Hi Tom / Amelia,
No, I think what Amelia is saying is that she first looked at the
whole brain, and nothing showed up with corrected p-values, but some
areas did with uncorrected. On the basis of this she identified some
logical regions, like L_Cuneus, which contained some uncorrected
significant voxels, and then ran testing within that.
Amelia, I'm afraid that this is still slightly dodgy, as you only
identified those regions on the basis of the uncorrected testing of
the same data, so the stats is still a little too 'circular' to be
safe.......unless you predicted that you were interested in this area
before running the original analysis.
Does this make sense Tom / Amelia?
Cheers.
On 17 Mar 2008, at 22:06, Thomas Nichols wrote:
> Amelia,
>
> I haven't shed any tears yet, but I'm afraid I don't quite
> understand your question either.
>
> Is it this: You are surprised that using a tightly constrained ROI
> doesn't increase your sensitivity when using FDR (relative to a more
> generous region)? This is not surprising, especially if you have a
> tiny region. The reason is that FDR is an adaptive method and works
> best with there are many 100's or 1000's of voxels, and when most of
> them are null voxels with no signal. With a tiny number of voxels
> (17?), I think your better off just averaging the data and then
> fitting a model with, e.g. SPSS.
>
> Was this the issue?
>
> -Tom
>
> On Sun, Mar 16, 2008 at 2:52 PM, Versace, Amelia <[log in to unmask]>
> wrote:
> I am afraid I wasn't clear enough.... Let me try to make it clear...
> I didn't try to run fdr in the same volume (number of voxels
> significantly 'uncorrected'), but I defined the anatomical WM tract
> whom my 'uncorrected' roi belong to.
> I.e.: WM-mask in the L_Cuneus (about 1500 voxels) for an roi
> (17vxls) placed in the L_optical radiation (my uncorrected roi).
> I thought in this way I can say that this region doesn't survive for
> multiple comparisons at whole brain level, but it does within the
> anatomical area it belongs to.
> I can't see why this means cheating, but ...."of course I don't want
> make Tom cry...". :-), so please, could you suggest some references
> to understand these concepts better??
>
> In the mean time, I'll try the suggested approach.
>
> Thank you very much for your attention!!!
> Amelia
>
>
>
>
> Hi - I'm afraid you're not allowed to reduce your set of considered
> voxels (in order to reduce the effects of multiple comparisons) using
> the same data before and after - that's cheating and will make Tom
> cry.
>
> You _are_ for example, allowed to find a (corrected) significant ROI
> in the FA, and then only test the MD in that ROI.
>
> But you're NOT allowed to find an (uncorrected) 'significant' ROI in
> FA, and then only test within there for multiple comparisons - this
> goes against the whole reason for needing to do multiple comparisons
> on the original full set of voxels.
>
> If you're needing to boost significance I would just recommend testing
> the -tfce option (probably using H=1 and E=1 and just 500 permutations
> to start with)
>
> Cheers.
>
>
>
> On 11 Mar 2008, at 20:59, Versace, Amelia wrote:
>
> > Dear FSL experts,
> >
> > I am trying to do small volume correction for multiple comparison in
> > DTI data, because I got significant results just in tbss_*_voxtstat*
> > image (uncorrected p value).
> >
> > I was wondering if the following steps are correct:
> >
> > 1. run tbss -i all_FA.nii.gz -o tbss_* -m mean_FA_skeletonized _mask
> > -d design.mat -t design.con -c 3 -n 10000 -v 5
> >
> > 2. define 1-voxtstat* image (fslmaths tbss_*_voxtstat* -mul -1 -add
> > 1 tbss_*_1-voxtstat*)
> >
> > 3. define a WM-mask (accordingly with mean_FA_skeleton_mask)
> > surrounding a significant roi (group of voxels with p>0.999).
> >
> > 2. run fdr -i tbss_*_1-voxtstat* -m WM_mask -q 0.05
> >
> > 4.if the output is >0, can I consider that roi as small volume
> > corrected for multiple comparison??
> >
> >
> > About point 3, is there any size limitation of WM-mask in order to
> > use FDR properly??
> >
> >
> > If this is not the proper way, can anybody suggest a better one?
> > Many thanks for your help!
> > Amelia
> >
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
> --
> ____________________________________________
> Thomas Nichols, PhD
> Director, Modelling & Genetics
> GlaxoSmithKline Clinical Imaging Centre
>
> Senior Research Fellow
> Oxford University FMRIB Centre
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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