Modified version Ferath's script to threshhold and print SPM5 results. The script prints glass brains and rendered activations as well as the first page of the results table. The lines in block (3) are the ones you need to (or are most likely to want to) change. Originally modified by DannyMitchell and subsequently by IanNimmoSmith.

1. The program needs files attachment:cls_getRes.m and attachment:cls_getSPM2.m . For CBU people the following line should find them, otherwise you need to download them and point to their path. addpath /imaging/dm01/MoreTools/spm2Batch

2. Last updated 02/07 by DannyMitchell

3. dataroot = ''; % path to data, and where the results are printed
   outputdir=''; % name of folder, in above directory, where analysis is
   cond_dir={''}; % cell array of folder names in outputdir, containing the SPMs for each contrast
   outputfilesuffix='_RFX_Rendered.ps'
   %{set the following variable to 'yes' to do a 2-tailed test and show
   % rendered activations and deactivations (assumes that positive and negative
   % second level contrasts have already been calculated; Glass brains will
   % only show positive activations). Set it to 'no' to to a 1-tailed test
   % and only calculate positive activations. %}
   ShowDeactivations = 'no';
   Threshold=0.05; % p threshold
   ExtentThreshold=0; % minimum number of contiguous voxels
   addpath /imaging/dm01/MoreTools/spm2Batch %{the program needs files cls_getRes.m and cls_getSPM2.m. For CBU people this line will find them, otherwise you need to download them and point to their path.%}
   MCC='FDR'; % method for correcting for multiple comparisons : 'FWE','FDR', or 'none'
   Brain='/imaging/local/spm/spm5/rend/render_smooth_average.mat'%render_single_subj.mat' %render_smooth_average.mat'; % the brain on which you want to render the results
   Style=1; % Rendering Style: NaN=old, 1=normal, <1=brighter

4. %%%%%%% Do it:
   if exist(fullfile(dataroot,strcat(outputdir,outputfilesuffix)))==2
       delete(fullfile(dataroot,strcat(outputdir,outputfilesuffix)));
   end;
   spm_defaults;
   global defaults
   defaults.modality='FMRI';
   try q=defaults.units{3}; catch; defaults.units={'mm','mm','mm'}; end; % for some reason I had to add this line 15/01/07
   
   %--------------------------------------------------------------------
   %- xSPM is a structure for the parameters

5. xSPM = struct( ...
       'swd', '', ... % full path to SPM.mat file
       'Ic', [], ... % no of contrast (or contrasts for conjunction)
       'Im', [],... % no of contrast to mask with. Empty for no masking
       'pm', [],... % masking contrast uncorrected p
       'Ex', [],... % whether masking is inclusive or exclusive
       'title', '',... % if empty results in default contrast title
       'Mcp', MCC,... % Mutiple comp method: FWE|FDR|none
       'u', Threshold,... % threshold (corrected or uncorrected, as above)
       'k', ExtentThreshold); % extent threshold
   
   clear SPM

6. for i = 1:size(cond_dir,2)
       condir = fullfile(dataroot,outputdir,cond_dir{i});
       cd(condir);
       xSPM.spmmat = fullfile(condir,'SPM.mat'); % Get SPM path
       if lower(ShowDeactivations(1))=='y'
           xSPM.u=Threshold/2; % 2-tailed
           TailText=strcat('2-tailed, p<',num2str(Threshold));
       else
           xSPM.u=Threshold; % 1-tailed
           TailText=strcat('1-tailed, p<',num2str(Threshold));
       end
       xSPM.k=ExtentThreshold;
       bck_xSPM=xSPM;
       delete(gcf) % this is a bit annoying, but for some reason I had problems without it
       nc=0;
       for i=2:-1:1
           xSPM=bck_xSPM; % Reset xSPM to default
           xSPM.Ic=i; %Set the current contrast Index
           try
               [hReg,xSPM,SPM] = csl_getRes(xSPM);
               nc=nc+1;
               dat(nc) = struct( 'XYZ', xSPM.XYZ,...
                   't', xSPM.Z',...
                   'mat', xSPM.M,...
                   'dim', xSPM.DIM);
           catch
               ShowDeactivations = 'no'; % only found one contrast
               xSPM.u=Threshold; % 1-tailed
               TailText=strcat('1-tailed, p<',num2str(Threshold));
           end
       end
       clear flipdat
       flipdat(1)=dat(2);
       if lower(ShowDeactivations(1))=='y'
           flipdat(2)=dat(1);
       end
       try
           spm_render(flipdat,Style,Brain);
           ann1=annotation('textbox',[0 .94 1 .06],'Color','r','String',{strcat('RFX results (',TailText,' correction=',MCC,', red=positive)'),strcat('Data:...',condir),strcat('Date:...',datestr(now,0))},'edge','none');
       catch
           try
               spm_render(flipdat(1),Style,Brain);
               ann1=annotation('textbox',[0 .94 1 .06],'Color','r','String',{strcat('RFX results (',TailText,' correction=',MCC,', red=positive)'),strcat('Data:...',condir),strcat('Date:...',datestr(now,0))},'edge','none');
           catch
               try
                   spm_render(flipdat(2),Style,Brain);
                   ann1=annotation('textbox',[0 .94 1 .06],'Color','r','String',{strcat('RFX results (',TailText,' correction=',MCC,', RED=NEGATIVE)'),strcat('Data:...',condir),strcat('Date:...',datestr(now,0))},'edge','none');
               catch
                   ann1=annotation('textbox',[0 .94 1 .06],'Color','r','String',{strcat('RFX results (',TailText,' correction=',MCC,') No significant effects'),strcat('Data:...',condir),strcat('Date:...',datestr(now,0))},'edge','none');
               end
           end
       end
       spm_print(fullfile(dataroot,strcat(outputdir,outputfilesuffix)));
       TabDat=spm_list('List',xSPM,hReg);
       tot=0;
       for r=1:size(TabDat.dat,1)
           if ~isempty(TabDat.dat{r,4}); tot=tot+TabDat.dat{r,4};end
       end
       if tot>0
           delete(ann1);
           ann1=annotation('textbox',[0 .94 1 .06],'Color','r','String',{strcat('RFX results (',TailText,' correction=',MCC,')'),strcat('Data:...',condir),strcat('Date:...',datestr(now,0))},'edge','none');
           ann2=annotation('textbox',[0 0 1 .02],'Color','r','String',strcat('First page of table only. Total number of significant voxels=',num2str(tot)),'edge','none');
           spm_print(fullfile(dataroot,strcat(outputdir,outputfilesuffix)));
           delete(ann2);
       end
       xSPM= bck_xSPM; % Reset xSPM to default
       delete(ann1);
   end
   fprintf('\nFinished.\nResults saved to: %s.\r',fullfile(dataroot,strcat(outputdir,outputfilesuffix)));