Modified version Ferath's script (BatchRenderRFX.m) 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.
The program needs files cls_getRes.m and 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. Also, you should add a path to the custom spm_render_dm, which solves some of the issues of the default spm_render command addpath /imaging/dm01/MEG/aaMEG. Finally, if you are using AAL, you should add the path to its toolkit, e.g.
Last updated 03/08 by DannyMitchell and AlejandroVicenteGrabovetsky
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 (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 coi=[29, -57, 45] % coordinate of interest for check_reg if no significant voxels%%%%%%% Do it: for j = 1:size(anadirs,2) outputdir=anadirs{j}; spm_defaults; global defaults defaults.modality='FMRI'; try q=defaults.units{3}; catch; defaults.units={'mm','mm','mm'}; end;%- 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 SPMfor 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') 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 -ve tail first, so that glass brain ends up showing +ve 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 if ignore_empty == 0 %%(AVG) Probably no need to draw, so do next contrast rather than print this one continue; else %%(djm) Overlay the results of individual subjects spm_check_registration(char(SPM.xY.P)); spm_orthviews('reposition',coi) ann1=annotation('textbox',[0 .94 1 .06],'Color','r','String',{strcat('RFX results (',TailText,' correction=',MCC,') No significant voxels; showing all subjects at %s'),strcat('Data:...',condir),strcat('Date:...',datestr(now,0))},'edge','none',mat2str(coi)); end end end end drawnow 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'); 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