Hi Stephen,
Can you explain why ttologp() conversion needs a variance (varcope) as
input? --- Would t-stats and dof be sufficient to decide a p-value?
Please kindly advise.
Best,
Leo
On Thu, Aug 12, 2010 at 3:31 AM, Stephen Smith <[log in to unmask]> wrote:
> Hi - use the tstat in place of cope1 and make a copy full of ones for
> varcope.
> Cheers.
>
>
> On 11 Aug 2010, at 23:20, Yiou Li wrote:
>
> Hi All,
>
> I used a third party software to obtain t-stats map and now I wan to
> calculate the FDR using the following code:
> ********************************************************
> ttologp -logpout logp1 varcope1 cope1 `cat dof`
> (this outputs the log(p) image)
>
> fslmaths logp1 -exp p1
> (this creates the p-value image)
>
> fdr -i p1 -m ../mask -q 0.05
> Probability Threshold is:
> 0.00339819
> (this tells you the FDR threshold - p-values below 0.00339819 are
> significant)
>
> fslmaths p1 -mul -1 -add 1 -thr .99660181 -mas ../mask thresh_1_minus_p1
> (this creates a 1-p image for ease of display, thresholds that at
> 1-thresh and then remasks)
> ***************************************************************
> However, I don't have the varcope1 and cope1 values since I didn't use
> FEAT to generate the t stat maps.
>
> Could you please advise what how can I work it around?
>
> Best,
> Leo
>
>
>
> ---------------------------------------------------------------------------
> 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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