Hi Suzanna,
> Hi Gwenaelle,
>
> Thank you for such a prompt reply.
>
> >> 2) Generate a ROI mask and use that with the -m
> >> function in
> >> randomise, with or without the TFCE option.
> > Right. With TFCE or cluster-based correction,
> you're
> > still looking at "voxel-skeleton wise" results and
> not
> > at the significance of the global change of FA
> within
> > your ROI...
>
> So, if I interpret you, and the list correctly,
> there's three ways of
> analysing ROIs:
> 1) use voxel-wise tbss analysis
> 2) don't use tbss, but use fslmaths to find the mean
> FA within the
> whole cerebellum including grey matter.
> 3) use the skeleton output from tbss but generate a
> mean of the FA in
> the ROI. ALthough it's probably better to do 1).
>
> Are there restrictions about doing 1)?
So far, I can see only one: if you're interested in
change of diffusion indices (e.g. FA) outside the
white matter tracts, so mainly in the subcortical grey
matter structures.
> Would
> randomise results be
> valid for voxel-wise analysis of a small ROI?
Yes, and I don't feel like your ROI would be so
small...
> Thanks for your other advice, I'll give the masking
> procedures a go.
No problem!
Cheers,
Gwen
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