[pymvpa] Preprocessing/Analyzing physiological data with python/pyMVPA

jdemanet jelle.demanet at ugent.be
Fri May 29 21:04:00 UTC 2015

> Op 29-mei-2015, om 22:32 heeft Christopher J Markiewicz <effigies at bu.edu> het volgende geschreven:
> On 05/29/2015 04:09 PM, jdemanet wrote:
>> Hello all,
>> I am looking for a elegant way to preprocess physiological data in python/pyMVPA. Does anyone know a good way to preprocess and analyse, heart rate, pupil size, skin conductance in python, possibly with pyMVPA?
>> I really want to avoid using MATLAB for that.
> What are you looking to do with them? And what formats are they coming
> in? NumPy (http://www.numpy.org/) will get you pretty far with loading
> and saving text files and doing linear algebra. With a little more work
> you can handle binary files.

They are coming from a Biopac system but this is not the main problem.
Im especially looking for algorithms that can be used to calculate HRV and heart rate frequency of the heart beats, respiration frequency of respiration data, handle and filter out blinks in the pupil data. So i wondered if there is a toolbox or set of functions which can handle/preprocess all kinds of physiological data. If not, maybe there is a tutorial somewhere how to preprocess these kinds of data in existing python libraries, such as numpy, scipy,..?

> Just as a warning: if you're used to MATLAB, numpy can be a bit
> surprising at times, particularly with regard to matrix operations.
> Without knowing more, I can't help further.
> -- 
> Christopher J Markiewicz
> Ph.D. Candidate, Quantitative Neuroscience Laboratory
> Boston University
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