[pymvpa] PyMVPA surface searchlight

John Baublitz jbaub at bu.edu
Sat Jun 27 10:35:16 UTC 2015

Hi all,
I am working on a Python script using PyMVPA to read in FreeSurfer
recon-all processed data and run a surface-based searchlight analysis. I am
running into some problems both with running the searchlight and returning
the resulting dataset to the original NIftI space. I've seen some questions
about this on the mailing list but there have been no answers to those
sharing my exact error messages.

This is the link to my script on github:

This script gives me a warning and an error. The warning happens while
actually running the searchlight and it is:

WARNING: Detected incorrect (nan) scl_ fields. Resetting to scl_slope=1.0
and scl_inter=0.0
 * Please note: warnings are printed only once, but underlying problem
might occur many times *

The error happens while using map2nifti to map the data back to NIftI space
and that is:

ValueError: shape mismatch: value array of shape (1,112320) could not be
broadcast to indexing result of shape (14166,1)

I have played around with a number of different tweaks to try to get at the
problem but I can't seem to get around either of these issues. These
1. Specifying the imghdr in map2nifti
2. Using the mapper from the original dataset and samples from the
searchlight-processed data
3. Following both the tutorial on the surface and volume-based searchlight

Also of note is that it WILL save the dataset in a SUMA-readable format but
SUMA errors out while trying to load it at the first line of the file
header which seems to be malformed. Any ideas?

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