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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| function [aap,resp]=aamod_CoSMoMVPA(aap,task,subj) | ||
| resp=''; | ||
|
|
||
| switch task | ||
| case 'report' | ||
| % localpath = aas_getpath_bydomain(aap,aap.tasklist.currenttask.domain,[subj,sess]); | ||
| % | ||
| % fdiag = dir(fullfile(localpath,'diagnostic_*.jpg')); | ||
| % if isempty(fdiag) | ||
| % streams=aas_getstreams(aap,'output'); | ||
| % for streamind=1:length(streams) | ||
| % % obtain output | ||
| % outputfnames = aas_getfiles_bystream(aap,aap.tasklist.currenttask.domain,[subj sess],streams{streamind},'output'); | ||
| % | ||
| % % perform diagnostics | ||
| % do_diag(outputfnames); | ||
| % end | ||
| % fdiag = dir(fullfile(localpath,'diagnostic_*.jpg')); | ||
| % end | ||
| % | ||
| % for d = 1:numel(fdiag) | ||
| % aap = aas_report_add(aap,subj,'<table><tr><td>'); | ||
| % imgpath = fullfile(localpath,fdiag(d).name); | ||
| % aap=aas_report_addimage(aap,subj,imgpath); | ||
| % aap = aas_report_add(aap,subj,'</td></tr></table>'); | ||
| % end | ||
| case 'doit' | ||
| %% Prepare data | ||
| RSAROOT = fullfile(aas_getsubjpath(aap,subj),'RSA'); | ||
| aas_makedir(aap,RSAROOT); | ||
|
|
||
| inps = aas_getstreams(aap,'input'); | ||
| inps = inps(logical(cellfun(@(x) exist(aas_getinputstreamfilename(aap,'subject',subj,x),'file'), inps))); | ||
| struct_fn = aas_getfiles_bystream(aap,'subject',subj,inps{1}); | ||
|
|
||
| fnMask = cellfun(@(x) aas_getfiles_bystream(aap,'subject',subj,x), inps(cell_index(inps,'firstlevel_brainmask')),'UniformOutput',false); | ||
| fnSPM = cellfun(@(x) aas_getfiles_bystream(aap,'subject',subj,x), inps(cellfun(@(x) ~isempty(regexp(x,'firstlevel_spm$', 'once')), inps)),'UniformOutput',false); | ||
| fnTmaps = cellfun(@(x) aas_getfiles_bystream(aap,'subject',subj,x), inps(cell_index(inps,'firstlevel_spmts')),'UniformOutput',false); | ||
|
|
||
| if numel(fnSPM) > 1 | ||
| brain_mask = spm_imcalc(spm_vol(char(fnMask)),fullfile(RSAROOT,'brain_mask.nii'),'min(X)',{1}); | ||
| else | ||
| brain_mask.fname = char(fnMask); | ||
| end | ||
|
|
||
| ITEMS = aas_getsetting(aap,'itemList'); | ||
| fnT = {}; | ||
| for run = 1:numel(fnSPM) | ||
| load(fnSPM{run}); | ||
| conNames = {SPM.xCon.name}'; | ||
| for it = 1:numel(ITEMS) | ||
| ITEMS{it} = cellstr(ITEMS{it}); | ||
| fnT{end+1} = fnTmaps{run}(sum(cellfun(@(x) cell_index(conNames,x), ITEMS{it})),:); | ||
| end | ||
| end | ||
| spm_file_merge(fnT,fullfile(RSAROOT,'glm_T_stats_perrun.nii')); | ||
|
|
||
| %% Initialise Cosmo | ||
| oldPath = path; | ||
| cosmo_set_path | ||
| cosmo_check_external('-tic'); | ||
|
|
||
| % Data | ||
| ds=cosmo_fmri_dataset(fullfile(RSAROOT,'glm_T_stats_perrun.nii'),'mask',brain_mask.fname,... | ||
| 'targets',repmat(1:numel(ITEMS),1,numel(fnSPM))'); | ||
| ds=cosmo_fx(ds, @(x)mean(x,1), 'targets', 1); | ||
| ds.sa.labels=cellfun(@(x) x{1}, ITEMS, 'UniformOutput', false)'; | ||
| ds.sa.set=(1:numel(ITEMS))'; | ||
| cosmo_check_dataset(ds); | ||
|
|
||
| % Searchlight | ||
| nbrhood=cosmo_spherical_neighborhood(ds,'count',aas_getsetting(aap,'searchlightVox')); | ||
|
|
||
| % Model | ||
| target_dsm=importdata(aas_getsetting(aap,'bsMatrix')); | ||
| measure=@cosmo_target_dsm_corr_measure; | ||
| measure_args=struct(); | ||
| measure_args.target_dsm=target_dsm; | ||
|
|
||
| %% Info | ||
| aas_log(aap,false,'INFO:Dataset input:'); cosmo_disp(ds); | ||
| aas_log(aap,false,'INFO:Searchlight neighborhood definition:'); cosmo_disp(nbrhood); | ||
| aas_log(aap,false,'INFO:Target DSM:'); disp(target_dsm); | ||
|
|
||
| % imagesc(target_dsm) | ||
| % set(gca,'XTick',1:size(ds.samples,1),'XTickLabel',ds.sa.labels,... | ||
| % 'YTick',1:size(ds.samples,1),'YTickLabel',ds.sa.labels) | ||
|
|
||
| %% Run | ||
| ds_rsm_behav=cosmo_searchlight(ds,nbrhood,measure,measure_args); | ||
|
|
||
| % cosmo_plot_slices(ds_rsm_behav); | ||
|
|
||
| % store results | ||
| rsa_fn=fullfile(RSAROOT,'RSAmap.nii'); | ||
| cosmo_map2fmri(ds_rsm_behav,rsa_fn); | ||
|
|
||
| %% Cleanup | ||
| path(oldPath); | ||
|
|
||
| aap=aas_desc_outputs(aap,'subject',subj,'RSAmap',rsa_fn); | ||
|
|
||
| case 'checkrequirements' | ||
|
|
||
| otherwise | ||
| if isempty(which('cosmo_set_path')), aas_log(aap,true,sprintf('CoSMoMVPA cannot be found!\n Make sure you add <CoSMoMVPA directory>/mvpa to aap.directory_conventions.spmtoolsdir.')); end | ||
| reqInps = {'firstlevel_brainmask' 'firstlevel_spm' 'firstlevel_spmts'}; | ||
| inps = aas_getstreams(aap,'input'); | ||
| missingInps = reqInps(cellfun(@(x) ~any(cell_index(inps,x)), reqInps)); | ||
| if ~isempty(missingInps), aas_log(aap,true,['Inputs not specified:' sprintf(' %s',missingInps{:})]); end | ||
| end |
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