[pymvpa] Using PyMVPA for preprocessing only

Yaroslav Halchenko debian at onerussian.com
Sun Mar 6 23:45:57 UTC 2016

On Sun, 06 Mar 2016, Adrian Smith wrote:

> I’m a student researcher working with the Haxby ds105 data from OpenfMRI. I’m not planning on using PyMVPA for my whole analysis of the data, but wanted to use it in order to denoise, mask and detrend the data. What I want is to input a 4D NIfTI (or group of NIfTIs), run some preprocessing on each file like shown in http://www.pymvpa.org/tutorial_mappers.html <http://www.pymvpa.org/tutorial_mappers.html>, and then output a processed NIfTI for each input NIfTI. How can I do that with PyMVPA?
> I’ve read through the tutorial, but it is written for someone trying to operate their entire pipeline within PyMVPA, and I couldn’t find anything that was what I am looking for.

I guess such toolkits as AFNI, SPM, Nipy, Nipype would be a better
choice for preprocessing, and generally PyMVPA wouldn't be sufficient
anyways since we do not provide e.g. motion correction and rely on those
toolkits for that to be done first. Well -- ds105 iirc was already
motion corrected so that state we shared it with openfmri indeed should
be sufficient to carry out MVPA right away.

So since you have asked, after you are done with your 'preprocessing' in
PyMVPA you can just map2nifti that dataset back in its entirety, or per
each chunk with a little loop.

Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        

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