[pymvpa] Preprocessing in FSL, question on specifics

Mike E. Klein michaeleklein at gmail.com
Wed Jul 13 02:57:48 UTC 2011

Hi all,

Thanks so much for your quick and thoughtful suggestions! I'm still
processing all the info, and will most likely try out a few different
methods (all of this in tandem with learning the PyMVPA software, itself!).
I hadn't previously considered the smoothing effects of interpolation from
using a double motion correction procedure. My next step will probably be to
try fiddling with the MCFLIRT parameters on the single concatenated file.


On Tue, Jul 12, 2011 at 7:32 PM, Michael Hanke <mih at debian.org> wrote:

> On Tue, Jul 12, 2011 at 04:50:04PM -0500, J.A. Etzel wrote:
> > Volume order within a session definitely matters: I had a dataset in
> > which the volumes were entered in the wrong order (due to a
> > numerical vs. alphabetical file naming mixup) and the motion
> > correction was extremely abnormal and poor. Once the file naming was
> > fixed the motion correction looked fine.
> According to my experience, most software uses some sort of running
> guess on the transformation matrix with heavy constraints on the
> translation/rotation magnitude between volume (for speed reasons).
> Reverse order of volumes shouldn't have much of an effect, but random
> order would. For heavy between session motion (maybe people got out of
> the scanner) it might be better to compute a cross-session alignment and
> combine that with within session motion correction. But again, that is
> nothing MVPA specific.
> Michael
> --
> Michael Hanke
> http://mih.voxindeserto.de
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