[pymvpa] General fMRI question - coregistering three EPI sequences

Thorsten Kranz thorstenkranz at googlemail.com
Wed Aug 24 09:13:15 UTC 2011

Hi all,

I have a question that is a little bit off-topic, please excuse me if
I exploit this mailing list ;-). I'm even cross-posting on nipy and
PyMVPA mailing lists...

We are doing an fMRI experiment consisting of three "blocks", each
block being a separate fMRI-session with some minutes of break in
between. We want to do some MVPA on all three blocks together and
therefore want to coregister all EPIs. Schematically, the schedule
looks like:

|Task 1|  -> |Task 2| -> |Task 1+2| -> |Structural T1|

Each arrow is a break of some minutes (out of the scanner). We are
trying to do cross-block cross-validation, e.g. train on Block 1+2 and
validate on Block 3.

My main question now is: what is the recommended way to coregister all
three EPIs? Obvious possibilties are:

1. Register all three EPIs to T1
    -> voxel-dimensions increased, not good for MVPA
2. Register Block1 and Block2 on Block3
    -> Block 3 is not transformed and thus not interpolated, thus the
blocks are not treated equally. 1 and 2 will be blurred, 3 not.
3. Register all three blocks to a common "average" of the three blocks
    -> how to choose the best coordinate system for this? Using T1? We
want to keep voxel-dimensions low, see 1.

Maybe somebody already had similar problems and knows a simple
solution. We used FSL for our previous tries, but if there is a better
choice, we're happy to switch. Maybe it would be possible to use nipy
for this? AffineImage?

Thanks in advance,


More information about the Pkg-ExpPsy-PyMVPA mailing list