[pymvpa] searchlight analysis

Yaroslav Halchenko debian at onerussian.com
Fri Sep 8 12:53:10 UTC 2017

On Fri, 08 Sep 2017, Pegah Kassraian Fard wrote:

>    That would be great.
>    - Files (whole brain - not yet masked) are here
>    - Targets/labels are in the labels.mat file, it is binary classification,
>    so one classes' samples are labeled by "1", the other classes by "2", the
>    "7" are just the head movement parameters and can be ignored for
>    classification
>    - I have included a struct image of the subject (subject2_struct.nii), as
>    well as a mask for primary sensory cortex (S1_mask.nii)
>    I was attempting to reproduce this:
>    http://www.pymvpa.org/examples/searchlight.html
>    including the plots, but my highest accuracies (1-error) were 1. outside
>    of the brain:)) 

;)  that is the fun of using all data (not just masked) -- you could
potentially discover interesting aspects of your data/design/code ;-)
does the rest of the map look "feasible" given your experiment?

but before we get that excited, let's indeed see the code:

> 2. I was not sure what the necessary background files were
>    (I tried to guess and use similar ones I found elsewhere, but there was a
>    dimension mismatch - is there a resampling method in the toolbox to match
>    the dimensions?)
>    Many thanks, let me know if I can provide my (buggy?) script

sure -- just paste it in here (make sure no wrapping) or post it
somewhere online 

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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