's Introduction

The project is nolonger maintained!

Updates

Python implementation of RETROICOR (Glover et al., 2000) - physiology regressors for fMRI preprocessing.

Dependencies

The required dependencies to use the software are:

  • Python >= 3.5
  • NumPy >= 1.18
  • Nibabel >= 2.5

Install

First make sure you have installed all the dependencies listed above. Then you can install pyretroicor by running the following command in a command prompt:

pip install -U --user pyretroicor

Reference

Glover, G. H., Li, T. Q., & Ress, D. (2000). Image‐based method for retrospective correction of physiological motion effects in fMRI: RETROICOR. Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine, 44(1), 162-167.

MATLAB implementation from: https://github.com/mkassinopoulos/PRF_estimation

Support

Please use GitHub issues for questions, bug reports or feature requests.

License

This project is licensed under BSD-3-Clause.

pyretroicor's People

Contributors

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Watchers

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pyretroicor's Issues

Slice timing correction

This library is only for creating regressors rather than the full preprocessing.
It might be a good idea to add slice-timing correction for the regressor output.
I don't really know how to structure the output.
Another part I will need help with is multiband acquisitions.

Things to do

To-do list in the order of priority:

  • r peak detection for cardiac data
  • Construct TR timing (based on BIDS)
  • Set-up file
  • Example data (possibly from NKI/LEMON?)
  • Tutorial
  • Write test
  • CI

n_vol value from wrong axis

Hi, I know this is probably a work in progress right now, but it looks the value "n_vol" is taken from the wrong axis. The time axis in nibabel is usually the last dimension, which means "n_vol = func.shape[0]" should be "n_vol = func.shape[-1]". Thanks for the package!

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