Hi Josh
It should be relatively straightforward to calculate the mean displacement
of your data, given the .par file.
What you will need to do is calculate the root mean square error
associated with the motion parameters of each volume (i.e. each
single-line entry in the .par file) according to the method described in
the FMRIB Technical Report TR99MJ1, available at:
http://www.fmrib.ox.ac.uk/analysis/techrep/
This method allows you to calculate an average error measurement (in mm)
for each volume. You can then average this measure across all the volumes
in your timeseries to obtain the mean displacement.
Depending on your FSL installation, there should be a version of the
program which implements the method described in the technical report.
On my system, it is /usr/local/fsl/bin/rmsdiff
Hope this helps
Peter
You can then calculate the displacement
> Hi,
> It would be available in the .feat/mc/* files, but I typically run
> mcflirt outside of feat, and thus have not generated those files...all I
> have is the mc.par file. Is there any way to recreate the other files
> that feat would normally make?
Thanks, and Happy New Year,
> Josh
>
> -----Original Message-----
> From: Stephen Smith [mailto:[log in to unmask]]
> Sent: Thu 1/1/2004 3:58 PM
> To: [log in to unmask]
> Cc:
> Subject: Re: [FSL] mcflirt mean displacement
>
>
>
> Hi - I'm not quite sure what you are asking for that is not available
> in
the .feat/mc/index.html or other .feat/mc/* files?
>
> Thanks, Steve.
>
>
> On Mon, 29 Dec 2003, Joshua Korn wrote:
>
> > Hi,
> >
> > Just wondering if there was any way to get mean displacement based
> on
the mc.par (and a template image if necessary) without having to
> rerun
mcflirt.
> > Thanks,
> >
> > Josh Korn
> >
>
> Stephen M. Smith DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
>
--
Signal Processing and Artificial Neural Networks Engineering Research Group
University of Oxford, Parks Road, Oxford OX1 3PJ
+44 (0)1865 273121 - [log in to unmask] - http://www.robots.ox.ac.uk/~prb
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