BatchRenderRfx - MRC CBU Imaging Wiki

Revision 1 as of 2006-10-01 20:12:08

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Modified version Ferath's script to threshhold and print SPM5 results. The script prints rendered activations as well as a list of coordinates. The first six blocks of lines are the ones you need to (or are most likely to want to) change. Originally modified by DannyMitchell and subsequently by IanNimmoSmith.

  1. Path to data, and where the results are printed

    dataroot = '/imaging/dm01/TestReCon';

  2. Name of folder, in above directory, where analysis is

    outputdir='';

  3. Cell array of folder names in outputdir, containing the SPMs for each contrast

    cond_dir={'EarlySmoothNoReCon'};

  4. 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';

  5. p threshold

    Threshold=0.05;

  6. Minimum number of contiguous voxels

    ExtentThreshold=0;

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.

addpath /imaging/dm01/MoreTools/spm2Batch

Method for correcting for multiple comparisons : 'FWE','FDR', or 'none' MCC='FDR';

The brain on which you want to render the results Brain='/imaging/local/spm/spm5/rend/render_smooth_average.mat';

{{{%%%%%%% Do it: if exist(fullfile(dataroot,strcat(outputdir,'_RFX_Rendered.ps')))==2

  • delete(fullfile(dataroot,strcat(outputdir,'_RFX_Rendered.ps')));

end; disp(strcat('Printing results to:...',fullfile(dataroot,strcat(outputdir,'_RFX_Rendered.ps')))) spm_defaults; global defaults defaults.modality='FMRI';

%

%- 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}); cd(condir); xSPM.spmmat = fullfile(condir,'SPM.mat'); % Get SPM path

    if ShowDeactivations(1)=='y'

    • xSPM.u=0.025; % 2-tailed

      TailText='2-tailed, p<0.05';

    else
    • xSPM.u=0.05; % 1-tailed

      TailText='1-tailed, p<0.05';

    end xSPM.k=0; bck_xSPM=xSPM; delete(gcf) % this is a bit annoying, but for some reason I had problems without it for i=2:-1:1
    • xSPM= bck_xSPM; % Reset xSPM to default xSPM.Ic=i; %Set the current contrast Index [hReg,xSPM,SPM] = csl_getRes(xSPM); dat(3-i) = struct( 'XYZ', xSPM.XYZ,...
      • 't', xSPM.Z',... 'mat', xSPM.M,... 'dim', xSPM.DIM);
    end clear flipdat flipdat(1)=dat(2);

    if ShowDeactivations(1)=='y'

    • flipdat(2)=dat(1);
    end try
    • spm_render(flipdat,0.5,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),0.5,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),0.5,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,'_RFX_Rendered.ps'))); spm_list('List',xSPM,hReg); spm_print(fullfile(dataroot,strcat(outputdir,'_RFX_Rendered.ps'))); xSPM= bck_xSPM; % Reset xSPM to default delete(ann1);

end }}}