[pymvpa] How do people get the preprocessed .nii.gz before throwing it into the pyMVPA?

[Yaroslav Halchenko]

to raise the curtain a bit:
 Michael has started a script which is to be the one to help with
 preprocessing of the data. Script does make use of FSL tools, so you have to
 have FSL installed.

 You can check that script out -- it is in mh/master and now yoh/master
 branches in our git repository and located under
 bin/mvpa-prep-fmri. Suggestions and fixes (patches) are welcome ;-)

As for doing preprocessing with other tools -- the choice is yours, but
I found that some times preprocessing methods tailored toward GLM
analysis might ruin some effects which might be useful in case of
multivariate analysis (e.g. smth like despekling), so you better
be cautious about them.

in general only minimalistic preprocessing with outside tools is
necessary: pretty much just motion correction. Spatial filtering can be
also favorable if effects are believed to be not very localized (like
distributed patterns within fusiform). Detrending, zscoring can be done
within PyMVPA. How much of benefit from field inhomogenuity correction
methods, I have no clue.

you might also have look at

LaConte, S., Strother, S., Cherkassky, V., Anderson, J. & Hu, X. (2005).
Support vector machines for temporal classification of block design fMRI data.
Neuroimage, 26, 317–329.

Comprehensive evaluation of preprocessing options with respect to
SVM-classifier (and others) performance on block-design fMRI data.

DOI: http://dx.doi.org/10.1016/j.neuroimage.2005.01.048


On Fri, 26 Dec 2008, Yune Lee wrote:

>     I attempted do the preprocessing using 4D nifti in SPM5, but
>    apprently, it didnt' work. So, below are two options that come up to my
>    mind in order to make the data files ready for myMVPA.

-- 
Yaroslav Halchenko
Research Assistant, Psychology Department, Rutgers-Newark
Student  Ph.D. @ CS Dept. NJIT
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