[pymvpa] zscore clarification and question
J.A. Etzel
jetzel at artsci.wustl.edu
Tue Nov 30 23:45:33 UTC 2010
I want to make sure I understand how zscore works, so will describe what
I think the behavior is, then add a question. Please correct any errors.
:) I'm assuming in all cases that the mean and standard deviation are
calculated by zscore, not passed.
I think zscore normalizes what I usually call column-wise: by default
(perchunk=True and pervoxel=True) the voxel time course is normalized (a
single voxel over the samples (volumes) in that chunk). So after
normalization each voxel has a mean of zero and standard deviation of
one within each chunk.
Setting perchunk=False and pervoxel=True normalizes the entire column:
each voxel has a mean of zero and standard deviation of one over all
volumes in the dataset.
Setting perchunk=False and pervoxel=False normalizes over all columns:
all voxels together have a mean of zero and standard deviation of one
over all volumes in the dataset.
Setting perchunk=True and pervoxel=False normalizes over all columns
within each chunk: all voxels together have a mean of zero and standard
deviation of one over all volumes in each chunk.
This gives various options for normalizing column-wise, but is it
possible to normalize row-wise? In other words, normalize so that the
voxels in each sample (volume) have a mean of zero and standard
deviation one? Chunks are irrelevant for this case, since each sample is
normalized separately. If this is already in pyMVPA, can you point me in
the right direction?
thanks,
Jo
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