I don't think it will make that much of a difference. Typically, I create models with only the useable runs in them, but all the runs were pre-processed. 

In some cases, it could make a difference. In particular, when the scan is so bad that it causes the data to be masked incorrectly and cuts of the brain or causes issues with normalization.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Mon, Jul 28, 2014 at 8:05 AM, Andy Yeung <[log in to unmask]> wrote:
Dear all,

For pilot study, I ran 3 sessions of experiment. I checked that subject moved a lot during session 3, which might negatively affect the results. I want to just check results from first 2 sessions.

At contrast manager, I redefined contrasts so that they only limit to first 2 sessions.

Else, I could re-pre-process the data right from the beginning: slice timing, realignment, coregistration... and so on.

Will I have more precise results using the latter method? Or both are the same?
Thanks for any advice.

Best,
Andy