[pymvpa] PyMVPA surface searchlight

[Nick Oosterhof]

On 30 June 2015 at 21:02, John Baublitz <jbaub at bu.edu> wrote:

> Thank you for the quick response! I met with my lab today and they are
> looking to have the option of either outputting a NIftI file, which was
> indeed solved using 'volume' for output_modality in the query engine OR,
> preferably, outputting a FreeSurfer-compatible surface file with the PyMVPA
> searchlight results as we are looking to visualize it ultimately on the
> surface. The former is working with your suggestion. The latter is not
> working. I am using surf.write() with an .asc extension for the output file
> but when passing in the surface-based searchlight output dataset, it errors
> out while trying to convert it to a surface.
>

.asc is for 'anatomical' surface files, that is surfaces that have vertices
(points in 3D space) and faces (lists of 3 node indices that define which
nodes make up a triangle together).

Surface-based searchlight results are stored in a PyMPVA dataset structure
that has, amongst other things, fields .samples and .fa. If "ds" is such a
dataset structure, you can write it using:

niml.write('output.niml.dset',ds);

assuming you imported the niml module (one way to do this is with "from
mvpa2.suite import *"). Also see [1]

I hope that clarifies matters.

[1] http://www.pymvpa.org/examples/searchlight_surf.html
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