Hi - just to add a couple of points.
As Christian suggests, the motion correction will be less accurate, but it
will also introduce another problem. That is, the different runs will be
shifted/rotated by dramatically different amounts in order to align them,
and therefore will be subject to very different amounts of interpolation
related smoothness. Hence the smoothness will vary through time in a step
like fashion (being roughly stationary through a single run but changeing
between runs). As all the stats in Feat assume that the smoothness is
stationary, this will introduce errors into the final stats ...
cheers
Tim
On Fri, 20 Dec 2002, Christian Beckmann wrote:
> Hi,
>
> I completely agree with Joe - concatenating the data is probably not
> what you want since it will result in suboptimal motion-correction. The
> reason is that (for 'typical' fmri experiments) the amount of motion
> within one run is considerably smaller than between runs. When data is
> concatenated mcflirt will register all the low-res fmri volumes to one
> reference image (by default the middle one) which for all volumes from
> the different runs other than the one that the ref. image belongs to
> will make motion-correction less accurate.
> If you really want to concatenate the data you'll probably have to do
> some clever shell scripting. Usin avwroi instead of avwsplit will make
> this a bit easier for you though...
>
> cheers,
> Christian
>
> Joe Devlin wrote:
> > Hi Russ,
> >
> >> hi all - I'm trying to motion-correct fMRI data collected over multiple
> >> runs, and it's not clear how to do this with mcflirt at the command
> >> line. Obviously I could do this using some combination of avwmerge and
> >> avwsplit but that seems rather awkward, particularly because I would
> >> have to reconstruct the numbering within the individual runs after
> >> avwsplitting the merged motion corrected image. Any suggestions would
> >> be greatly appreciated.
> >
> >
> > I know this isn't really an answer but I'm wondering why you want to motion
> > correct more than one run at a time? I typically motion-correct the runs
> > individually, analyse them individually at the first level, and enter them
> > into the second level as repeated measures now that Feat5 offers that
> > option. I've found it works pretty well.
> >
> > Cheers,
> > Joe
> >
> > Joseph Devlin, Ph. D.
> > FMRIB, Dept. of Clinical Neurology
> > University of Oxford
> > John Radcliffe Hospital
> > Headley Way, Headington
> > Oxford OX3 9DU, U.K.
> > Phone: +44 (0)1865 222 738
> > Fax: +44 (0)1865 222 717
> > Email: [log in to unmask]
> >
> >
>
> --
> Christian F. Beckmann
> Address: Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717 Mob: +44(0)7811 189123
>
--
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Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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