Hi,
On 30 Oct 2008, at 14:55, Yi-Shin Sheu wrote:
> Dear FSL experts,
>
> I am doing some preliminary analysis on 42 controls subjects that we
> have.
>
> After running randomise on FA skeleton by using the command:
>
> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d
> design.mat -t
> design.con -n 1000 --T2 -V -x
>
> I didn't get any significant results by looking at
> "tbss_tfce_corrp_tstat2.nii.gz" file (the
> corrected p stats file), which is expected, since the purpose of my
> analysis is basically
> exploring.
>
> So I look at the "tbss_tfce_p_tstat2.nii.gz" file (showing
> uncorrected p) in order to get a
> sense of what regions might show up. By set the threshold to (1-
> p)>0.99, and I did see
> two region that really support my hypothesis. But I do not know how
> to generate a
> report that show the cluster size of those regions.
You can use the 'cluster' program to produce output images that tell
you how large the clusters are. However, this isn't terribly useful -
this won't give you an 'independent' measure of significance, because
the TFCE enhancement already takes into account spatial extent.
> What I really would need is a command that might be similar to
> easythresh, which I can
> specify the threshold for "tbss_tfce_p_tstat2.nii.gz" and cluster
> size in a sensible way.
I'm afraid this would be even dodgier - easythresh inference is based
on Gaussian random field theory, which a) isn't applicable to the
_output_ of TFCE, and b) isn't in any case applicable in the case of
TBSS skeletons - sorry!
Is your main goal to try to 'boost' the significance of the regions
that you found, or to describe them concisely?
Cheers.
> I did try easythresh on the raw t-stats data, but it seems like
> there is a discrepancy
> between the generated outputs and what I see on the thresholded
> "tbss_tfce_p_tstat2.nii.gz". I am not sure which one makes more
> sense to look at. The
> command I tried with easythresh is:
> easythresh tbss_tstat2.nii.gz mean_FA.nii.gz 3.307 0.001
> mean_FA_mask.nii.gz
> Easythresh_3.307_0.001_tstat2
>
> Thank you for any input.
>
> Best wishes,
>
> Yi-Shin
>
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
|