I am curious about the number of permutations necessary for TFCE. 5000
takes a very long time (>3 days for us), yet I thought that reducing the
number of permutations basically results in widely varying p values if
the same analysis is run a second time. I remember snPM advertising 2000
permutations as a reasonable number. What is the current empirical
understanding of this?
Another question I have is the following. We have a single significant
voxel FWE corrected in one analysis, but when we try to do a fdr
corrected analysis, nothing comes out significant. Is this possible?
Stefano Marenco, NIMH
-----Original Message-----
From: Steve Smith [mailto:[log in to unmask]]
Sent: Thursday, March 13, 2008 3:29 AM
To: [log in to unmask]
Subject: Re: [FSL] SVC for multiple comparison
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
>
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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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