Hi - your suggestions are sensible, but given that you rightly say that
the artefacts are not simply limited to a single time-point each time, you
are probably best off subtracting the artefacts using MELODIC - identify
the aretfact components by eye and run the cleanup as described at
http://www.fmrib.ox.ac.uk/fslfaq/#melodic_filter
Let us know how you get on!
Cheers.
On Wed, 11 Feb 2004, Christopher Joseph Bailey wrote:
> Dear List,
>
> We have data from a long FMRI-session (896 volumes at 3.66 sec TR). In
> general, motion has not been a big problem (<1mm), but we have a handful
> of subjects with nasty point-like movement artefacts. They are higly
> likely due to coughing during a volume acquisition: the symptoms are a
> "grated" appearance, where, due to interleaved imaging, consecutive
> slices have different spin excitation histories. Timecourses of voxels
> show sharp intensity gradients.
>
> We would like not to have to throw these subjects away. Expectedly,
> mcflirt cannot cope with such radical events. My first instinct was
> simply to go through the data (in AFNI), mark the one or max two
> (consequtive) volumes with the "grated" appearance and splice them out
> with avwroi (naturally adjusting the design matrix accordingly). We
> would pretend those volumes were never acquired.
>
> However, a colleague pointed out that an option would be to interpolate
> the contaminated volumes, i.e. replace them with the average of the
> preceeding and succeeding volumes. This would then possibly not affect
> the autocorrelations in the data. This could, however, be considered
> more severe tampering of the data.
>
> Any comments appreciated,
>
> Christopher Bailey
> --
> Research Assistant (MSc)
> Center for Functionally Integrative Neuroscience (CFIN)
> Aarhus University Hospital, Denmark
> [log in to unmask]
> phn: +45 89 49 43 78
> fax: +45 89 49 44 00
>
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
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