Hi Leo,
Yes, you are right. But ttologp compute logp not directly from t value,
but from cope and varcope. If I am correct the equation is:
t = cope/varcope. Then based on the dof, logp will be calculated.
So if you have a t-map, you can feed the program along with a map with
ones, so:
t(program) = t(your map)/1. And the calculation will be performed as usual.
Bests,
Auer, Tibor M.D. Ph.D.
Biomedizinische NMR Forschungs GmbH
am Max-Planck Institut für Biophysikalische Chemie
Am Fassberg 11
37077 Göttingen
Germany
Phone/Work: +49-(0)551-201-1725
Phone/Home: +49-(0)551-387-0076
Mobile: +49-(0)176-8012-7921
Mail: [log in to unmask]
2010.08.13. 20:23 keltezéssel, Yiou Li írta:
> 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
>> ---------------------------------------------------------------------------
>>
>>
>>
>>
|