diff --git a/lead_group.m b/lead_group.m index c291b4638..f36ed8427 100644 --- a/lead_group.m +++ b/lead_group.m @@ -2174,37 +2174,45 @@ function lc_SPM_Callback(hObject, eventdata, handles) % hObject handle to lc_SPM (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) +M=getappdata(handles.lg_figure,'M'); + +gecs=get(handles.lc_graphmetric,'String'); +[~,gecs]=fileparts(gecs{M.ui.lc.graphmetric}); +parc=get(handles.labelpopup,'String'); +parc=parc{get(handles.labelpopup,'Value')}; -spmdir=[M.ui.groupdir,'connectomics',filesep,get(handles.labelpopup,'String'),filesep,'graph',filesep,gecs,filesep,'SPM']; +spmdir=[M.ui.groupdir,'connectomics',filesep,parc,filesep,'graph',filesep,gecs,filesep,'SPM']; +try rmdir(spmdir,'s'); +end mkdir([M.ui.groupdir,'connectomics']); -mkdir([M.ui.groupdir,'connectomics',filesep,get(handles.labelpopup,'String')]); -mkdir([M.ui.groupdir,'connectomics',filesep,get(handles.labelpopup,'String'),filesep,'graph']); -gecs=get(handles.lc_graphmetrics,'String'); -[~,gecs]=gecs{M.ui.lc.graphmetrics}; -mkdir([M.ui.groupdir,'connectomics',filesep,get(handles.labelpopup,'String'),filesep,'graph',filesep,gecs]); +mkdir([M.ui.groupdir,'connectomics',filesep,parc]); +mkdir([M.ui.groupdir,'connectomics',filesep,parc,filesep,'graph']); + +mkdir([M.ui.groupdir,'connectomics',filesep,parc,filesep,'graph',filesep,gecs]); mkdir(spmdir); for sub=1:length(M.patient.list) - if M.ui.lc.normalize==1; + if M.ui.lc.normalization==1; zzz=''; - elseif M.ui.lc.normalize==2; + elseif M.ui.lc.normalization==2; zzz='z'; - ea_histnormalize([M.patient.list{sub},'connectomics',filesep,get(handles.labelpopup,'String'),filesep,'graph',filesep,gecs,'.nii,1'],2); - elseif M.ui.lc.normalize==3; + ea_histnormalize([M.patient.list{sub},filesep,'connectomics',filesep,parc,filesep,'graph',filesep,gecs,'.nii,1'],2); + elseif M.ui.lc.normalization==3; zzz='k'; - ea_histnormalize([M.patient.list{sub},'connectomics',filesep,get(handles.labelpopup,'String'),filesep,'graph',filesep,gecs,'.nii,1'],3); + ea_histnormalize([M.patient.list{sub},filesep,'connectomics',filesep,parc,filesep,'graph',filesep,gecs,'.nii,1'],3); end if M.ui.lc.smooth sss='s'; - ea_smooth([M.patient.list{sub},'connectomics',filesep,get(handles.labelpopup,'String'),filesep,'graph',filesep,zzz,gecs,'.nii,1']); + ea_smooth([M.patient.list{sub},filesep,'connectomics',filesep,parc,filesep,'graph',filesep,zzz,gecs,'.nii,1']); else sss=''; end - fis{sub}=[M.patient.list{sub},'connectomics',filesep,get(handles.labelpopup,'String'),filesep,'graph',filesep,sss,zzz,gecs,'.nii,1']; + fis{sub}=[M.patient.list{sub},filesep,'connectomics',filesep,parc,filesep,'graph',filesep,sss,zzz,gecs,'.nii,1']; end + %% model specification: matlabbatch{1}.spm.stats.factorial_design.dir = {spmdir}; matlabbatch{1}.spm.stats.factorial_design.des.t1.scans = fis'; @@ -2305,16 +2313,20 @@ function lc_smooth_Callback(hObject, eventdata, handles) function ea_histnormalize(fname,zzz) nii=ea_load_nii(fname); [pth,fn,ext]=fileparts(fname); -vals=nii.img(~isnan(nii.img)); + +msk=isnan(nii.img); +msk=msk+(nii.img==0); +vals=nii.img(~msk); +ext=ext(1:end-2); switch zzz case 2 % zscore - nii.fname=[pth,'z',fn,ext]; + nii.fname=[pth,filesep,'z',fn,ext]; vals=zscore(vals(:)); case 3 % albada - nii.fname=[pth,'k',fn,ext]; - vals=ea_normal(vals(:)); + nii.fname=[pth,filesep,'k',fn,ext]; + vals=ea_normal(vals(:)); end -nii.img(~isnan(nii.img))=vals; +nii.img(~msk)=vals; spm_write_vol(nii,nii.img); function ea_smooth(fname)