[pymvpa] searchlight on ER data

Anna Manelis anna.manelis at gmail.com
Wed Dec 29 17:16:02 UTC 2010

I am trying to use searchlight on event-related fMRI data. The error message
suggests that there is a problem with assigning metrics to MappedDataset.
I submitted the question related to this problem a week ago and did not receive
any response. I repeat my request with the hope that somebody knows how to
deal with the problem.

In order to test the searchlight method on ER data,  I combined two scripts
provided with pymvpa (version 0.4.5): eventrelated.py
and searchlight_2d.py.
The combined script looks like that

from mvpa.suite import *

fmri_src = os.path.join(pymvpa_dataroot, 'bold.nii.gz')
mask = NiftiImage(os.path.join(pymvpa_dataroot, 'mask.nii.gz'))
attr = SampleAttributes(
verbose(1, "Load data for preprocessing")
pre_ds = NiftiImage(fmri_src)
pre_ds = NiftiDataset(samples=fmri_src, labels=attr.labels,
                      chunks=attr.chunks, mask=mask)
detrend(pre_ds, perchunk=True, model='linear')
evs = [ev for ev in attr.toEvents()
            if ev['label'] in ['face', 'house']]
for ev in evs:
    ev['onset'] -= 1
    ev['duration'] = 4
ds = ERNiftiDataset(samples=pre_ds.map2Nifti(),
                    labels_map={'face': 1,
                                'house': 2})
zscore(ds, perchunk=True)

# Run Searchlight
clf = LinearNuSVMC()
cv = CrossValidatedTransferError(TransferError(clf),
for radius in [1,5,10]:

    print "Running searchlight with radius: %i ..." % (radius)
    sl = Searchlight(cv, radius=radius)
    sl_map = sl(ds)


The code fails with the following message:

Traceback (most recent call last):
  File "eventrelated_original_SL.py", line 158, in <module>
    sl_map = sl(ds)
  File "/usr/lib/pymodules/python2.6/mvpa/measures/base.py", line 105, in
    result = self._call(dataset)
  File "/usr/lib/pymodules/python2.6/mvpa/measures/searchlight.py", line 77,
in _call
    raise ValueError, "Searchlight only works with MappedDatasets " \
ValueError: Searchlight only works with MappedDatasets that has metric

Could you please advise on how to make the code work by assigning metric to
MappedDatasets or in any other way.

Thank you,
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/attachments/20101229/38476f85/attachment.htm>

More information about the Pkg-ExpPsy-PyMVPA mailing list