Hi - yes, as I said yesterday, as long as you didn't decide to place
this ROI _after_ seeing the initial uncorrected results, then that's
fine - that would be true for this situation AND in FMRI.
Cheers, Steve.
On 18 Mar 2008, at 20:41, Versace, Amelia wrote:
> Not really…
> I just wanted to check that the approach I'm using to control for
> multiple tests for small regions that emerge as significant
> (p<0.001, uncorrected) in my TBSS analyses is OK.
>
> The approach I'm using for a small volume correction is essentially
> the same as the small volume correction approach employed for fMRI
> and VBM structural data I've used with SMP5. I'm using an
> anatomically-defined regional mask for the small volume correction.
> Thus, for example, for the left optic radiation cluster, I use an
> optic radiation mask for which the search volume is approx.. 1500
> voxels. I test the significance of my 17-voxel cluster against that
> mask. Is this approach OK for TBSS data? I cannot think of another
> method of employing a small volume correction approach.
>
> Thank you in advance for your advice here!
> Best Regards
> Amelia
>
>
> Amelia Versace, MD
> Loeffler Building
> 121 Meyran Avenue, room 202
> Pittsburgh, PA 15213
> Phone 412- 383-8202
> Fax 412-383-8336
>
>
> CONFIDENTIAL UPMC HEALTH SYSTEM INFORMATION Any unauthorized or
> improper disclosure, copying, distribution, or use of the contents
> of this email or attached documents is PROHIBITED. The information
> contained in this e-mail message is intended only for the personal
> and confidential use of the recipient(s) named above. If you have
> received this communication in error, please notify the sender
> IMMEDIATELY by e-mail and DELETE the original message.
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Thomas Nichols
> Sent: Monday, March 17, 2008 6:07 PM
> To: [log in to unmask]
> Subject: Re: [FSL] SVC for multiple comparisons
>
> 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
---------------------------------------------------------------------------
|