[pymvpa] outputting p-values from searchlight

[William Graves]

Dear PyMVPA Experts:

In trying to do an RSA analysis using PyMVPA, I have to say your tools are really great. One issue I’ve run into though is that I can’t figure out from your documentation how to output both correlation coefficients and p-values into a NIfTI file to view the output.

Here’s what I’ve done so far:

Set up a comparison matrix for eventually testing against each searchlight:
tdm = rsa.pdist(ds.sa.orth, 'correlation’)

Set up the target similarity comparison:
dsm = rsa.PDistTargetSimilarity(tdm, comparison_metric='spearman', corrcoef_only=True)

Set up the searchlight:
sl = sphere_searchlight(dsm, radius=3, enable_ca='ca.pvalues’)

Run it:
slres = sl(ds)

And finally output the results in NIfTI format:
map2nifti(slres, imghdr=ds.a.imghdr).to_filename('meansubj.rsa_orth_sl.nii.gz’)

From your documentation, it seems like there’s a way to output not only correlation coefficients for each voxel, but also p-values. I just can’t figure out how to set it up properly, even after searching the mailing list. I’d appreciate any help you could give.

Best,
Will

---
William W. Graves, Ph.D.
Assistant Professor, Department of Psychology
Rutgers, The State University of New Jersey
Smith Hall, Room 337
101 Warren Street, Newark, NJ  07102
Voice: 973-353-3947
Fax: 973-353-1171
http://lbbil.rutgers.edu