Hi - the first example shows how to bring up the cluster p-values and
threshold them; in the second example, the example fslview command is
bringing up the raw tstat images, and the text after that example
command line call is describing how also to load in the pvalue images
(maxc) and threshold them.
Cheers.
On 14 May 2007, at 17:55, R Huang wrote:
> Dear All,
>
>
> I am puzzled by the descriptions of TBSS--fslview
> in the practical and the TBSS-website.
>
>
> (1) In the practical of 'Analysis of Diffusion-Weighted MR Data
> (the last paragraph of
> http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt/
> index.htm),
>
> ... Thresholding clusters at 0.949 (corresponding to thresholding the
> p-values at 0.05, because randomise outputs p-values as 1-p for
> convenience of display - so that higher values are more
> significant) shows
> several areas of reduced FA in the MS patients.
> The following shows unthresholded t-stats in red-yellow and
> thresholded
> clusters in blue:
>
> fslview MNI152 mean_FA_skeleton -l Green -b 2000,8000 tbss_tstat1 -l
> Red-Yellow -b 1.5,3 tbss_maxc_tstat1 -l Blue-Lightblue -b 0.949,1
>
> (2) But in the TBSS
> (http://www.fmrib.ox.ac.uk/fsl/tbss/index.html), the description
>
> fslview MNI152 mean_FA_skeleton -l Green -b 2000,8000 tbss_tstat1 -l
> Red-Yellow -b 3,6 tbss_tstat2 -l Blue-Lightblue -b 3,6
>
> ...The cluster p-value images (fully corrected for multiple
> comparisons
> across space) are tbss_maxc_tstat1 and tbss_maxc_tstat2 (note,
> these are
> actually 1-p for convenience of display, so thresholding at .95 gives
> significant clusters).
>
>
> Does any one know why 'fslview' in the two locations use different
> '-b'
> values?
>
> Many thanks in advance
>
> Rhuang
>
>
>
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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)
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