% Modified version of Ferath's script to threshhold and print SPM5 second % level results. % Prints rendered activations as well as a list of coordinates. % The first 11 lines are the ones you need to (or are most likely to % want to) change. % djm 03/08 dataroot = ''; % path to data anadirs = {''}; % name of folder(s), in above directory, where analysis is (useful if you have used several models in analysis) cond_dir={''}; % cell array of folder names in outputdir, containing the SPMs for each contrast % %%(AVG) Alternatively, save the data from your 'aamod_firstlevel_contrasts.m' file onto a 'contrast_names.mat' file and do the following: % load contrast_names % cond_dir=cname; %cname is the array of contrast names and their directory names in your second level analysis folder 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 (0.75 = light, 0.5 = more, 0.25 = lots) % for results table num=3; % number of maxima per cluster dis=8; % distance among clusters (mm) doaal = 0; % Label anatomical clusters with AAL? 1=yes 0=no ignore_empty = 1 % (AVG) Create a file if there are no significant voxels? 1=yes 0=no %%%%%%% Do it: for j = 1:size(anadirs,2) outputdir=anadirs{j}; 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 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 for i = 1:size(cond_dir,2) condir = fullfile(dataroot,outputdir,cond_dir{i}); % Checks if there is a rendered file made for this contrast and deletes the old one if exist(strcat(condir,outputfilesuffix),'file')==2 delete(strcat(condir,outputfilesuffix)); end; cd(condir); xSPM.spmmat = fullfile(condir,'SPM.mat'); % Get SPM path %%%%%%%%% modified 080308 to run 2nd level contrasts if not found % Set significance thresholds and run t-tests if not done already load(xSPM.spmmat) if isempty(SPM.xCon) SPM.xCon = spm_FcUtil('Set',cond_dir{i},'T','c',1,SPM.xX.xKXs); end if lower(ShowDeactivations(1))=='y' xSPM.u=Threshold/2; % 2-tailed TailText=strcat('2-tailed, p<',num2str(Threshold)); if length(SPM.xCon)<2 SPM.xCon(end+1) = spm_FcUtil('Set',strcat('Negative_',cond_dir{i}),'T','c',-1,SPM.xX.xKXs); end else xSPM.u=Threshold; % 1-tailed TailText=strcat('1-tailed, p<',num2str(Threshold)); end if isempty(SPM.xCon(1).Vcon) spm_contrasts(SPM); end %%%%%%%%%%%%%% xSPM.k=ExtentThreshold; bck_xSPM=xSPM; delete(gcf) % this is a bit annoying, but for some reason I had problems without it clear dat for con=2:-1:1 % get any negative tail first, so that glass brain ends up showing positive tail xSPM=bck_xSPM; % Reset xSPM to default xSPM.Ic=con; %Set the current contrast Index if strcmp(ShowDeactivations,'no') && con==2; continue; end; try [hReg,xSPM,SPM] = csl_getRes(xSPM); if exist('dat','var') dat(end+1) = struct('XYZ', xSPM.XYZ,'t', xSPM.Z','mat', xSPM.M,'dim', xSPM.DIM); else dat(1) = struct('XYZ', xSPM.XYZ,'t', xSPM.Z','mat', xSPM.M,'dim', xSPM.DIM); end catch xSPM.u=Threshold; % 1-tailed TailText=strcat('1-tailed, p<',num2str(Threshold)); end end dat=circshift(dat,[1 1]); try % should work if all tails tested have significant voxels spm_render_dm(dat,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 % just render +ve tail if no significant -ve voxels spm_render_dm(dat(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 % just render -ve tail if no significant +ve voxels dat(1)=dat(2); dat(1).t=zeros(length(dat(1).XYZ),1); % set dat(1) as empty dat(2) spm_render_dm(dat,Style,Brain); ann1=annotation('textbox',[0 .94 1 .06],'Color','r','String',{strcat('RFX results (',TailText,' correction=',MCC,', blue=negative)'),strcat('Data:...',condir),strcat('Date:...',datestr(now,0))},'edge','none'); catch % probably no significant voxels 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'); if ignore_empty == 0 %%(AVG) Alternatively: probably no need to draw, so do next contrast rather than print this one continue; end end end end try spm_print(strcat(condir,outputfilesuffix)); catch fprintf('\nFailed to print! (check write permissions?)'); return end TabDat=spm_list('List',xSPM,hReg,num, dis); 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'); try spm_print(strcat(condir,outputfilesuffix)); catch fprintf('\nFailed to print! (check write permissions?)'); return end delete(ann2); end %Following section borrowed from Mirjana Bozic's script if doaal == 1 % SPM_print anatomical labels for clusters using batch-enabled AAL scripts gin_clusters_plabels_auto('List',xSPM); spm_print(strcat(condir,outputfilesuffix)); end xSPM= bck_xSPM; % Reset xSPM to default delete(ann1); end fprintf('\nFinished.\nResults saved to: %s.\r',strcat(condir,outputfilesuffix)); end