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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. |
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. |
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1. Path to data, and where the results are printed |
1. Path to data, and where the results are printed |
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1. 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. | 1. 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 do a 1-tailed test and only calculate positive activations. |
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1. Minimum number of contiguous voxels {{{ExtentThreshold=0;}}} |
1. Minimum number of contiguous voxels {{{ExtentThreshold=0;}}} |
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* 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. |
1. 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. |
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* Method for correcting for multiple comparisons : 'FWE','FDR', or 'none' {{{MCC='FDR';}}} |
1. Method for correcting for multiple comparisons : 'FWE','FDR', or 'none' {{{MCC='FDR';}}} |
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* The brain on which you want to render the results | 1. The brain on which you want to render the results |
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* Do it: | 1. Do it: |
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xSPM.u=0.025; % 2-tailed TailText='2-tailed, p<0.05'; |
xSPM.u=Threshold/2; % 2-tailed TailText=strcat('2-tailed, p<',Threshold); |
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xSPM.u=0.05; % 1-tailed TailText='1-tailed, p<0.05'; |
xSPM.u=Threshold; % 1-tailed TailText=strcat('1-tailed, p<',Threshold); |
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xSPM.k=0; | xSPM.k=ExtentThreshold; |
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delete(gcf) % this is a bit annoying, but for some reason I had problems without it for i=2:-1:1 |
delete(gcf) % this is a bit annoying, but for some reason I had problems without it for i=2:-1:1 |
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spm_render(flipdat,0.5,Brain); | spm_render(flipdat,0.5,Brain); % change the middle parameter to play with brightness of activations |
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.
- Path to data, and where the results are printed
dataroot = '/imaging/yourname/TestReCon';
- Name of folder, in above directory, where analysis is
outputdir='';
- Cell array of folder names in outputdir, containing the SPMs for each contrast
cond_dir={'EarlySmoothNoReCon'};
- 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 do a 1-tailed test and only calculate positive activations.
ShowDeactivations = 'no';
- p threshold
Threshold=0.05;
- 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=Threshold/2; % 2-tailed TailText=strcat('2-tailed, p<',Threshold); else xSPM.u=Threshold; % 1-tailed TailText=strcat('1-tailed, p<',Threshold); end xSPM.k=ExtentThreshold; 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); % change the middle parameter to play with brightness of activations 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