[pymvpa] PyMVPA surface searchlight

John Baublitz jbaub at bu.edu
Tue Jun 30 19:02:23 UTC 2015

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. Here is the error:

/projectnb/somerslab/john/python/PyMVPA/mvpa2/support/nibabel/surf.pyc in
write(fn, s, overwrite)
   2222     if fn.endswith('.asc'):
   2223         from mvpa2.support.nibabel import surf_fs_asc
-> 2224         surf_fs_asc.write(fn, s, overwrite=overwrite)
   2225     elif fn.endswith('.gii'):
   2226         if not fn.endswith('.surf.gii'):

in write(fn, surface, overwrite, comment)
    119     s.append(comment)
--> 121     nv, nf = surface.nvertices, surface.nfaces,
    122     v, f = surface.vertices, surface.faces

AttributeError: 'Dataset' object has no attribute 'nvertices'

Any suggestions? If you need to take a look at the code, again the updated
code is accessible at this link:


Thank you so much for your quick and comprehensive support!

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