[pymvpa] Searchligh SVM on fMRI Beta Values in PyMVPA

Yaroslav O Halchenko yoh at onerussian.com
Thu May 23 21:44:45 BST 2019

On Fri, 24 May 2019, Alireza Karami wrote:

>    Hi
>    I have a dataset of an fMRI experiment and I have preprocessed the data
>    and done first level analysis. Now, I want to do searchlight SVM on the
>    beta values like the demo fmri searchlight lda [1] in CoSMoMVPA. I want to
>    do this with PyMVPA. I know how to do searchlight SVM on raw fMRI data in

you probably never want to do searchlight SVM on truly "raw" data -- at
least motion correction etc should be done ;)

>    PyMVPA [2] but I do not know how to import beta values as a dataset in
>    PyMVPA and do searchlight SVM on them.

nothing should change for your code -- just load from your .nii.gz with
beta values (the same fmri_dataset, can give it a list of filenames with
betas), assign targets/chunks, might want to do zscoring or not
depending on how many categories and total # of betas etc, and do
whatever you were doing on "raw" data.

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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