Dear Micael,
Concerning the first problem raised by Ged (negative RESEL counts
creating an error later on), it seems to me that this can be fixed by
changing l.30 of spm_uc_RF.m so that:
u = spm_u((a/max(R))^(1/n),df,STAT); % and not mean(R)
Hopefully it provides a fix for most of the errors reported in the last
years on that topic:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?S2=SPM&q=betainc
Please report any situation that will still create an error after this fix.
Concerning the use of spm_P_RF for very low thresholds, you should then
get NaN, which, even if accidental, is not such a bad answer given that
the assumption that the expected Euler characteristic is close to the
number of blobs does not hold any more (the threshold should at least
correspond to a Z score of 3). Answering NaN, instead of 1, can then be
seen as a reminder that you are out of the range of application of the
RFT. In which context would you go for such low thresholds?
Also, are you reporting that in some instances, spm_P_RF returns a real
value smaller than 0 when you would be expecting NaN (or 1)? If so, with
which input parameters to spm_P_RF?
Best regards,
Guillaume.
Micael Andersson wrote:
> Dear Ged and other SPM-users
>
> I have noticed the same phenomena that you point out at "*" below. The
> negativeness of the fourth EC-density makes the FWE-corrected p-value to
> become low in a short intervall of small t-values when it should
> obviously be 1 (about from t=0.7 to t=1). Perhaps one should set EM =
> max(0,EM)? It is problably not a big problem since voxel thresholds
> shouldn't be that low, but it might affect other applications of the
> spm_P_RF. I noticed it when making a function for conjunction by
> maximizing p-values.
>
>
> At 10:57 2007-04-16, Ged Ridgway wrote:
>> Dear RFT experts,
>>
>> I've noticed that for a couple of VBM studies with normal-looking
>> FWE-corrected results, when I came to check xSPM.R I saw that the
>> first two resel counts are negative.
>>
>> While it seems reasonable (or at least possible) that the Euler
>> Characteristic might be negative, I'm confused as to how the caliper
>> diameter (xSPM.R(2)) could possibly be negative. Any comments?
>>
>> It seems possible from spm_P_RF that negative resel counts might
>> produce a negative Em,* which produces a NaN from spm_Pcdf. This might
>> possibly be the cause of a later error. E.g. maybe in this apparently
>> unanswered post:
>> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=SPM&P=R775760
>>
>> Perhaps line 106 of spm_P_RF should be replaced with something like
>> lam = max(eps, Em*p);
>> P = 1 - spm_Pcdf(c - 1, lam);
>>
>> to return p-values of 1 instead?
>>
>> *(also, the fourth EC density at line 160 of spm_P_RF can be negative
>> for t less than 1 -- or near 1, and small DF, e.g.
>> v = 10; t = 1.05;
>> (v-1)*(t.^2)/v - 1 < 0
>> It's probably daft to ask for the corrected p-value of such low
>> t-values, but I would guess that it would be better to return p=1
>> than p=NaN)
>>
>> All the best,
>> Ged.
>
>
> /Micael
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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