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How do you separate the eye movements (rotations), per se, from the RF artifacts they might generate, in the phase direction? These are often clearly seen in the T1 of a high res anatomical, in the phase direction, but does the BOLD EPI sequence suffer from similar artifacts? Quoting Peter Hansen <[log in to unmask]>: > Peter - for some reason my mail system won't allow me to reply to > [log in to unmask] > Could you forward this for me, please. > > > I have tried to use mcflirt for exactly this same reason, in data from a > tracking task where we know the ocular target position and know the > subjects will have been tracking that with eye movement. > I first choose a very small volume around one eye, from data that had > been mcflirted to remove overall head motion, but got poor mcflirt > output of this "eye movement" data. I got better results by masking the > eye within a larger volume - 10x20x5 voxels within 30x30x10 I think, as > the flirt seems to need moderately sized volumes. Mcflirt seemed to work > fine on this data, but I am not convinced that the motion output > resemble anything like real eye movement. > If you look carefully at figure 2B of Tregallas et al, you will see no > noise at all on the reconstructed eye position data. In my hands, the > correlation between "eye position" and target position after mcflirt was > very poor. I'm not sure why they get such enormous effects of eye > movement in their data, but it seems that the FMRIB scanner doesn't have > a strong eye movement signal, unfortunately. > -- > Regards, > Chris > _____________________________________________________________ > Chris Miall Tel: +44 1865 282162 > Professor of Neuroscience Fax: +44 1865 272469 > University Laboratory of Physiology Mobile: 07815 296483 > Parks Road [log in to unmask] > Oxford OX1 3PT, U.K. http://www.physiol.ox.ac.uk/~rcm > ============================================================= > Arun Bokde wrote: > > > > Hello FSLers, > > > > A recent paper (Tregellas J et al, HBM, vol 17: 237-243) shows that a > > measure of eye movement can be obtained by using the standard EPI > > sequences. I am interested in trying it out using FLIRT, as the method > > described basically is a rigid body registration process on the time > > series of each eye. Is there any reason that FLIRT would have problems > > with a time series file that has perhaps 10 x 10 voxels per slice and > > 4-5 slices ? Is there a program that could produce a 4D avw file from > > another 4D avw file based on an ROI ? I was looking at avwroi but the > > help info is not very clear to me. > > > > TIA > > > > Cheers, Arun > > -- Darren L. Weber, BSc(Hons), BA PhD student, Cognitive Neuroscience Laboratory, School of Psychology, The Flinders University of South Australia, GPO Box 2100, Adelaide SA 5001 PH: (61 8) 8201 3998, FAX: (61 8) 8201 3887 WWW: http://brain.mhri.edu.au/~dlw/homepages/