Hi
On 3 Apr 2008, at 16:54, Carlos Faraco wrote:
> Steve,
>
> Thank you for your reply. Just have a few more questions though.
>
> 1) In the FSL manual it says to use MELODIC before the data is
> processed
> (and BETed I imagine). I guess this is supposed to make it easier to
> detect
> motion if you see "activity" closer to the skull. My question then
> is, does
> it matter when MELODIC is applied?
This also is an area where one can argue both ways - if you want to
use artefact related to the MR physics (slice dropouts, say) then in
most cases you want to be as close to the original data as possible
and use the non pre-processed data without betting/mc/smoothing. If -
like in the case of head motion - you want to correct for artefact
over and above what you can achieve with other approaches (i.e. rigid
body motion correction) then clearly you'd want to perform these steps
first.
>
>
> 2) Are there any pictorial representations of what motion in the
> MELODIC
> output would look like? As I stated previously, I feel very hesitant
> to just
> go in there and start judging things as motion without any type of
> criteria.
>
these typically look like rim-like artefacts - see the melodic course
talk for some examples (http://www.fmrib.ox.ac.uk/fslcourse/lectures/melodic.pdf
)
> 3)If motion parameters are added to the GLM, does this have to be
> done for
> all subjects (since the degrees of freedom would be reduced)? Would
> the same
> be true for MELODIC noise removal, even though in that case the
> number of
> reduced DFs might vary per subject?
>
Differences in the DOFs between subjects are accounted for in the
higher level analysis of FEAT, i.e. adding motion regressors for some
but not all subjects is OK. When using melodic denoising then this
more difficult, though you can adjust the dofs explicitly on the
command line when using ttoz for first level analysis - for the higher
level analysis you'd want to adjust the dof files using fslmaths
before running higher-level analysis.
hth
Christian
> Thank you,
>
> Carlos Faraco
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