[pymvpa] Preprocessing in FSL, question on specifics
J.A. Etzel
jetzel at artsci.wustl.edu
Tue Jul 12 21:50:04 UTC 2011
Perhaps this various with software. I usually use SPM for preprocessing,
and you have the option to motion correct to a (session-wise) mean image
or single volume (the first, or whichever).
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.
Jo
On 7/12/2011 4:02 PM, Yaroslav Halchenko wrote:
>
> On Tue, 12 Jul 2011, Mike E. Klein wrote:
>> before being run a second time on the concatenated file. While there is
>> very little head motion within each session, there looks to be
>> considerably more between sessions, which probably comes as no
>> surprise. A test of running motion correction a single time (after
>> concatenation) looks like it does not perform very well: there is still
>> a large amount of motion visible to the naked eye.
>
> ha -- that is interesting to me: afaik (correct me if I am wrong) motion
> correction is just a re-alignment/slicing to a reference 3D volume extracted
> (or computed, e.g. mean of representative volumes), i.e. no temporal
> order between volumes should matter... and now you are getting worse results
> if you concatenate them all into a single 4D series (which is what I usually
> do, to eliminate double-smoothing/error others pointed out) :
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