June 03, 2010

SPM2 Gem 4: –log10 P–values from T images

P-value images are difficult to visualize since "important" values are small and clumped near zero. A -log10 transformation makes for much better visualization while still having interpretability (e.g. a value of 3 cooresponds to P=0.001).

This function, T2nltP, will create -log10 P-value image based on either a contrast number (which must be a T contrast) or a T statistic image and the degrees of freedom.

This version for SPM2 was created Michael Moffitt, based on the SPM99 function of the same name for SPM99. Note that Michael's version can easily be changed to create P-values instead of -log10 P-values.

T2nltP.m

function T2nltP(a1,a2)
% Write image of P-values (spm_nltP_?) for a T image
%
% FORMAT T2nltP
% SPM will ask you which spmT_? file you want to convert to spm_nltP_?
%
% FORMAT T2nltP(Timg,df)
% Timg  Filename of T image
% df    Degrees of freedom
%
%
% As per SPM convention, T images are zero masked, and so zeros will have
% P-value NaN.
%
% @(#)T2nltP.m  1.2 T. Nichols 03/07/15
% Modified 04/01/20 by MAM - for SPM2 compatibility

if nargin==0

     % Ask user for SPM.mat file and specific contrast
     [SPM,xSPM]=spm_getSPM;

     % If a 'T' contrast, get degrees of freedom (df) and fname of spmT_?
     if xSPM.STAT ~= 'T', error('Not a T contrast'); end
     df=xSPM.df(2);
     Tnm=xSPM.Vspm.fname;

elseif nargin==2
   Tnm = a1;
   df  = a2;
end


Tvol = spm_vol(Tnm);

Pvol        = Tvol;
Pvol.dim(4) = spm_type('float');
Pvol.fname  = strrep(Tvol.fname,'spmT','spm_nltP');
if strcmp(Pvol.fname,Tvol.fname)
   Pvol.fname = fullfile(spm_str_manip(Tvol.fname,'H'), ...
                         ['nltP' spm_str_manip(Tvol.fname,'t')]);
end


Pvol = spm_create_vol(Pvol);

for i=1:Pvol.dim(3),
   img         = spm_slice_vol(Tvol,spm_matrix([0 0 i]),Tvol.dim(1:2),0);
   img(img==0) = NaN;
   tmp         = find(isfinite(img));
   if ~isempty(tmp)
       % Create map of P values
       %img(tmp)  = (max(eps,1-spm_Tcdf(img(tmp),df)));

       % Create map of -log10(P values)
       img(tmp)  = -log10(max(eps,1-spm_Tcdf(img(tmp),df)));
   end
   Pvol        = spm_write_plane(Pvol,img,i);
end;

spm_close_vol(Pvol);

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