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/
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