[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.


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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