[pymvpa] Rapid ER design

Jeffrey Bloch jeffreybloch1 at gmail.com
Fri Mar 27 22:55:29 UTC 2015

Dear All,

Hello!  I am in the middle of setting up a rapid event-related design
analysis, and was hoping I could ask a few questions.  I've been working
through this for a while, but to no avail.  Thanks in advance!

My main confusion(s) stem from the fact that my design has events that are
not multiples of the TR.  Namely, there are 110 events (of 3s duration),
but my TR is 2s.  So, technically, any volume could have multiple
conditions, and/or conditions can spread over more than one TR.  What is
the best way of dealing with this when setting up the analysis?

1.  PyMVPA knows that my nifti file has 179 volumes, so it keeps getting
mad when I try to create an attribute that has fewer items (say, a
condition for each of the 110 events).  How can I make the software forget
about the volumes and just focus on the timepoints of my events?  The
original attribute file (with just chunks and condition) has to be 179
items long, but 110 doesn't fit into 179 very nicely!  :)

2. I am trying to get GLM estimates (per event/volume) using
'eventrelated_design' with 'hrf'.  I understand that it is possible to
bring in betas from outsidePyMVPA, but I was hoping to keep it all "in
house."  Even if I make my event list by multiplying by TR (as in the
tutorial), the original dataset need is still 179 volumes, so the events
and attributes don't line up.

3.  I find that my "time_coords" are always blank (all zeros) when I create
my datasets, but several functions seem to require this information.
Similarly, the time_indices are always 179 due to the nifti volumes, but
that's not very useful for me (again, 110 events, sorry to be repetitive).

Lastly (I hope!), is it possible using eventrelated_dataset to get
parameters for each event (instead of each target)?  I was hoping to be
able to tease apart relationships at an event by event basis.

Thank you all very much for your time!

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