Dear Steve,
Many thanks for your explanation.
In reality, I would like to know that for the given tstat images or the pvalue
images (maxc), how to choose the range of [-b] value if I use fslview to
display p<0.05 result? (see the example in TBSS-website
(http://www.fmrib.ox.ac.uk/fsl/tbss/index.html),
Cheers
Rhuang
On Tuesday 15 May 2007 09:39, you wrote:
> 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
>
> ------------------------------------------------------------------------
> ---
> 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
> ------------------------------------------------------------------------
> ---
|