AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Isaac Schwabacher
February 20, 2015 12:03PM
If you look at 3dcalc -help, you'll find this: 

 The following 27 functions are used for statistical conversions,
 as in the program 'cdf':
   fico_t2p(t,a,b,c), fico_p2t(p,a,b,c), fico_t2z(t,a,b,c),
   fitt_t2p(t,a)    , fitt_p2t(p,a)    , fitt_t2z(t,a)    ,
   fift_t2p(t,a,b)  , fift_p2t(p,a,b)  , fift_t2z(t,a,b)  ,
   fizt_t2p(t)      , fizt_p2t(p)      , fizt_t2z(t)      ,
   fict_t2p(t,a)    , fict_p2t(p,a)    , fict_t2z(t,a)    ,
   fibt_t2p(t,a,b)  , fibt_p2t(p,a,b)  , fibt_t2z(t,a,b)  ,
   fibn_t2p(t,a,b)  , fibn_p2t(p,a,b)  , fibn_t2z(t,a,b)  ,
   figt_t2p(t,a,b)  , figt_p2t(p,a,b)  , figt_t2z(t,a,b)  ,
   fipt_t2p(t,a)    , fipt_p2t(p,a)    , fipt_t2z(t,a)    .

 See the output of 'cdf -help' for documentation on the meanings of
 and arguments to these functions.  The two functions below use the
 NIfTI-1 statistical codes to map between statistical values and
 cumulative distribution values:
   cdf2stat(val,code,p1,p2,p3) -- val is between 0 and 1
   stat2cdf(val,code,p1,p2,p3) -- val is legal for the given distribution
 where code is
   2 = correlation statistic     p1 = DOF
   3 = t statistic (central)     p1 = DOF
   4 = F statistic (central)     p1 = num DOF, p2 = den DOF
   5 = N(0,1) statistic          no parameters (p1=p2=p3=0)
   6 = Chi-squared (central)     p1 = DOF
   7 = Beta variable (central)   p1 = a , p2 = b
   8 = Binomial variable         p1 = #trials, p2 = prob per trial
   9 = Gamma distribution        p1 = shape, p2 = scale
  10 = Poisson distribution      p1 = mean
  11 = N(mu,variance) normal     p1 = mean, p2 = scale
  12 = noncentral F statistic    p1 = num DOF, p2 = den DOF, p3 = noncen
  13 = noncentral chi-squared    p1 = DOF, p2 = noncentrality parameter
  14 = Logistic distribution     p1 = mean, p2 = scale
  15 = Laplace distribution      p1 = mean, p2 = scale
  16 = Uniform distribution      p1 = min, p2 = max
  17 = noncentral t statistic    p1 = DOF, p2 = noncentrality parameter
  18 = Weibull distribution      p1 = location, p2 = scale, p3 = power
  19 = Chi statistic (central)   p1 = DOF
  20 = inverse Gaussian variable p1 = mu, p2 = lambda
  21 = Extreme value type I      p1 = location, p2 = scale
  22 = 'p-value'                 no parameters
  23 = -ln(p)                    no parameters
  24 = -log10(p)                 no parameters
When fewer than 3 parameters are needed, the values for later parameters
are still required, but will be ignored.  An extreme case is code=5,
where the correct call is (e.g.) cdf2stat(p,5,0,0,0)

Which means that you can use ccalc (which is 3dcalc for individual numbers instead of datasets) to compute what you want: 

3dclust -1noneg -1thresh `ccalc -expr 'fizt_p2t(.01)'` -dxyz=1 1.01 10 brik.nii   # 1sided
3dclust -1thresh `ccalc -expr 'fizt_p2t(.01/2)'` -dxyz=1 1.01 10 brik.nii   # 2sided

Unfortunately, it doesn't look like there's an easy way to do the bisided case. You would have to run the program twice, once with positive and once with negative input, and then merge the results together.
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Subject Author Posted

New 3dClustSim

kickan February 20, 2015 04:03AM

Re: New 3dClustSim

Isaac Schwabacher February 20, 2015 12:03PM