Metadata-Version: 2.1
Name: niphlem
Version: 0.0.2
Summary: Physiological Log Extraction for Modelling in Neuroimaging
Home-page: https://github.com/CoAxLab/niphlem
License: UNKNOWN
Project-URL: Bug Tracker, https://github.com/CoAxLab/niphlem/issues
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
License-File: LICENSE

# niphlem

*niphlem* toolbox extracts physiological recordings during MRI scanning and estimates the signal phases so that they can be used as a covariate in your general linear model (GLM) with fMRI data.

*niphlem* can generate multiple models of physiological noise to include as regressors in your GLM model from either ECG, pneumatic breathing belt or pulse-oximetry data.  These are described in Verstynen and Deshpande (2011).

Briefly, niphlem implements three two of models:

- *RETROICOR*:  A phasic decomposition method that isolates the fourier series that best describes the spectral properties of the input signal.  This was first described by Glover and colleagues. 
- *Variation Models*:  For low frequency signals (like the pneumatic belt and low-pass filtered pulse-oximetry) this does the combined respiration variance and response function described by Birn and colleagues (2008).  For high frequency signals (i.e., ECG or high-pass filtered pulse-oximetry), this generates the heart-rate variance and cardiac response function described by Chang and colleagues (2009).

*niphlem* can also extract cardiac and respiratory signals from the pulse-oximitry data stream itself, as described in Verstynen and Deshpande (2011).

## Dependencies

## Install

```pip install niphlem```

## References:
- Verstynen TD, Deshpande V. Using pulse oximetry to account for high and low frequency physiological artifacts in the BOLD signal. Neuroimage. 2011 Apr 15;55(4):1633-44.
- Chang C, Cunningham JP, Glover GH. Influence of heart rate on the BOLD signal: the cardiac response function. Neuroimage. 2009 Feb 1;44(3):857-69.
- Birn RM, Smith MA, Jones TB, Bandettini PA. The respiration response function: the temporal dynamics of fMRI signal fluctuations related to changes in respiration. Neuroimage. 2008;40(2):644-654.



