function varargout=conn_process(options,varargin)
global CONN_x
if nargin<1, options=[]; end
if ischar(options),
switch(lower(options)),
case 'all', disp(['CONN: RUNNING ALL ANALYSIS STEPS']); conn_process([0:14]);
case 'all_voxel', disp(['CONN: RUNNING ALL ANALYSIS STEPS (voxel-based analyses only)']); conn_process([0:3,5:6,9:10,12:13]);
case 'all_roi', disp(['CONN: RUNNING ALL ANALYSIS STEPS (roi-based analyses only)']); conn_process([0:2,4:5,7,9,11,14]);
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:5]);
case 'setup_roi', disp(['CONN: RUNNING SETUP STEP (roi-based analyses only)']); conn_process([0:2,4:5]);
case 'preprocessing', disp(['CONN: RUNNING PREPROCESSING STEP']); conn_process([5:9],varargin{:});
case 'preprocessing_gui',disp(['CONN: RUNNING PREPROCESSING STEP']); conn_process([6:9],varargin{:});
case 'preprocessing_roi',disp(['CONN: RUNNING PREPROCESSING STEP (roi-based analyses only)']); conn_process([5,7,9],varargin{:});
case 'analyses', disp(['CONN: RUNNING ANALYSIS STEP']); conn_process([9,10:14],varargin{:});
case 'analyses_seed', disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([9,10,12],varargin{:});
case 'analyses_vv', disp(['CONN: RUNNING ANALYSIS STEP (voxel-to-voxel analyses)']); conn_process([9,13],varargin{:});
case 'analyses_roi', disp(['CONN: RUNNING ANALYSIS STEP (roi-based analyses only)']); conn_process([9,11,14],varargin{:});
case 'analyses_gui', disp(['CONN: RUNNING ANALYSIS STEP']); conn_process([10:14],varargin{:});
case 'analyses_gui_seed',disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10:12,14],CONN_x.Analysis);
case 'analyses_gui_vv', disp(['CONN: RUNNING ANALYSIS STEP (voxel-to-voxel analyses)']); conn_process([13],varargin{:});
case 'prepare_results', conn_process(13:14,varargin{:});
case 'prepare_results_roi',conn_process(14,varargin{:});
case 'results', conn_process(15:16,varargin{:});
case 'results_voxel', [varargout{1:nargout}]=conn_process(15,varargin{:});
case 'results_roi', [varargout{1:nargout}]=conn_process(16,varargin{:});
case 'update', conn gui_setup_saveas; conn_process all; conn save;
end
return;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Checks dimensionality of setup files
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==0),
ERR={};
if isempty(CONN_x.filename)||isempty(dir(CONN_x.filename)),ERR{end+1}=['WARNING: Project not saved or empty project information']; end
try, conn_updatefilepaths; catch, ERR{end+1}=['ERROR: Files not found. Check that all your functional/structural/ROIs/first-level covariate files point to existing files.']; end
nl1covariates=length(CONN_x.Setup.l1covariates.names)-1;
nconditions=length(CONN_x.Setup.conditions.names)-1;
nrois=length(CONN_x.Setup.rois.names)-1;
if nconditions<1, ERR{end+1}=['ERROR: No conditions defined. You must define at least one condition (use onset=0; duration=inf; for encompassing the entire scanning session)']; end
for nsub=1:CONN_x.Setup.nsubjects,
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
if nsess<1,ERR{end+1}=['ERROR: Subject ',num2str(nsub),' has no functional data assigned (number of sessions = 0); increase the number of sessions in Setup->Basic or remove this subject']; end
if numel(CONN_x.Setup.conditions.values)<nsub, ERR{end+1}=['ERROR: Subject ',num2str(nsub),' has no experimental conditions defined']; end
if numel(CONN_x.Setup.conditions.values)>=nsub&&numel(CONN_x.Setup.conditions.values{nsub})<nconditions, ERR{end+1}=['ERROR: Missing experimental conditions on Subject ',num2str(nsub)]; end
okconditions=false(1,nconditions);
for nses=1:nsess,
if length(CONN_x.Setup.nscans)<nsub, ERR{end+1}=['ERROR: Subject ',num2str(nsub),' has no functional data defined'];
elseif length(CONN_x.Setup.nscans{nsub})<nses, ERR{end+1}=['ERROR: Subject ',num2str(nsub),' has no functional data defined for session ',num2str(nses)];
else,
nscans=CONN_x.Setup.nscans{nsub}{nses};
if isempty(nscans),ERR{end+1}=['ERROR: Subject ',num2str(nsub),' Session ',num2str(nses), ' functional data has not been defined'];
elseif nscans<2, ERR{end+1}=['ERROR: Subject ',num2str(nsub),' Session ',num2str(nses), ' functional data has ',num2str(nscans),' time-points (scans) defined']; end
for nroi=1:nrois,
if numel(CONN_x.Setup.rois.files)<nsub||numel(CONN_x.Setup.rois.files{nsub})<nroi||numel(CONN_x.Setup.rois.files{nsub}{nroi})<3||isempty(CONN_x.Setup.rois.files{nsub}{nroi}{1}),
ERR{end+1}=['ERROR: Subject ',num2str(nsub),' ROI ',num2str(nroi), ' file has not been defined'];
end
end
for nl1covariate=1:nl1covariates,
filename=CONN_x.Setup.l1covariates.files{nsub}{nl1covariate}{nses}{1};
switch(filename),
case '[raw values]',
data=CONN_x.Setup.l1covariates.files{nsub}{nl1covariate}{nses}{3};
otherwise,
data=load(filename);
if isstruct(data), tempnames=fieldnames(data); data=data.(tempnames{1}); end
end
names=CONN_x.Setup.l1covariates.names{nl1covariate};
if size(data,1)~=nscans, ERR{end+1}=['ERROR: Subject ',num2str(nsub),' Session ',num2str(nses), ' first-level covariate ',names,' mismatched dimensions (',num2str(size(data,1)),' rows, while functional data has ',num2str(nscans),' scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)']; end
end
for ncondition=1:nconditions,
if numel(CONN_x.Setup.conditions.values)>=nsub&&numel(CONN_x.Setup.conditions.values{nsub})>=ncondition&&(numel(CONN_x.Setup.conditions.values{nsub}{ncondition})<nses||numel(CONN_x.Setup.conditions.values{nsub}{ncondition}{nses})<2),
disp(['warning: Subject ',num2str(nsub),' condition ',CONN_x.Setup.conditions.names{ncondition},' has not been defined for session ',num2str(nses),'. Assuming this condition is not present in this session']);
CONN_x.Setup.conditions.values{nsub}{ncondition}{nses}={[],[]};
else
okconditions(ncondition)=okconditions(ncondition)|(~isempty(CONN_x.Setup.conditions.values{nsub}{ncondition}{nses}{1})&&~isempty(CONN_x.Setup.conditions.values{nsub}{ncondition}{nses}{2}));
end
end
end
end
if any(~okconditions)
for ncondition=find(~okconditions);
ERR{end+1}=['ERROR: Subject ',num2str(nsub),' does not have any scan associated with condition ',CONN_x.Setup.conditions.names{ncondition}];
end
end
end
if ~isempty(ERR),
disp('SOME ERROR FOUNDS!: Please revise the Setup information');
disp(strvcat(ERR));
return;
end
% check coregistration of reference files
CONN_x.Setup.normalized=1;
if CONN_x.Setup.spatialresolution~=1
ok=1;
for nsub=1:CONN_x.Setup.nsubjects,
switch(CONN_x.Setup.spatialresolution)
case 2, v=CONN_x.Setup.structural{nsub}{3}.dim;
case 3, v=CONN_x.Setup.functional{nsub}{1}{3}.dim;
end
if nsub==1, vref=v;
elseif any(v~=vref), ok=0;
end
end
if ~ok,
switch(CONN_x.Setup.spatialresolution)
case 2, vname='structural';
case 3, vname='functional';
end
txt=sprintf('Warning: %s volumes do not have the same dimensions. Multi-subject voxel-level analyses will NOT be performed. Choose ''same as template'' option in ''spatial resolution'' field if you wish to resample the data to a common voxel-resolution instead',vname);
if isfield(CONN_x,'gui')&&isnumeric(CONN_x.gui)&&CONN_x.gui,
answ= questdlg(txt,'','Continue', 'Stop','Stop');
if strcmp(answ,'Stop'), return; end
CONN_x.Setup.normalized=0;
else
disp(txt);
CONN_x.Setup.normalized=0;
end
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Segments structural data if appropriate
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==1),
h=conn_waitbar(0,['Step ',num2str(sum(options<=1)),'/',num2str(length(options)),': Segmentation']);
[path,name,ext]=fileparts(CONN_x.filename);
for nsub=1:CONN_x.Setup.nsubjects,
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
dosegm=0;for n1=1:3,if length(CONN_x.Setup.rois.files{nsub})<n1||isempty(CONN_x.Setup.rois.files{nsub}{n1})||~iscell(CONN_x.Setup.rois.files{nsub}{n1})||isempty(CONN_x.Setup.rois.files{nsub}{n1}{1}),dosegm=1;end;end;
if dosegm,
file=deblank(CONN_x.Setup.structural{nsub}{1});
if (~conn_existfile(conn_prepend(['c',num2str(1)],file)))||(~conn_existfile(conn_prepend(['c',num2str(2)],file)))||(~conn_existfile(conn_prepend(['c',num2str(3)],file))),
V=spm_vol(file);
res=spm_preproc(V);
[sn,isn]=spm_prep2sn(res);
savefields(conn_prepend('',deblank(CONN_x.Setup.structural{nsub}{1}),'_seg_sn.mat'),sn);
savefields(conn_prepend('',deblank(CONN_x.Setup.structural{nsub}{1}),'_seg_inv_sn.mat'),isn);
opts=struct('biascor',0,'GM',[0 0 1],'WM',[0 0 1],'CSF',[0 0 1],'cleanup',0);
spm_preproc_write(sn,opts);
end
for n1=1:3,
ffile=conn_prepend(['c',num2str(n1)],file);
[V,str,icon]=conn_getinfo(ffile);
CONN_x.Setup.rois.files{nsub}{n1}={ffile,str,icon};
end
end
conn_waitbar(nsub/CONN_x.Setup.nsubjects,h);
end
conn_waitbar('close',h);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates COV_Subject###_Session###.mat files (first-level temporal covariate values)
% Creates COND_Subject###_Session###.mat files (temporal samples included in each condition)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==2),
[path,name,ext]=fileparts(CONN_x.filename);
%[ok,nill]=mkdir(path,name);
%[ok,nill]=mkdir(fullfile(path,name),'data');
%filepath=fullfile(path,name,'data');
filepath=CONN_x.folders.data;
h=conn_waitbar(0,['Step ',num2str(sum(options<=2)),'/',num2str(length(options)),': Importing covariates']);
REDO=[];
nl1covariates=length(CONN_x.Setup.l1covariates.names)-1;
nconditions=length(CONN_x.Setup.conditions.names)-1;
N=sum(CONN_x.Setup.nsessions); if length(CONN_x.Setup.nsessions)==1, N=N*CONN_x.Setup.nsubjects; end
N=N*(nl1covariates+nconditions);
maxdims=[];n=0;
for nsub=1:CONN_x.Setup.nsubjects,
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
for nses=1:nsess,
filename=fullfile(filepath,['COND_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
if isempty(REDO)&&~isempty(dir(filename)),
if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
end
if strcmp(REDO,'Yes')||isempty(dir(filename)),
clear data names;
clear samples weights;
nscans=CONN_x.Setup.nscans;
for nl1covariate=1:nl1covariates,
filename=CONN_x.Setup.l1covariates.files{nsub}{nl1covariate}{nses}{1};
switch(filename),
case '[raw values]',
data{nl1covariate}=CONN_x.Setup.l1covariates.files{nsub}{nl1covariate}{nses}{3};
otherwise,
data{nl1covariate}=load(filename);
if isstruct(data{nl1covariate}), tempnames=fieldnames(data{nl1covariate}); data{nl1covariate}=data{nl1covariate}.(tempnames{1}); end
end
names{nl1covariate}=CONN_x.Setup.l1covariates.names{nl1covariate};
n=n+1;
conn_waitbar(n/N,h);
end
for ncondition=1:nconditions,
onset=CONN_x.Setup.conditions.values{nsub}{ncondition}{nses}{1};
durat=CONN_x.Setup.conditions.values{nsub}{ncondition}{nses}{2};
rt=CONN_x.Setup.RT/10;
durat=max(rt,min(CONN_x.Setup.RT*CONN_x.Setup.nscans{nsub}{nsess},durat));
hrf=spm_hrf(rt);
x=zeros(ceil(CONN_x.Setup.nscans{nsub}{nses}*CONN_x.Setup.RT/rt),1);
for n1=1:length(onset), x(round(1+onset(n1)/rt+(0:durat(min(length(durat),n1))/rt-1)))=1; end
if CONN_x.Setup.acquisitiontype==1,
x=convn(x,hrf);
end
x=mean(reshape(x(1:10*CONN_x.Setup.nscans{nsub}{nses}),[10,CONN_x.Setup.nscans{nsub}{nses}]),1)';%x=x(1+10*(0:CONN_x.Setup.nscans{nsub}{nses}-1));
data{nl1covariates+ncondition}=x;
names{nl1covariates+ncondition}=['Effect of ',CONN_x.Setup.conditions.names{ncondition}];
samples{ncondition}=[]; weights{ncondition}=cell(1,2);
idx1=find(x>0); idx2=[0;find(diff(idx1)>1);length(idx1)];
for n1=1:length(idx2)-1,
idx=idx1(idx2(n1)+1:idx2(n1+1));
samples{ncondition}=cat(1,samples{ncondition},idx(:));
weights{ncondition}{1}=cat(1,weights{ncondition}{1},x(idx(:)));
weights{ncondition}{2}=cat(1,weights{ncondition}{2},conn_hanning(length(idx)));
end
n=n+1;
conn_waitbar(n/N,h);
end
filename=fullfile(filepath,['COV_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
save(filename,'data','names');
% if str2num(version('-release'))>=14, save(filename,'-V6','data','names');
% else, save(filename,'data','names'); end
for n1=1:length(data), if length(maxdims)<n1, maxdims(n1)=size(data{n1},2); else, maxdims(n1)=max(maxdims(n1),size(data{n1},2)); end; end
names={CONN_x.Setup.conditions.names{1:nconditions}};
filename=fullfile(filepath,['COND_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
save(filename,'samples','weights','names');
% if str2num(version('-release'))>=14, save(filename,'-V6','samples','weights','names');
% else, save(filename,'samples','weights','names'); end
end
end
end
conn_waitbar('close',h);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates DATA_Subject###_Session###.mat files (percentage signal change data at analysis mask)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==3) && any(CONN_x.Setup.steps([2,3])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.data;
h=conn_waitbar(0,['Step ',num2str(sum(options<=3)),'/',num2str(length(options)),': Importing functional data']);
REDO='Yes';filename=fullfile(filepath,['DATA_Subject',num2str(1,'%03d'),'_Session',num2str(1,'%03d'),'.mat']);
if ~isempty(dir(filename)),if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end; end
N=sum(CONN_x.Setup.nsessions); if length(CONN_x.Setup.nsessions)==1, N=N*CONN_x.Setup.nsubjects; end
n=0;
if CONN_x.Setup.analysismask==1,%CONN_x.Setup.normalized,
filename=fullfile(fileparts(which('spm')),'apriori','brainmask.nii');
Vmask=spm_vol(filename);
elseif 0,%isfield(CONN_x.Setup,'usebrainmask')&&CONN_x.Setup.usebrainmask,
Vmask1=spm_vol(CONN_x.Setup.rois.files{nsub}{1}{1});
Vmask2=spm_vol(CONN_x.Setup.rois.files{nsub}{2}{1});
Vmask3=spm_vol(CONN_x.Setup.rois.files{nsub}{3}{1});
Vmask=struct('mat',Vmask1.mat,'dim',Vmask1.dim,'fname',conn_prepend('mask_',CONN_x.Setup.functional{nsub}{1}{1}(1,:)),...
'dt',[spm_type('uint8') spm_platform('bigend')]);
a=spm_read_vols(Vmask1)+spm_read_vols(Vmask2)+spm_read_vols(Vmask3);
try,
spm_write_vol(Vmask,a>0);
catch,
[temp_path,temp_filename,temp_ext]=fileparts(Vmask.fname);
Vmask.fname=fullfile(pwd,[temp_filename,temp_ext]);
spm_write_vol(Vmask,a>0);
end
Vmask=spm_vol(Vmask.fname);
else, Vmask=[]; end
for nsub=1:CONN_x.Setup.nsubjects,
switch CONN_x.Setup.spatialresolution
case 1, filename=fullfile(fileparts(which('spm')),'apriori','brainmask.nii');
case 2, filename=deblank(CONN_x.Setup.structural{nsub}{1});
case 3, filename=deblank(CONN_x.Setup.functional{nsub}{1}{1}(1,:));
end
Vref=spm_vol(filename);
Vref=Vref(1);
CONN_x.Setup.spatialresolutionvolume{nsub}=Vref;
% if ~CONN_x.Setup.normalized,
% filename=deblank(CONN_x.Setup.structural{nsub}{1});
% Vref=spm_vol(filename);
% end
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
sfile=[];%conn_prepend('',CONN_x.Setup.structural{nsub}{1},'_seg_inv_sn.mat');
for nses=1:nsess,
filename=fullfile(filepath,['DATA_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
if strcmp(REDO,'Yes')||isempty(dir(filename)),
warning off;Vsource=spm_vol(CONN_x.Setup.functional{nsub}{nses}{1});warning on;
CONN_x.Setup.nscans{nsub}{nses}=prod(size(Vsource));
if CONN_x.Setup.analysismask==2&&nses==1,%~CONN_x.Setup.normalized&&(isempty(Vmask)), % computes analysis mask
Vmask=Vsource(1);
Vmask.fname=conn_prepend('mask_',CONN_x.Setup.functional{nsub}{1}{1}(1,:));
Vmask.dt=[spm_type('uint8') spm_platform('bigend')];
a=ones(Vmask.dim(1:3));
[gridx,gridy,gridz]=ndgrid(1:Vmask.dim(1),1:Vmask.dim(2),1:Vmask.dim(3));xyz=Vmask.mat*[gridx(:),gridy(:),gridz(:),ones(numel(gridx),1)]';
for nsest=1:nsess,
if nsest==nses,Vsourcet=Vsource;else,warning off;Vsourcet=spm_vol(CONN_x.Setup.functional{nsub}{nsest}{1});warning on;end
for nt=1:numel(Vsourcet),
b=reshape(spm_get_data(Vsourcet(nt),pinv(Vsourcet(nt).mat)*xyz),Vmask.dim(1:3)); %b=spm_read_vols(Vsourcet(nt));
mb=mean(b(b>mean(b(~isnan(b)))/8));
a=a&(b>0.80*mb);
end
end
try,
spm_write_vol(Vmask,a);
catch,
[temp_path,temp_filename,temp_ext]=fileparts(Vmask.fname);
Vmask.fname=fullfile(pwd,[temp_filename,temp_ext]);
spm_write_vol(Vmask,a);
end
end
V=conn_create_vol(filename,Vsource,[],Vref,sfile,Vmask);
end
n=n+1;
conn_waitbar(n/N,h);
end
end
conn_waitbar('close',h);
clear data;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates sDATA_Subject###_Session###.mat files (smoothed functional data)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0,%any(options==2.5),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.data;
h=conn_waitbar(0,['Step ',num2str(sum(options<=3)),'/',num2str(length(options)),': Smoothing functional data']);
N=sum(CONN_x.Setup.nsessions); if length(CONN_x.Setup.nsessions)==1, N=N*CONN_x.Setup.nsubjects; end
n=0;
for nsub=1:CONN_x.Setup.nsubjects,
[spath,sfile,sext]=fileparts(deblank(CONN_x.Setup.structural{nsub}{1}));
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
for nses=1:nsess,
filename=fullfile(filepath,['DATA_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
fileout=fullfile(filepath,['sDATA_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
Y0=conn_vol(filename);
conn_reslice(fileout,Y0.matdim.mat,Y0.matdim.dim,Y0,[],CONN_x.Setup.fwhm);
n=n+1;
conn_waitbar(n/N,h);
end
end
conn_waitbar('close',h); ;
clear data;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates ROI_Subject###_Session###.mat files (activation timecourses for each roi)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==4),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.data;
h=conn_waitbar(0,['Step ',num2str(sum(options<=4)),'/',num2str(length(options)),': Importing ROI data']);
REDO='Yes';filename=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Session',num2str(1,'%03d'),'.mat']);
if ~isempty(dir(filename)),if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end; end
nrois=length(CONN_x.Setup.rois.names)-1;
N=sum(CONN_x.Setup.nsessions); if length(CONN_x.Setup.nsessions)==1, N=N*CONN_x.Setup.nsubjects; end
N=N*nrois;
n=0;
for nsub=1:CONN_x.Setup.nsubjects,
clear Vmask; for nroi=1:nrois, Vmask{nroi}=CONN_x.Setup.rois.files{nsub}{nroi}{1}; end
ERODE=1; % erosing level for white/csf masks (voxels) (set to 0 for no erosion)
if ERODE>0,
for nroi=2:3,
Vmask{nroi}=conn_prepend('e',CONN_x.Setup.rois.files{nsub}{nroi}{1});
if (~conn_existfile(conn_prepend('e',CONN_x.Setup.rois.files{nsub}{nroi}{1}))),
[nill,nill,ext]=fileparts(Vmask{nroi});
switch(ext),
case {'.img','.nii','.hdr'},
V0=spm_vol(CONN_x.Setup.rois.files{nsub}{nroi}{1}); % mask
X0=spm_read_vols(V0);
idx1=find(X0(:)>.5);
[idxx,idxy,idxz]=ind2sub(size(X0),idx1);
idxt=find(idxx>ERODE&idxx<size(X0,1)+1-ERODE&idxy>ERODE&idxy<size(X0,2)+1-ERODE&idxz>ERODE&idxz<size(X0,3)+1-ERODE);
for n1=1:length(idxt), if (sum(sum(sum(X0(idxx(idxt(n1))+(-ERODE:ERODE),idxy(idxt(n1))+(-ERODE:ERODE),idxz(idxt(n1))+(-ERODE:ERODE))<.5,3),2),1))>1, idxt(n1)=0; end; end
idxt=idxt(idxt>0);
idx1=idx1(idxt);
X1=zeros(size(X0));X1(idx1)=1;V0.fname=conn_prepend('e',CONN_x.Setup.rois.files{nsub}{nroi}{1});spm_write_vol(V0,X1);
otherwise,
Vmask{nroi}=CONN_x.Setup.rois.files{nsub}{nroi}{1};
end
end
end
end
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
for nses=1:nsess,
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
if ~isempty(dir(filename)),
old=load(filename);%,'data','names','source','xyz','sampledata');
else, old=[]; end
filename=fullfile(filepath,['COV_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
covariates=load(filename);covariates=cat(2,covariates.data{:});
source=fullfile(filepath,['DATA_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
Vsource=CONN_x.Setup.functional{nsub}{nses}{1};
Vsource2=[];
for n1=1:size(Vsource,1),
[Vsourcepath,Vsourcename,Vsourceext]=fileparts(Vsource(n1,:));
if Vsourcename(1)~='s' || (~conn_existfile(fullfile(Vsourcepath,[Vsourcename(2:end),Vsourceext]))), Vsource2=[]; break; end
Vsource2=strvcat(Vsource2,fullfile(Vsourcepath,[Vsourcename(2:end),Vsourceext])); % exists un-smooth data?
end
if strcmp(REDO,'Yes')||isempty(old)||~isfield(old,'sampledata'),
sampledata=conn_rex(Vsource,Vmask{1},'dims',256,'level','subsetvoxels','scaling','roi','select_clusters',0,'output_type','none');
else, sampledata=old.sampledata; end
if ~isempty(Vsource2), Vsource=Vsource2; end
clear data names xyz;
nroi1=1;
for nroi=1:nrois,
%if nroi>=5&&nroi<=8,REDO='Yes';else REDO='No'; end
if ~isfield(CONN_x.Setup.rois,'mask') || length(CONN_x.Setup.rois.mask)<nroi, CONN_x.Setup.rois.mask(nroi)=0; end
if ~isfield(CONN_x.Setup.rois,'multiplelabels') || length(CONN_x.Setup.rois.multiplelabels)<nroi, CONN_x.Setup.rois.multiplelabels(nroi)=0; end
if ~isfield(CONN_x.Setup.rois,'regresscovariates') || length(CONN_x.Setup.rois.regresscovariates)<nroi, CONN_x.Setup.rois.regresscovariates(nroi)=double(CONN_x.Setup.rois.dimensions{nrois}>1); end
failed=0;
if ~strcmp(REDO,'Yes')&&~isempty(old),
if CONN_x.Setup.rois.multiplelabels(nroi),
[roi_path_dir,roi_path_name]=fileparts(Vmask{nroi});
idx=strmatch([CONN_x.Setup.rois.names{nroi},'.'],old.names);
%idx=strmatch([roi_path_name,'.'],old.names);
if isempty(idx) failed=1;
else
if isempty(dir(fullfile(roi_path_dir,[roi_path_name,'.txt']))),
if CONN_x.Setup.rois.mask(nroi), mask=CONN_x.Setup.rois.files{nsub}{1}{1}; else, mask=''; end
if CONN_x.Setup.rois.multiplelabels(nroi), level='clusters'; else, level='rois'; end
if CONN_x.Setup.rois.regresscovariates(nroi), entercovariates=covariates; else, entercovariates=[]; end
[nill,tnames]=conn_rex(Vmask{nroi},Vmask{nroi},'summary_measure','mean','conjunction_mask',mask,'level',level,'scaling','roi','select_clusters',0,'covariates',entercovariates,'output_type','saverex');
for n1=1:numel(tnames)
if ~isempty(strmatch(roi_path_name,tnames{n1})), tnames{n1}=[tnames{n1}(numel(roi_path_name)+2:end)]; end
end
else
tnames=textread(fullfile(roi_path_dir,[roi_path_name,'.txt']),'%s','delimiter','\n');
end
clear tidx; for n1=1:length(tnames),
tidx{n1}=strmatch([CONN_x.Setup.rois.names{nroi},'.',tnames{n1}],old.names,'exact');
if isempty(tidx{n1}), failed=1; else, tidx{n1}=tidx{n1}(1); end
end
if ~failed,
for n1=1:length(tnames),
data{nroi1}=old.data{tidx{n1}};
names{nroi1}=old.names{tidx{n1}};
xyz{nroi1}=old.xyz{tidx{n1}};
nroi1=nroi1+1;
end
end
end
else,
idx=strmatch(CONN_x.Setup.rois.names{nroi},old.names,'exact');
if isempty(idx), failed=1;
else,
idx=idx(1);
data{nroi1}=old.data{idx};
names{nroi1}=old.names{idx};
xyz{nroi1}=old.xyz{idx};
nroi1=nroi1+1;
end
end
end
if strcmp(REDO,'Yes')||isempty(old)||failed,
%disp(nroi);
if CONN_x.Setup.rois.mask(nroi), mask=CONN_x.Setup.rois.files{nsub}{1}{1}; else, mask=''; end
if CONN_x.Setup.rois.multiplelabels(nroi), level='clusters'; else, level='rois'; end
if CONN_x.Setup.rois.regresscovariates(nroi), entercovariates=covariates; else, entercovariates=[]; end
if isfield(CONN_x.Setup,'extractSVD')&&CONN_x.Setup.extractSVD
[data{nroi1},namesroi{nroi},params]=conn_rex(Vsource,Vmask{nroi},'summary_measure','eigenvariate','PCA',0,'dims',CONN_x.Setup.rois.dimensions{nroi},'conjunction_mask',mask,'level',level,'scaling','roi','select_clusters',0,'covariates',entercovariates,'output_type','saverex');
else
if CONN_x.Setup.rois.dimensions{nroi}>1,
[data{nroi1},namesroi{nroi},params]=conn_rex(Vsource,Vmask{nroi},'summary_measure','eigenvariate','dims',CONN_x.Setup.rois.dimensions{nroi},'conjunction_mask',mask,'level',level,'scaling','roi','select_clusters',0,'covariates',entercovariates,'output_type','saverex');
else,
[data{nroi1},namesroi{nroi},params]=conn_rex(Vsource,Vmask{nroi},'summary_measure','mean','conjunction_mask',mask,'level',level,'scaling','roi','select_clusters',0,'covariates',entercovariates,'output_type','saverex');
end
end
[data{nroi1},ok]=conn_nan(data{nroi1});
data{nroi1}=detrend(data{nroi1},'constant');
if CONN_x.Setup.rois.multiplelabels(nroi),
datatemp=data{nroi1};
[Vmaskfilepath,Vmaskfilename,Vmaskfileext]=fileparts(Vmask{nroi});
for n1=1:size(datatemp,2),
data{nroi1}=datatemp(:,n1); names{nroi1}=namesroi{nroi}{n1};
if ~isempty(strmatch(Vmaskfilename,names{nroi1})), names{nroi1}=[CONN_x.Setup.rois.names{nroi},names{nroi1}(numel(Vmaskfilename)+1:end)]; end
Z=params.ROIinfo.basis{params.ROIinfo.trans{n1}{1}}{params.ROIinfo.trans{n1}{2}}(params.ROIinfo.trans{n1}{4},params.ROIinfo.trans{n1}{3});
XYZ=params.ROIinfo.voxels{params.ROIinfo.trans{n1}{1}}{params.ROIinfo.trans{n1}{2}}(params.ROIinfo.trans{n1}{4},:);
xyz{nroi1}=mean(XYZ(Z==max(Z),:),1);
nroi1=nroi1+1;
end
else,
names{nroi1}=CONN_x.Setup.rois.names{nroi};
n1=1;
Z=params.ROIinfo.basis{params.ROIinfo.trans{n1}{1}}{params.ROIinfo.trans{n1}{2}}(params.ROIinfo.trans{n1}{4},params.ROIinfo.trans{n1}{3});
XYZ=params.ROIinfo.voxels{params.ROIinfo.trans{n1}{1}}{params.ROIinfo.trans{n1}{2}}(params.ROIinfo.trans{n1}{4},:);
xyz{nroi1}=mean(XYZ(Z==max(Z),:),1);
nroi1=nroi1+1;
end
filename=fullfile(filepath,['REX_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'_ROI',num2str(nroi),'.mat']);
load('REX.mat');save(filename,'params');
end
n=n+1;
conn_waitbar(n/N,h);
end
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
save(filename,'data','names','source','xyz','sampledata');
% if str2num(version('-release'))>=14, save(filename,'-V6','data','names','source','xyz','sampledata');
% else, save(filename,'data','names','source','xyz','sampledata');end
end
end
% eliminates ROIs not present in all subjects/sessions
for nsub=1:CONN_x.Setup.nsubjects,
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
for nses=1:nsess,
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
load(filename,'names');
if nsub==1&&nses==1,ROInamesall=names;
else,
temp=zeros(1,length(ROInamesall));
for n1=1:length(ROInamesall),
idx=strmatch(ROInamesall{n1},names,'exact');
temp(n1)=~isempty(idx);
end
if ~all(temp),
idx=find(~temp);
for n1=1:length(idx), disp(['Warning: ROI ',ROInamesall{idx(n1)},' missing from Subject ',num2str(nsub),' Session ',num2str(nses)]); end
end
ROInamesall={ROInamesall{find(temp)}};
end
end
end
tmp=[];
for nsub=1:CONN_x.Setup.nsubjects,
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
for nses=1:nsess,
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
load(filename,'data','names','source','xyz','sampledata');
temp=zeros(1,length(names));
for n1=1:length(names),
idx=strmatch(names{n1},ROInamesall,'exact');
temp(n1)=~isempty(idx);
end
if ~all(temp),
if isempty(tmp), tmp=questdlg('Remove regions with incomplete data?','','Yes', 'No', 'Yes'); end
if strcmp(tmp,'Yes'),
data={data{find(temp)}};
names={names{find(temp)}};
xyz={xyz{find(temp)}};
save(filename,'data','names','source','xyz','sampledata');
% if str2num(version('-release'))>=14, save(filename,'-V6','data','names','source','xyz','sampledata');
% else, save(filename,'data','names','source','xyz','sampledata');end
end
end
end
end
conn_waitbar('close',h); ;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% updates CONN_x.Preproc structure with a subset of ROIs plus all covariates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==5),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.data;
filename1=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Session',num2str(1,'%03d'),'.mat']);
filename2=fullfile(filepath,['COV_Subject',num2str(1,'%03d'),'_Session',num2str(1,'%03d'),'.mat']);
if isempty(dir(filename1)), disp(['Not ready to process step conn_process_5']); return; end
x1=load(filename1);
x2=load(filename2);
CONN_x.Preproc.variables.names=cat(2,x1.names,x2.names);
CONN_x.Preproc.variables.types=cat(2,repmat({'roi'},[1,length(x1.names)]),repmat({'cov'},[1,length(x2.names)]));
CONN_x.Preproc.variables.deriv=cat(2,repmat({0},[1,length(x1.names)]),repmat({1},[1,length(x2.names)]));
CONN_x.Preproc.variables.dimensions={};
for n1=1:length(x1.names), CONN_x.Preproc.variables.dimensions{end+1}=size(x1.data{n1},2)*ones(1,2); end
for n1=1:length(x2.names), CONN_x.Preproc.variables.dimensions{end+1}=size(x2.data{n1},2)*ones(1,2); end
N1=length(x1.names);N2=length(x2.names);
for nsub=1:CONN_x.Setup.nsubjects,
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
for nses=1:nsess,
filename2=fullfile(filepath,['COV_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
x2=load(filename2);
for n1=1:N2, CONN_x.Preproc.variables.dimensions{N1+n1}=max(CONN_x.Preproc.variables.dimensions{N1+n1},size(x2.data{n1},2)*ones(1,2)); end
end
end
if isfield(CONN_x.Preproc.confounds,'names') && ~isempty(CONN_x.Preproc.confounds.names), initial=CONN_x.Preproc.confounds.names; dims=CONN_x.Preproc.confounds.dimensions; ders=CONN_x.Preproc.confounds.deriv;
else, initial={'White Matter','CSF',x2.names{:}};dims={5,5}; ders={}; end
CONN_x.Preproc.confounds.names={};
CONN_x.Preproc.confounds.types={};
CONN_x.Preproc.confounds.deriv={};
CONN_x.Preproc.confounds.dimensions={};
for n1=1:length(initial), idx=strmatch(initial{n1},CONN_x.Preproc.variables.names,'exact'); if ~isempty(idx),
CONN_x.Preproc.confounds.names{end+1}=CONN_x.Preproc.variables.names{idx};
CONN_x.Preproc.confounds.types{end+1}=CONN_x.Preproc.variables.types{idx};
if length(ders)>=n1&&~isempty(ders{n1}), CONN_x.Preproc.confounds.deriv{end+1}=ders{n1}; else, CONN_x.Preproc.confounds.deriv{end+1}=CONN_x.Preproc.variables.deriv{idx};end
if length(dims)>=n1&&~isempty(dims{n1}), CONN_x.Preproc.confounds.dimensions{end+1}=[min(dims{n1}(1),CONN_x.Preproc.variables.dimensions{idx}(1)),CONN_x.Preproc.variables.dimensions{idx}(1)]; else, CONN_x.Preproc.confounds.dimensions{end+1}=CONN_x.Preproc.variables.dimensions{idx}; end
end
end
if ~isfield(CONN_x.Preproc,'filter')||isempty(CONN_x.Preproc.filter), CONN_x.Preproc.filter=[0,1/(2*CONN_x.Setup.RT)]; end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates DATA_Subject###_Condition###.mat files (whole-brain data after removal of confounding effects & filtering)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==6) && any(CONN_x.Setup.steps([2,3])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.data;
filepathresults=CONN_x.folders.preprocessing;
nconditions=length(CONN_x.Setup.conditions.names)-1;
h=conn_waitbar(0,['Step ',num2str(sum(options<=6)),'/',num2str(length(options)),': Preprocessing functional data']);
REDO='Yes';filename=fullfile(filepathresults,['DATA_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if ~isempty(dir(filename)),if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end; end
N=CONN_x.Setup.nsubjects; %sum(CONN_x.Setup.nsessions); if length(CONN_x.Setup.nsessions)==1, N=N*CONN_x.Setup.nsubjects; end
n=0;
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepathresults,['DATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if strcmp(REDO,'Yes')||isempty(dir(filename)),
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
clear Y X iX X1 X2 C;
for nses=1:nsess, % loads all ROI COV COND data for this subject
filename=fullfile(filepath,['DATA_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_6']); conn_waitbar('close',h); return; end
Y{nses}=conn_vol(filename);
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
X1{nses}=load(filename);
filename=fullfile(filepath,['COV_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
X2{nses}=load(filename);
filename=fullfile(filepath,['COND_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
C{nses}=load(filename);
X{nses}=conn_designmatrix(CONN_x.Preproc.confounds,X1{nses},X2{nses});
%X{nses}=conn_filter(CONN_x.Setup.RT,CONN_x.Preproc.filter,X{nses});
if size(X{nses},1)~=CONN_x.Setup.nscans{nsub}{nses}, error('Wrong dimensions'); end
iX{nses}=pinv(X{nses});
end
clear nsamples time0 dataroi conditionsweights;
for ncondition=1:nconditions, % computes number of samples per condition
nsamples{ncondition}=0; for nses=1:nsess, nsamples{ncondition}=nsamples{ncondition}+length(C{nses}.samples{ncondition}); end
% dataroi{ncondition}=cell(1,length(X1{1}.data));
conditionsweights{ncondition}=cell(1,length(C{1}.weights{ncondition}));
for nses=1:nsess,
for nweight=1:length(C{nses}.weights{ncondition}),
conditionsweights{ncondition}{nweight}=cat(1,conditionsweights{ncondition}{nweight},C{nses}.weights{ncondition}{nweight});
end
end
end
clear Yout;
for ncondition=1:nconditions,
filename=fullfile(filepathresults,['DATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
Yout{ncondition}=Y{1}; Yout{ncondition}.fname=filename;
Yout{ncondition}.size.Nt=nsamples{ncondition};
Yout{ncondition}.conditionsweights=conditionsweights{ncondition};
Yout{ncondition}=conn_init_vol(Yout{ncondition});
end
B=[];
for slice=1:Y{1}.matdim.dim(3),
Bb=[];
if 1, % analyses per slice (all sessions together, faster but requires more memory)
clear y;
for nses=1:nsess,
[y{nses},idx]=conn_get_slice(Y{nses},slice);
if size(y{nses},1)~=CONN_x.Setup.nscans{nsub}{nses}, error('Wrong dimensions'); end
if slice==1&&rank(X{nses})>=size(y{nses},1), disp(['Warning: Over-determined model (no degrees of freedom for subject ',num2str(nsub),' session ',num2str(nses),'). Please consider reducing the number, dimensions, or covariates order of the confounds or disregarding this subject/session']); end
b=iX{nses}*y{nses};
y{nses}=y{nses}-X{nses}*b;
y{nses}=conn_filter(CONN_x.Setup.RT,CONN_x.Preproc.filter,y{nses});
if isfield(CONN_x.Setup,'outputfiles')&&numel(CONN_x.Setup.outputfiles)>=1&&CONN_x.Setup.outputfiles(1),
Bb=cat(1,Bb,b);
end
end
for ncondition=1:nconditions,
ytemp=[]; for nses=1:nsess, ytemp=cat(1,ytemp,y{nses}(C{nses}.samples{ncondition},:)); end
conn_write_slice(Yout{ncondition},ytemp,slice);
end
else, % analyses per slice/session (slower but requires less memory)
for nses=1:nsess,
[y,idx]=conn_get_slice(Y{nses},slice);
if size(y,1)~=CONN_x.Setup.nscans{nsub}{nses}, error('Wrong dimensions'); end
if slice==1&&rank(X{nses})>=size(y,1), disp(['Warning: Over-determined model (no degrees of freedom for subject ',num2str(nsub),' session ',num2str(nses),'). Please consider reducing the number, dimensions, or covariates order of the confounds or disregarding this subject/session']); end
b=iX{nses}*y;
y=y-X{nses}*b;
y=conn_filter(CONN_x.Setup.RT,CONN_x.Preproc.filter,y);
if isfield(CONN_x.Setup,'outputfiles')&&numel(CONN_x.Setup.outputfiles)>=1&&CONN_x.Setup.outputfiles(1),
Bb=cat(1,Bb,b);
end
for ncondition=1:nconditions,
if nses==1, time0{ncondition}=1; end
conn_write_slice(Yout{ncondition},y(C{nses}.samples{ncondition},:),slice,time0{ncondition});
time0{ncondition}=time0{ncondition}+length(C{nses}.samples{ncondition});
end
end
end
if isfield(CONN_x.Setup,'outputfiles')&&numel(CONN_x.Setup.outputfiles)>=1&&CONN_x.Setup.outputfiles(1),
if 0, %%% 0 to avoid memory errors
B=cat(2,B,Bb);
else
if slice==1
V=struct('mat',Y{1}.matdim.mat,'dim',Y{1}.matdim.dim,'pinfo',[1;0;0],'fname',fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'.nii']),...
'dt',[spm_type('float32') spm_platform('bigend')]);
%V=CONN_x.Setup.structural{nsub}{3}; V=V(1);
%if isfield(V,'dt'), V.dt=[spm_type('float32') spm_platform('bigend')];
%elseif length(V.dim)>3, V.dim(4)=spm_type('float32'); end
%V.fname=fullfile(filepathresults,['BETA_Subject',num2str(nsub),'.nii']);
V=repmat(V,[size(Bb,1),1]);for nh=1:numel(V),V(nh).n=[nh,1];end
V=spm_create_vol(V);
% for n1=1:size(Bb,1)
% V(n1)=V(1);
% V(n1).fname=fullfile(filepathresults,['BETA_Subject',num2str(nsub),'_Regressor',num2str(n1,'%04d'),'.nii']);
% V(n1)=spm_create_vol(V(n1));
% end
end
t=nan+zeros(Y{1}.matdim.dim(1:2));
for n1=1:size(Bb,1),
t(idx)=Bb(n1,:);
V(n1)=spm_write_plane(V(n1),t,slice);
end
end
end
conn_waitbar((n+slice/Y{1}.matdim.dim(3))/N,h);
end
if 0,%%% 0 to avoid memory errors
if isfield(CONN_x.Setup,'outputfiles')&&numel(CONN_x.Setup.outputfiles)>=1&&CONN_x.Setup.outputfiles(1),
t=nan+zeros(Y{1}.matdim.dim);
V=struct('mat',Y{1}.matdim.mat,'dim',Y{1}.matdim.dim,'pinfo',[1;0;0],'fname','',...
'dt',[spm_type('float32') spm_platform('bigend')]);
%V=CONN_x.Setup.structural{nsub}{3}; V=V(1);
%if isfield(V,'dt'), V.dt=[spm_type('float32') spm_platform('bigend')];
%elseif length(V.dim)>3, V.dim(4)=spm_type('float32'); end
for n1=1:size(B,1),
t(Y{1}.voxels)=B(n1,:);
V.fname=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Regressor',num2str(n1,'%04d'),'.nii']);
spm_write_vol(V,t);
end
end
end
if isfield(CONN_x.Setup,'outputfiles')&&numel(CONN_x.Setup.outputfiles)>=2&&CONN_x.Setup.outputfiles(2),
for ncondition=1:nconditions,
conn_matc2nii(Yout{ncondition}.fname,0);
end
end
end
n=n+1;
conn_waitbar(n/N,h);
end
conn_waitbar('close',h);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates ROI_Subject###_Condition###.mat files (roi data after removal of confounding effects & filtering)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==7) && any(CONN_x.Setup.steps([1,2])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.data;
filepathresults=CONN_x.folders.preprocessing;
nconditions=length(CONN_x.Setup.conditions.names)-1;
h=conn_waitbar(0,['Step ',num2str(sum(options<=7)),'/',num2str(length(options)),': Preprocessing ROI data']);
%REDO='Yes';filename=fullfile(filepathresults,['ROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
%if ~isempty(dir(filename)),if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end; end
REDO=[];
N=CONN_x.Setup.nsubjects; %sum(CONN_x.Setup.nsessions); if length(CONN_x.Setup.nsessions)==1, N=N*CONN_x.Setup.nsubjects; end
n=0;
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepathresults,['ROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if isempty(REDO)&&~isempty(dir(filename)),
if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
end
if strcmp(REDO,'Yes')||isempty(dir(filename)),
nsess=CONN_x.Setup.nsessions(min(length(CONN_x.Setup.nsessions),nsub));
clear Y X iX X1 X2 C;
for nses=1:nsess, % loads all ROI COV COND data for this subject
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_7']); conn_waitbar('close',h); return; end
X1{nses}=load(filename);
filename=fullfile(filepath,['COV_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
X2{nses}=load(filename);
filename=fullfile(filepath,['COND_Subject',num2str(nsub,'%03d'),'_Session',num2str(nses,'%03d'),'.mat']);
C{nses}=load(filename);
X{nses}=conn_designmatrix(CONN_x.Preproc.confounds,X1{nses},X2{nses});
%X{nses}=conn_filter(CONN_x.Setup.RT,CONN_x.Preproc.filter,X{nses});
if size(X{nses},1)~=CONN_x.Setup.nscans{nsub}{nses}, error('Wrong dimensions'); end
iX{nses}=pinv(X{nses});
end
clear nsamples time0 dataroi d1dataroi d2dataroi conditionsweights;
for ncondition=1:nconditions, % computes number of samples per condition
nsamples{ncondition}=0; for nses=1:nsess, nsamples{ncondition}=nsamples{ncondition}+length(C{nses}.samples{ncondition}); end
dataroi{ncondition}=cell(1,length(X1{1}.data)+length(X2{1}.data));
d1dataroi{ncondition}=cell(1,length(X1{1}.data)+length(X2{1}.data));
d2dataroi{ncondition}=cell(1,length(X1{1}.data)+length(X2{1}.data));
conditionsweights{ncondition}=cell(1,length(C{1}.weights{ncondition}));
for nses=1:nsess,
for nweight=1:length(C{nses}.weights{ncondition}),
conditionsweights{ncondition}{nweight}=cat(1,conditionsweights{ncondition}{nweight},C{nses}.weights{ncondition}{nweight});
end
end
end
for nroi=1:length(X1{1}.data),
for nses=1:nsess,
y=X1{nses}.data{nroi};
if size(y,1)~=CONN_x.Setup.nscans{nsub}{nses}, error('Wrong dimensions'); end
b=iX{nses}*y;
y=y-X{nses}*b;
y=conn_filter(CONN_x.Setup.RT,CONN_x.Preproc.filter,y);
d1y=convn(cat(1,y(1,:),y,y(end,:)),[1;0;-1]/2,'valid');
d2y=convn(cat(1,d1y(1,:),d1y,d1y(end,:)),[1;0;-1]/2,'valid');
for ncondition=1:nconditions,
dataroi{ncondition}{nroi}=cat(1,dataroi{ncondition}{nroi},y(C{nses}.samples{ncondition},:));
d1dataroi{ncondition}{nroi}=cat(1,d1dataroi{ncondition}{nroi},d1y(C{nses}.samples{ncondition},:));
d2dataroi{ncondition}{nroi}=cat(1,d2dataroi{ncondition}{nroi},d2y(C{nses}.samples{ncondition},:));
end
end
end
for ncov=1:length(X2{1}.data),
for nses=1:nsess,
y=X2{nses}.data{ncov};
if size(y,1)~=CONN_x.Setup.nscans{nsub}{nses}, error('Wrong dimensions'); end
b=iX{nses}*y;
y=y-X{nses}*b;
y=conn_filter(CONN_x.Setup.RT,CONN_x.Preproc.filter,y);
d1y=convn(cat(1,y(1,:),y,y(end,:)),[1;0;-1]/2,'valid');
d2y=convn(cat(1,d1y(1,:),d1y,d1y(end,:)),[1;0;-1]/2,'valid');
for ncondition=1:nconditions,
if size(y,2)>size(dataroi{ncondition}{length(X1{1}.data)+ncov},2)&&size(dataroi{ncondition}{length(X1{1}.data)+ncov},2)>0,
dataroi{ncondition}{length(X1{1}.data)+ncov}=cat(2,dataroi{ncondition}{length(X1{1}.data)+ncov}, zeros(size(dataroi{ncondition}{length(X1{1}.data)+ncov},1),size(y,2)-size(dataroi{ncondition}{length(X1{1}.data)+ncov},2)));
d1dataroi{ncondition}{length(X1{1}.data)+ncov}=cat(2,d1dataroi{ncondition}{length(X1{1}.data)+ncov}, zeros(size(d1dataroi{ncondition}{length(X1{1}.data)+ncov},1),size(y,2)-size(d1dataroi{ncondition}{length(X1{1}.data)+ncov},2)));
d2dataroi{ncondition}{length(X1{1}.data)+ncov}=cat(2,d2dataroi{ncondition}{length(X1{1}.data)+ncov}, zeros(size(d2dataroi{ncondition}{length(X1{1}.data)+ncov},1),size(y,2)-size(d2dataroi{ncondition}{length(X1{1}.data)+ncov},2)));
end
if size(y,2)<size(dataroi{ncondition}{length(X1{1}.data)+ncov},2),
y=cat(2,y,zeros(size(y,1),size(dataroi{ncondition}{length(X1{1}.data)+ncov},2)-size(y,2)));
d1y=cat(2,d1y,zeros(size(d1y,1),size(d1dataroi{ncondition}{length(X1{1}.data)+ncov},2)-size(d1y,2)));
d2y=cat(2,d2y,zeros(size(d2y,1),size(d2dataroi{ncondition}{length(X1{1}.data)+ncov},2)-size(d2y,2)));
end
dataroi{ncondition}{length(X1{1}.data)+ncov}=cat(1,dataroi{ncondition}{length(X1{1}.data)+ncov},y(C{nses}.samples{ncondition},:));
d1dataroi{ncondition}{length(X1{1}.data)+ncov}=cat(1,d1dataroi{ncondition}{length(X1{1}.data)+ncov},d1y(C{nses}.samples{ncondition},:));
d2dataroi{ncondition}{length(X1{1}.data)+ncov}=cat(1,d2dataroi{ncondition}{length(X1{1}.data)+ncov},d2y(C{nses}.samples{ncondition},:));
end
end
end
for ncondition=1:nconditions,
data=dataroi{ncondition};
d1data=d1dataroi{ncondition};
d2data=d2dataroi{ncondition};
names=cat(2,X1{1}.names,X2{1}.names);
xyz=cat(2,X1{1}.xyz,repmat({[nan,nan,nan]},[1,length(X2{1}.data)]));
%voxels=X1{1}.voxels;
%weights=X1{1}.weights;
source=X1{1}.source;
conditionname=C{1}.names{ncondition};
conditionweights=conditionsweights{ncondition};
filename=fullfile(filepathresults,['ROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
save(filename,'data','d1data','d2data','names','xyz','source','conditionweights','conditionname');
% if str2num(version('-release'))>=14, save(filename,'-V6','data','names','xyz','source','conditionweights','conditionname');
% else, save(filename,'data','names','xyz','source','conditionweights','conditionname');end
end
end
n=n+1;
conn_waitbar(n/N,h);
end
conn_waitbar('close',h);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates vvPC_Subject###_Condition###.mat files (voxel-to-voxel first-level SVD decomposition)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==8) && any(CONN_x.Setup.steps([3])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
nconditions=length(CONN_x.Setup.conditions.names)-1;
h=conn_waitbar(0,['Step ',num2str(sum(options<=8)),'/',num2str(length(options)),': preprocessing voxel-to-voxel covariance']);
REDO=[];
% filename=fullfile(fileparts(which('spm')),'apriori','brainmask.nii');
% Vmask=spm_vol(filename);
% THR_MASK=.25;
MAXDIMS=256;
filename=fullfile(filepath,['DATA_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_8']); return; end
Y=conn_vol(filename);
N=1.1*CONN_x.Setup.nsubjects*nconditions*Y.matdim.dim(3);n=0;
for nsub=1:CONN_x.Setup.nsubjects,
for ncondition=1:nconditions,
%filename=fullfile(filepath,['vvPCcov_SubjectA',num2str(nsub,'%03d'),'_SubjectB',num2str(nsub,'%03d'),'_ConditionA',num2str(ncondition,'%03d'),'_ConditionB',num2str(ncondition,'%03d'),'.mat']);
filename=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
if isempty(REDO)&&~isempty(dir(filename)),
if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
end
if strcmp(REDO,'Yes')||(isempty(dir(filename))),
filename=fullfile(filepath,['DATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_8']); return; end
Y=conn_vol(filename);
if isfield(Y,'conditionsweights')
clear X1;
X1.conditionweights=Y.conditionsweights;
else
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
X1=load(filename);
end
DOF=max(0,Y.size.Nt*(min(1/(2*CONN_x.Setup.RT),CONN_x.Preproc.filter(2))-max(0,CONN_x.Preproc.filter(1)))/(1/(2*CONN_x.Setup.RT))+1);
Cy=0;Cidx=[];
for slice=1:Y.matdim.dim(3),
[y,idx]=conn_get_slice(Y,slice);
%[xyzx,xyzy]=ind2sub(Y.matdim.dim(1:2),idx);xyz=Y.matdim.mat*[xyzx,xyzy,zeros(size(xyzx))+slice,ones(size(xyzx))]';
%z=spm_get_data(Vmask,pinv(Vmask(1).mat)*xyz);
%idxt=find(z>THR_MASK&~any(isnan(y),1));
idxt=find(~any(isnan(y),1));
if ~isempty(idxt),
Cidx=cat(1,Cidx,idx(idxt)+(slice-1)*Y.matdim.dim(1)*Y.matdim.dim(2));
y=detrend(y(:,idxt),'constant');
y=y.*repmat(X1.conditionweights{1},[1,size(y,2)]);
y=y.*repmat(sqrt(1./max(eps,sum(abs(y).^2,1))),[size(y,1),1]);
Cy=Cy+y*y';
end
n=n+.1;
conn_waitbar(n/N,h);
end
[Q1,D]=svd(Cy);
D=diag(D);
DIMS=min([MAXDIMS,ceil(DOF),sum(D>1e-8)]);
Q1=Q1(:,1:DIMS);
D=D(1:DIMS);
filename_D=fullfile(filepath,['vvPCeig_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
save(filename_D,'D');
% filename_A=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']); % spatial base
% Yout_A=struct('fname',filename_A,'mat',Y.matdim.mat,'dim',Y.matdim.dim,'pinfo',[1;0;0],'n',[1,1],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip','conn SVD (spatial base)');
% Yout_A=repmat(Yout_A,[DIMS,1]);for nh=1:DIMS,Yout_A(nh).n=[nh,1];end
% Yout_A=spm_create_vol(Yout_A);
filename_A=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']); % spatial base
Yout_A=Y; Yout_A.fname=filename_A;Yout_A.size.Nt=DIMS;Yout_A.DOF=DOF; Yout_A.BASE.Q1=Q1;Yout_A.BASE.D=D;
Yout_A=conn_init_vol(Yout_A,Cidx);
for slice=1:Y.matdim.dim(3),
[y,idx]=conn_get_slice(Y,slice);
%[xyzx,xyzy]=ind2sub(Y.matdim.dim(1:2),idx);xyz=Y.matdim.mat*[xyzx,xyzy,zeros(size(xyzx))+slice,ones(size(xyzx))]';
%z=spm_get_data(Vmask,pinv(Vmask(1).mat)*xyz);
%idxt=find(z>THR_MASK&~any(isnan(y),1));
idxt=find(~any(isnan(y),1));
if ~isempty(idxt),
y=detrend(y(:,idxt),'constant');
y=y.*repmat(X1.conditionweights{1},[1,size(y,2)]);
y=y.*repmat(sqrt(1./max(eps,sum(abs(y).^2,1))),[size(y,1),1]);
Q2=Q1'*y;
e=sum(abs(y).^2,1);
conn_write_slice(Yout_A,Q2,slice);
% Fplane=zeros(Y.matdim.dim(1:2));
% for ndim=1:DIMS,
% Fplane(idx(idxt))=Q2(ndim,:);
% Yout_A(ndim)=spm_write_plane(Yout_A(ndim),Fplane,slice);
% % conn_write_slice(Yout_A,Q2(ndim,:),slice,ndim);
% end
% else
% Fplane=zeros(Y.matdim.dim(1:2));
% for ndim=1:DIMS,
% Yout_A(ndim)=spm_write_plane(Yout_A(ndim),Fplane,slice);
% end
end
n=n+1;
conn_waitbar(n/N,h);
end
else, n=n+1.1*Y.matdim.dim(3); end
end
end
conn_waitbar('close',h);
% if nconditions>1
% N=CONN_x.Setup.nsubjects*(nconditions-1);n=0;
% h=conn_waitbar(0,['Step ',num2str(sum(options<=8)),'/',num2str(length(options)),': preprocessing subject-to-subject covariance']);
% for nsub=1:CONN_x.Setup.nsubjects,
% for ncondition=2:nconditions,
% filename=fullfile(filepath,['vvPCeig_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
% %filename=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
% if isempty(REDO)&&~isempty(dir(filename)),
% if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
% end
% if strcmp(REDO,'Yes')||(isempty(dir(filename))),
% % filename_A=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
% % Yout_A=spm_vol(filename_A);
% filename_A=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
% Yout_A=conn_vol(filename_A);
% % [gridx,gridy]=ndgrid(1:Yout_A(1).dim(1),1:Yout_A(1).dim(2));xyz=[gridx(:),gridy(:),ones(numel(gridx),2)]';
% Dall=zeros(Yout_A.size.Nt,Yout_A.size.Nt,ncondition);
% for slice=1:Yout_A.size.Ns,
% % xyz(3,:)=slice;
% yA=conn_get_slice(Yout_A,slice);
% for ncondition2=1:ncondition-1,
% filename_B=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition2,'%03d'),'.mat']);
% Yout_B=conn_vol(filename_B);
% yB=conn_get_slice(Yout_B,slice);
% Dall(:,:,ncondition2)=Dall(:,:,ncondition2)+yA*yB';
% end
% end
% for ncondition2=1:ncondition-1,
% D=Dall(:,:,ncondition2);
% filename_D=fullfile(filepath,['vvPCeig_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Condition',num2str(ncondition2,'%03d'),'.mat']); % between-condition cross-product
% save(filename_D,'D');
% end
% n=n+1;
% conn_waitbar(n/N,h);
% else, n=n+1; end
% end
% end
% conn_waitbar('close',h);
% end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% updates CONN_x.Analyses structure with all ROIs
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==9),
if any(CONN_x.Setup.steps([1,2]))
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
filename1=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if isempty(dir(filename1)), disp(['Not ready to process step conn_process_9']); return; end
x1=load(filename1);
if nargin>1,analyses=varargin{1}; % selected analysis only
else, analyses=1:length(CONN_x.Analyses); end;
doanalyses=analyses>0;
analyses=analyses(doanalyses);
analysisbak=CONN_x.Analysis;
for ianalysis=analyses,
CONN_x.Analysis=ianalysis;
if isempty(CONN_x.Analyses(ianalysis).name),CONN_x.Analyses(ianalysis).name=['ANALYSIS_',num2str(ianalysis,'%02d')]; end;
if ~exist(fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(ianalysis).name),'dir'), [ok,nill]=mkdir(CONN_x.folders.firstlevel,CONN_x.Analyses(ianalysis).name); end;
CONN_x.Analyses(ianalysis).variables.names={};
CONN_x.Analyses(ianalysis).variables.types={};
CONN_x.Analyses(ianalysis).variables.deriv={};
CONN_x.Analyses(ianalysis).variables.dimensions={};
for n1=1:length(x1.names), idx=strmatch(x1.names{n1},CONN_x.Preproc.confounds.names,'exact'); if isempty(idx),
CONN_x.Analyses(ianalysis).variables.names{end+1}=x1.names{n1};
CONN_x.Analyses(ianalysis).variables.types{end+1}='roi';
CONN_x.Analyses(ianalysis).variables.deriv{end+1}=0;
CONN_x.Analyses(ianalysis).variables.dimensions{end+1}=[size(x1.data{n1},2),size(x1.data{n1},2)];
end
end
if isfield(CONN_x.Analyses(ianalysis).regressors,'names') && ~isempty(CONN_x.Analyses(ianalysis).regressors.names), initial=CONN_x.Analyses(ianalysis).regressors.names; dims=CONN_x.Analyses(ianalysis).regressors.dimensions; ders=CONN_x.Analyses(ianalysis).regressors.deriv;
else, initial=CONN_x.Analyses(ianalysis).variables.names; dims={}; ders={}; end
CONN_x.Analyses(ianalysis).regressors.names={};
CONN_x.Analyses(ianalysis).regressors.types={};
CONN_x.Analyses(ianalysis).regressors.deriv={};
CONN_x.Analyses(ianalysis).regressors.dimensions={};
for n1=1:length(initial),
idx=strmatch(initial{n1},CONN_x.Analyses(ianalysis).variables.names,'exact');
if ~isempty(idx)&&~strcmp(initial{n1},'Grey Matter')&&~strcmp(initial{n1},'White Matter')&&~strcmp(initial{n1},'CSF'),
CONN_x.Analyses(ianalysis).regressors.names{end+1}=CONN_x.Analyses(ianalysis).variables.names{idx};
CONN_x.Analyses(ianalysis).regressors.types{end+1}=CONN_x.Analyses(ianalysis).variables.types{idx};
if length(ders)>=n1&&~isempty(ders{n1}), CONN_x.Analyses(ianalysis).regressors.deriv{end+1}=ders{n1}; else, CONN_x.Analyses(ianalysis).regressors.deriv{end+1}=CONN_x.Analyses(ianalysis).variables.deriv{idx};end
if length(dims)>=n1&&~isempty(dims{n1}), CONN_x.Analyses(ianalysis).regressors.dimensions{end+1}=[min(dims{n1}(1),CONN_x.Analyses(ianalysis).variables.dimensions{idx}(1)),CONN_x.Analyses(ianalysis).variables.dimensions{idx}(1)];
else, CONN_x.Analyses(ianalysis).regressors.dimensions{end+1}=CONN_x.Analyses(ianalysis).variables.dimensions{idx}; end
end
end
if ~isfield(CONN_x.Analyses(ianalysis),'measure') || isempty(CONN_x.Analyses(ianalysis).measure), CONN_x.Analyses(ianalysis).measure=1; end
if ~isfield(CONN_x.Analyses(ianalysis),'weight') || isempty(CONN_x.Analyses(ianalysis).weight), CONN_x.Analyses(ianalysis).weight=2; end
end
CONN_x.Analysis=analysisbak;
end
if any(CONN_x.Setup.steps([3]))&&(nargin<=1||any(varargin{1}==0)),
CONN_x.vvAnalyses.variables=conn_v2v('measures');
if isfield(CONN_x.vvAnalyses.regressors,'names') && ~isempty(CONN_x.vvAnalyses.regressors.names),
initial=CONN_x.vvAnalyses.regressors;
CONN_x.vvAnalyses.regressors=conn_v2v('empty');
for n1=1:numel(initial.names)
idx=strmatch(initial.names{n1},CONN_x.vvAnalyses.variables.names,'exact');
optionsnames=fieldnames(CONN_x.vvAnalyses.variables);
for n2=1:numel(optionsnames),
if ~isempty(idx)&&isempty(initial.(optionsnames{n2}){n1}), CONN_x.vvAnalyses.regressors.(optionsnames{n2}){n1}=CONN_x.vvAnalyses.variables.(optionsnames{n2}){idx(1)};
else CONN_x.vvAnalyses.regressors.(optionsnames{n2}){n1}=initial.(optionsnames{n2}){n1};
end
end
if isempty(idx), CONN_x.vvAnalyses.regressors.measuretype{n1}=1; end
end
else
CONN_x.vvAnalyses.regressors=CONN_x.vvAnalyses.variables;
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates resultsDATA_Subject###_Condition###.mat files (first-level voxel-to-voxel analysis)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0,%any(options==8.5),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
nconditions=length(CONN_x.Setup.conditions.names)-1;
h=conn_waitbar(0,['Step ',num2str(sum(options<=8.5)),'/',num2str(length(options)),': voxel-to-voxel first-level analyses']);
% workinprogress
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates resultsDATA_Subject###_Condition###_Source###.mat files (first-level ROI-to-voxel analysis)
% Creates BETA_Subject###_Condition###_Source###.mat files (first-level seed-to-voxel analyses)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==10) && any(CONN_x.Setup.steps([2])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
nconditions=length(CONN_x.Setup.conditions.names)-1;
filename=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_10']); return; end
X1=load(filename);
if nargin>1,analyses=varargin{1}; % selected analysis only
else, analyses=1:length(CONN_x.Analyses); end;
doanalyses=false(1,numel(analyses));
for nanalyses=1:numel(analyses),if analyses(nanalyses)>0&&any(CONN_x.Analyses(analyses(nanalyses)).type==[2,3]), doanalyses(nanalyses)=true; end; end
analyses=analyses(doanalyses);
h=conn_waitbar(0,['Step ',num2str(sum(options<=10)),'/',num2str(length(options)),': ROI-to-voxel first-level analyses']);
REDO=[];
analysisbak=CONN_x.Analysis;
for nanalyses=1:length(analyses),
ianalysis=analyses(nanalyses);
CONN_x.Analysis=ianalysis;
% ianalysis=CONN_x.Analysis;
filepathresults=fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(ianalysis).name);
[X,nill,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,X1,[]);
nrois=size(X,2)-1;
iroi=[];isnew=[];for nroi=1:nrois,[iroi(nroi),isnew(nroi)]=conn_sourcenames(names{nroi},'+');end
filename=fullfile(filepath,['DATA_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
Y=conn_vol(filename);
if nanalyses==1, N=CONN_x.Setup.nsubjects*nconditions*Y.matdim.dim(3)*length(analyses);n=0;end
for ncondition=1:nconditions,
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepath,['DATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
Y=conn_vol(filename);
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
X1=load(filename);
[X,nill,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,X1,[]);
clear Yout;
for nroi=1:nrois,
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.nii']);
%filename=fullfile(filepathresults,['resultsDATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.mat']);
isnew(nroi)=isnew(nroi)|isempty(dir(filename));
end
if any(isnew),
switch(CONN_x.Analyses(ianalysis).measure),
case {2,4}, %partial
isnew=ones(size(isnew));
end
end
if isempty(REDO)&&~all(isnew),
if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
end
if strcmp(REDO,'No'),
idxredo=find(isnew);
X=cat(2,X(:,1),X(:,1+idxredo));
else,
idxredo=1:nrois;
end
if length(idxredo)>0,
X=cat(2,X(:,1),detrend(X(:,2:end),'constant'));
switch(CONN_x.Analyses(ianalysis).weight),
case 1,
case 2, X=X.*repmat(X1.conditionweights{1},[1,size(X,2)]);
case 3, X=X.*repmat(X1.conditionweights{2},[1,size(X,2)]);
end
switch(CONN_x.Analyses(ianalysis).measure),
case {1,3}, %bivariate
iX=pinv(diag(diag(X'*X)));
DOF=max(0,Y.size.Nt*(min(1/(2*CONN_x.Setup.RT),CONN_x.Preproc.filter(2))-max(0,CONN_x.Preproc.filter(1)))/(1/(2*CONN_x.Setup.RT))-1);
case {2,4}, %partial
iX=pinv(X'*X);
DOF=max(0,Y.size.Nt*(min(1/(2*CONN_x.Setup.RT),CONN_x.Preproc.filter(2))-max(0,CONN_x.Preproc.filter(1)))/(1/(2*CONN_x.Setup.RT))-rank(X)+1);
end
filename=fullfile(filepathresults,['se_Subject',num2str(nsub),'_Condition',num2str(ncondition,'%03d'),'.nii']);
SEout=struct('mat',Y.matdim.mat,'dim',Y.matdim.dim,'fname',filename,'dt',[spm_type('float32') spm_platform('bigend')]);
SEout=spm_create_vol(SEout);
% filename=fullfile(filepathresults,['seDATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
% SEout=Y; SEout.fname=filename;
% SEout.size.Nt=1;%CONN_x.Setup.nsubjects;
% SEout.DOF=DOF;
% SEout=conn_init_vol(SEout);
for nroi=1:length(idxredo),
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(idxredo(nroi)),'%03d'),'.nii']);
Yout{nroi}=struct('mat',Y.matdim.mat,'dim',Y.matdim.dim,'fname',filename,'pinfo',[1;0;0],'n',[1,1],'dt',[spm_type('float32') spm_platform('bigend')]);
Yout{nroi}=spm_create_vol(Yout{nroi});
% filename=fullfile(filepathresults,['resultsDATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(idxredo(nroi)),'%03d'),'.mat']);
% Yout{nroi}=Y; Yout{nroi}.fname=filename;
% Yout{nroi}.size.Nt=1;%CONN_x.Setup.nsubjects;
% Yout{nroi}=conn_init_vol(Yout{nroi});
end
for slice=1:Y.matdim.dim(3),
[y,idx]=conn_get_slice(Y,slice);
y=detrend(y,'constant');
switch(CONN_x.Analyses(ianalysis).weight),
case 1,
case 2, y=y.*repmat(X1.conditionweights{1},[1,size(y,2)]);
case 3, y=y.*repmat(X1.conditionweights{2},[1,size(y,2)]);
end
B=iX*(X'*y);
e=sqrt(sum(abs(y).^2,1));
switch(CONN_x.Analyses(ianalysis).measure),
case {1,2}, %correlation
r=sqrt(diag(iX));
B=B./max(eps,r*e);
B=atanh(max(eps-1,min(1-eps,B)));
e(:)=1./max(eps,sqrt(DOF-3));
case {3,4}, %regression
e=e/max(eps,DOF);
end
%disp([slice,nsub])
% conn_write_slice(SEout,e,slice);%nsub);
% for nroi=1:length(idxredo);
% conn_write_slice(Yout{nroi},B(1+nroi,:),slice);%nsub);
% end
t=zeros(Y.matdim.dim(1:2));
t(idx)=e;
SEout=spm_write_plane(SEout,t,slice);
for nroi=1:length(idxredo);
t(idx)=B(1+nroi,:);
Yout{nroi}=spm_write_plane(Yout{nroi},t,slice);
end
n=n+1;
conn_waitbar(n/N,h);
end
else, n=n+Y.matdim.dim(3); end
end
end
CONN_x.Analyses(ianalysis).sources=names;
fileout=fullfile(filepathresults,'_list_sources.txt');
fh=fopen(fileout,'wt');
for n1=1:length(CONN_x.Analyses(ianalysis).sourcenames),fprintf(fh,'Source%03d = %s\n',n1,CONN_x.Analyses(ianalysis).sourcenames{n1});end
fclose(fh);
fileout=fullfile(filepathresults,'_list_conditions.txt');
fh=fopen(fileout,'wt');
for n1=1:nconditions,fprintf(fh,'Condition%03d = %s\n',n1,CONN_x.Setup.conditions.names{n1});end
fclose(fh);
end
CONN_x.Analysis=analysisbak;
conn_waitbar('close',h); ;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates resultsROI_Subject###_Condition###.mat files (first-level ROI-to-ROI analyses)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==11) && any(CONN_x.Setup.steps([1])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
if nargin>1,analyses=varargin{1}; % selected analysis only
else, analyses=1:length(CONN_x.Analyses); end;
doanalyses=false(1,numel(analyses));
for nanalyses=1:numel(analyses),if analyses(nanalyses)>0&&any(CONN_x.Analyses(analyses(nanalyses)).type==[1,3]), doanalyses(nanalyses)=true; end; end
analyses=analyses(doanalyses);
h=conn_waitbar(0,['Step ',num2str(sum(options<=11)),'/',num2str(length(options)),': ROI-to-ROI first-level analyses']);
analysisbak=CONN_x.Analysis;
for nanalyses=1:length(analyses),
ianalysis=analyses(nanalyses);
CONN_x.Analysis=ianalysis;
% ianalysis=CONN_x.Analysis;
filepathresults=fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(ianalysis).name);
nconditions=length(CONN_x.Setup.conditions.names)-1;
%REDO='Yes';filename=fullfile(filepathresults,['resultsROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
%if ~isempty(dir(filename)),if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end; end
if nanalyses==1, n=0; end
for ncondition=1:nconditions,
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepathresults,['resultsROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
if 1,%strcmp(REDO,'Yes')||isempty(dir(filename)),
filename=fullfile(filepath,['ROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_10']); conn_waitbar('close',h);return; end
X1=load(filename);
[X,nill,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,X1,[]);
nrois=size(X,2)-1;
[X2,nill,names2,xyz2]=conn_designmatrix({CONN_x.Analyses(ianalysis).variables,CONN_x.Analyses(ianalysis).regressors},X1,[]);
nrois2=size(X2,2)-1;
idxroi1roi2=zeros(1,nrois);
for n1=1:nrois,temp=strmatch(names{n1},names2,'exact'); idxroi1roi2(n1)=temp(1);end
X2=cat(2,X2(:,1),X2(:,1+idxroi1roi2),X2(:,1+setdiff(1:nrois2,idxroi1roi2)));
names2=cat(2,{names2{idxroi1roi2}},{names2{setdiff(1:nrois2,idxroi1roi2)}});
xyz=cat(2,{xyz2{idxroi1roi2}},{xyz2{setdiff(1:nrois2,idxroi1roi2)}});
if nanalyses==1&&nsub==1 && ncondition==1,N=CONN_x.Setup.nsubjects*nconditions*nrois2*length(analyses); nrois2bak=nrois2;
elseif nsub==1 && ncondition==1, N=N-CONN_x.Setup.nsubjects*nconditions*nrois2bak+CONN_x.Setup.nsubjects*nconditions*nrois2; end
Z=zeros(nrois,nrois2);%+diag(nan+zeros(nrois,1));
SE=zeros(1,nrois2);
X=cat(2,X(:,1),detrend(X(:,2:end),'constant'));X2=cat(2,X2(:,1),detrend(X2(:,2:end),'constant'));
switch(CONN_x.Analyses(ianalysis).weight),
case 1,
case 2, X=X.*repmat(X1.conditionweights{1},[1,size(X,2)]);X2=X2.*repmat(X1.conditionweights{1},[1,size(X2,2)]);
case 3, X=X.*repmat(X1.conditionweights{2},[1,size(X,2)]);X2=X2.*repmat(X1.conditionweights{2},[1,size(X2,2)]);
end
switch(CONN_x.Analyses(ianalysis).measure),
case {1,3}, %bivariate
DOF=max(0,size(X,1)*(min(1/(2*CONN_x.Setup.RT),CONN_x.Preproc.filter(2))-max(0,CONN_x.Preproc.filter(1)))/(1/(2*CONN_x.Setup.RT))-1);
case {2,4}, %partial
DOF=max(0,size(X,1)*(min(1/(2*CONN_x.Setup.RT),CONN_x.Preproc.filter(2))-max(0,CONN_x.Preproc.filter(1)))/(1/(2*CONN_x.Setup.RT))-rank(X)+1);
end
for nroi=1:nrois2,
y=X2(:,1+nroi);
switch(CONN_x.Analyses(ianalysis).measure),
case {1,3}, %bivariate
x=cat(2,X(:,1),X(:,1+setdiff(1:nrois,nroi)));
iX=pinv(diag(diag(x'*x)));
case {2,4}, %partial
x=cat(2,X(:,1),X(:,1+setdiff(1:nrois,nroi)));
iX=pinv(x'*x);
end
B=iX*(x'*y);
e=sqrt(sum(abs(y).^2,1));
switch(CONN_x.Analyses(ianalysis).measure),
case {1,2}, %correlation
r=sqrt(diag(iX));
B=B./max(eps,r*e);
B(~isnan(B))=atanh(max(eps-1,min(1-eps,B(~isnan(B)))));
SE(nroi)=1./max(eps,sqrt(DOF-3));
case {3,4},
SE(nroi)=e/max(eps,DOF);
end
Z(setdiff(1:nrois,nroi),nroi)=B(2:end);
if nroi<=nrois,Z(nroi,nroi)=nan;end
n=n+1;
conn_waitbar(n/N,h);
end
% xyz={}; %note: this assumes constant number of dimensions per subject for analysis regressors
% for n1=1:length(CONN_x.Analyses(ianalysis).variables.names),
% for n2=1:CONN_x.Analyses(ianalysis).variables.deriv{n1}+1,
% for n3=1:CONN_x.Analyses(ianalysis).variables.dimensions{n1}(1),
% idx=strmatch(CONN_x.Analyses(ianalysis).variables.names{n1},X1.names,'exact');
% if isempty(idx), xyz{end+1}=''; else, xyz{end+1}=X1.xyz{idx}; end
% end
% end;
% end
% xyz=cat(2,{xyz{idxroi1roi2}},{xyz{setdiff(1:nrois2,idxroi1roi2)}});
regressors=CONN_x.Analyses(ianalysis).regressors;
filename=fullfile(filepathresults,['resultsROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
save(filename,'Z','regressors','names','names2','xyz','SE','DOF');
end
end
end
end
CONN_x.Analysis=analysisbak;
conn_waitbar('close',h); ;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates BETA_Subject###_Condition###_Source###.mat files (first-level analysis results for SPM)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0,%any(options==12) && any(CONN_x.Setup.steps([2])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
if nargin>1,analyses=varargin{1}; % selected analysis only
else, analyses=1:length(CONN_x.Analyses); end;
doanalyses=false(1,numel(analyses));
for nanalyses=1:numel(analyses),if analyses(nanalyses)>0&&any(CONN_x.Analyses(analyses(nanalyses)).type==[2,3]), doanalyses(nanalyses)=true; end; end
analyses=analyses(doanalyses);
h=conn_waitbar(0,['Step ',num2str(sum(options<=12)),'/',num2str(length(options)),': Creating BETA volumes']);
analysisbak=CONN_x.Analysis;
for nanalyses=1:length(analyses),
ianalysis=analyses(nanalyses);
CONN_x.Analysis=ianalysis;
% ianalysis=CONN_x.Analysis;
filepathresults=fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(ianalysis).name);
nconditions=length(CONN_x.Setup.conditions.names)-1;
%nrois=0;for n1=1:length(CONN_x.Analyses.regressors.names), nrois=nrois+CONN_x.Analyses.regressors.dimensions{n1}(1)*(CONN_x.Analyses.regressors.deriv{n1}+1); end;
filename=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_11']); conn_waitbar('close',h);return; end
X1=load(filename);
[X,nill,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,X1,[]);
nrois=size(X,2)-1;
iroi=[];isnew=[];for nroi=1:nrois,[iroi(nroi),isnew(nroi)]=conn_sourcenames(names{nroi},'-');end
if any(isnew), error(['Non-existing ROI first-level data for ',names{find(isnew)},' subject ',num2str(nsub),'. Please repeat first-level analyses']); return; end
if nanalyses==1, REDO=[]; n=0; N=CONN_x.Setup.nsubjects*nconditions*nrois*length(analyses); nroisbak=nrois;
else N=N-CONN_x.Setup.nsubjects*nconditions*nroisbak+CONN_x.Setup.nsubjects*nconditions*nrois; end
clear Yout;
for ncondition=1:nconditions,
for nroi=1:nrois,
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.nii']);
if isempty(REDO)&&~(isnew(nroi)||isempty(dir(filename))),
if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
end
if strcmp(REDO,'Yes')||(isnew(nroi)||isempty(dir(filename))),
filename=fullfile(filepathresults,['resultsDATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.mat']);
Yout=conn_vol(filename);
t=nan+zeros(Yout.matdim.dim);
y=conn_get_time(Yout,1,[],false);%nsub);
%V0=spm_vol(deblank(CONN_x.Setup.functional{nsub}{1}{1}(1,:))); V0=V0(1);
%V=spm_vol(deblank(CONN_x.Setup.structural{nsub}{1})); V=V(1);
V=CONN_x.Setup.structural{nsub}{3}; V=V(1);
t(Yout.voxels)=y;
V.fname=fullfile(filepathresults,['BETA_Subject',num2str(nsub),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.nii']);
if isfield(V,'dt'), V.dt=[spm_type('float32') spm_platform('bigend')];
elseif length(V.dim)>3, V.dim(4)=spm_type('float32'); end
spm_write_vol(V,t);
if isfield(CONN_x.Setup,'outputfiles')&&numel(CONN_x.Setup.outputfiles)>=3&&CONN_x.Setup.outputfiles(3),
V.fname=fullfile(filepathresults,['corr_Subject',num2str(nsub),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.nii']);
t=tanh(t);
spm_write_vol(V,t);
end
end
n=n+1;
conn_waitbar(n/N,h);
end
end
end
CONN_x.Analyses(ianalysis).sources=names;
fileout=fullfile(filepathresults,'_list_sources.txt');
fh=fopen(fileout,'wt');
for n1=1:length(CONN_x.Analyses(ianalysis).sourcenames),fprintf(fh,'Source%03d = %s\n',n1,CONN_x.Analyses(ianalysis).sourcenames{n1});end
fclose(fh);
fileout=fullfile(filepathresults,'_list_conditions.txt');
fh=fopen(fileout,'wt');
for n1=1:nconditions,fprintf(fh,'Condition%03d = %s\n',n1,CONN_x.Setup.conditions.names{n1});end
fclose(fh);
end
CONN_x.Analysis=analysisbak;
conn_waitbar('close',h); ;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates BETA_Subject###_Condition###_Measure###.nii files (first-level voxel-to-voxel analyses)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==13) && any(CONN_x.Setup.steps([3])) && (nargin<=1||any(varargin{1}==0)),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
filepathresults=CONN_x.folders.firstlevel;
nconditions=length(CONN_x.Setup.conditions.names)-1;
REDO=[]; N=0;n=0;
h=conn_waitbar(0,['Step ',num2str(sum(options<=13)),'/',num2str(length(options)),': Voxel-to-voxel first-level analyses']);
measures=CONN_x.vvAnalyses.regressors;
[nill,idx]=sort(cat(1,measures.localsupport{:}));mfieldnames=fieldnames(measures);for nfieldnames=1:numel(mfieldnames), measures.(mfieldnames{nfieldnames})=measures.(mfieldnames{nfieldnames})(idx); end % make analyses with same kernel size consecutive for speed improvemnet (using conn_v2v local storage)
[measuretypes,idx]=sort(cat(1,measures.measuretype{:}));mfieldnames=fieldnames(measures);for nfieldnames=1:numel(mfieldnames), measures.(mfieldnames{nfieldnames})=measures.(mfieldnames{nfieldnames})(idx); end
nmeasures=numel(measures.names);
nmeasures2=sum(measuretypes==2);
nmeasures3=sum(measuretypes==3);
nmeasures1=nmeasures-nmeasures2-nmeasures3;
imeasure=[];isnew=[];for nmeasure=1:nmeasures,[imeasure(nmeasure),isnew(nmeasure)]=conn_v2v('match_measures',measures,nmeasure,'+');end
if nmeasures1>0
for nsub=1:CONN_x.Setup.nsubjects,
for ncondition=1:nconditions,
for nmeasure=1:nmeasures1,
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(1,'%03d'),'.nii']);
isnew(nmeasure)=isnew(nmeasure)|isempty(dir(filename));
end
if isempty(REDO)&&~all(isnew(1:nmeasures1)),
if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
end
if strcmp(REDO,'Yes')||any(isnew(1:nmeasures1)),
%filename_B1=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
%Y1=spm_vol(filename_B1);
filename_B1=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
Y1=conn_vol(filename_B1);
filename_D1=fullfile(filepath,['vvPCeig_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
D1=load(filename_D1,'D');
%if ~N, N=(CONN_x.Setup.nsubjects-nsub+1)*nconditions*numel(Y1); numelY1bak=numel(Y1);
%else, N=N-numelY1bak+numel(Y1);end
if ~N, N=(CONN_x.Setup.nsubjects-nsub+1)*nconditions*Y1.size.Nt; numelY1bak=Y1.size.Nt;
else, N=N-numelY1bak+Y1.size.Nt;end
params=cell(1,nmeasures1);
for nmeasure=1:nmeasures1,
if strcmp(REDO,'Yes')||isnew(nmeasure)
params{nmeasure}=conn_v2v('compute_start',measures,nmeasure,Y1.matdim.mat);
end
end
%[gridx,gridy,gridz]=ndgrid(1:Y1(1).dim(1),1:Y1(1).dim(2),1:Y1(1).dim(3));xyz=[gridx(:),gridy(:),gridz(:),ones(numel(gridx),1)]';
for ndim=1:Y1.size.Nt,%numel(Y1),
doneread=0;
for nmeasure=1:nmeasures1,
if (strcmp(REDO,'Yes')||isnew(nmeasure))&&ndim<=params{nmeasure}.dimensions_in,
if ~doneread
y1=conn_get_time(Y1,ndim);
%y1=reshape(spm_get_data(Y1(ndim),xyz),Y1(1).dim); %y1=spm_read_vols(Y1(ndim));
doneread=1;
end
params{nmeasure}=conn_v2v('compute_step',params{nmeasure},y1,D1.D(ndim));
end
end
n=n+1;
conn_waitbar(n/N,h);
end
for nmeasure=1:nmeasures1,
if strcmp(REDO,'Yes')||isnew(nmeasure)
d=conn_v2v('compute_end',params{nmeasure});
if iscell(d)
dsum=0;
for nout=1:numel(d)
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(nout,'%03d'),'.nii']);
Yout=struct('fname',filename,'mat',Y1.matdim.mat,'dim',Y1.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
%Yout=Y1(1);Yout.fname=filename;
spm_write_vol(Yout,d{nout});
dsum=dsum+abs(d{nout}).^2;
end
if numel(d)>1
dsum=sqrt(dsum);
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(0,'%03d'),'.nii']);
Yout=struct('fname',filename,'mat',Y1.matdim.mat,'dim',Y1.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
%Yout=Y1(1);Yout.fname=filename;
spm_write_vol(Yout,dsum);
end
else
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(1,'%03d'),'.nii']);
Yout=struct('fname',filename,'mat',Y1.matdim.mat,'dim',Y1.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
%Yout=Y1(1);Yout.fname=filename;
spm_write_vol(Yout,d);
end
end
end
end
end
end
end
conn_waitbar('close',h);
if nmeasures2>0,
MAXDIMS=256;
h=conn_waitbar(0,['Step ',num2str(sum(options<=13)),'/',num2str(length(options)),': connectome-level MVPA analyses']);
N=nconditions*nmeasures2;
n=0;
for ncondition=1:nconditions,
for nmeasure=nmeasures1+(1:nmeasures2),
filename=fullfile(filepathresults,['BETA_Subject',num2str(CONN_x.Setup.nsubjects,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(1,'%03d'),'.nii']);
isnew(nmeasure)=isnew(nmeasure)|isempty(dir(filename));
end
end
if isempty(REDO)&&~all(isnew(nmeasures1+(1:nmeasures2))),
if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
end
if strcmp(REDO,'Yes')||any(isnew(nmeasures1+(1:nmeasures2))),
% filename_D1=fullfile(filepath,['vvPCcov_SubjectA',num2str(1,'%03d'),'_SubjectB',num2str(1,'%03d'),'_ConditionA',num2str(ncondition,'%03d'),'_ConditionB',num2str(ncondition,'%03d'),'.mat']);
% D1=load(filename_D1,'D');
% filename_B1=fullfile(filepath,['vvPC_Subject',num2str(1,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
% Y1=spm_vol(filename_B1);
% sA=prod(Y1(1).dim);
% [gridx,gridy,gridz]=ndgrid(1:Y1(1).dim(1),1:Y1(1).dim(2),1:Y1(1).dim(3));xyz=[gridx(:),gridy(:),gridz(:),ones(numel(gridx),1)]';
filename_B1=fullfile(filepath,['vvPC_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
Y1=conn_vol(filename_B1);
sA=prod(Y1.matdim.dim);
for nmeasure=nmeasures1+(1:nmeasures2),
if strcmp(REDO,'Yes')||isnew(nmeasure)
Y1Nt=zeros(CONN_x.Setup.nsubjects,nconditions);
for nsub=1:CONN_x.Setup.nsubjects
for ncondition=1:nconditions,
filename=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
Yout=conn_vol(filename);
if ~isequal(Y1.matdim.dim,Yout.matdim.dim) || ~isequal(Y1.voxels,Yout.voxels), error('unequal analysis voxels across subjects'); end
Y1Nt(nsub,ncondition)=Yout.size.Nt;
end
end
NdimsIn=min(measures.dimensions_in{nmeasure},max(Y1Nt(:)));
h2=conn_waitbar(0,['computing subject x subject covariance']);
C=0;
for slice=1:Y1.size.Ns,
for nsub=1:CONN_x.Setup.nsubjects
for ncondition=1:nconditions,
Y1.fname=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
Y1.size.Nt=Y1Nt(nsub,ncondition);
temp=conn_get_slice(Y1,slice);
if nsub==1&&ncondition==1, x=zeros([size(temp,2),NdimsIn,CONN_x.Setup.nsubjects,nconditions]); end
if ~isempty(temp)
x(:,1:min(size(temp,1),NdimsIn),nsub,ncondition)=temp(1:min(size(temp,1),NdimsIn),:)';
end
end
end
x=x(:,:);
C=C+x'*x;
conn_waitbar(slice/Y1.size.Ns,h2);
end
close(h2);
filename=fullfile(filepathresults,['TEMPORAL1_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']);
save(filename,'C');
C=permute(reshape(C,[NdimsIn,CONN_x.Setup.nsubjects,nconditions,NdimsIn,CONN_x.Setup.nsubjects,nconditions]),[1,4,2,3,5,6]);
h2=conn_waitbar(0,['computing MVPA components']);
filename=fullfile(filepathresults,['TEMPORAL2_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']);
NdimsOut=min(CONN_x.Setup.nsubjects*nconditions,measures.dimensions_out{nmeasure});
Yout=Y1; Yout.fname=filename;Yout.size.Nt=CONN_x.Setup.nsubjects*nconditions*NdimsOut;
Yout=conn_init_vol(Yout);
for slice=1:Y1.size.Ns,
for nsub=1:CONN_x.Setup.nsubjects
for ncondition=1:nconditions,
Y1.fname=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
Y1.size.Nt=Y1Nt(nsub,ncondition);
temp=conn_get_slice(Y1,slice);
if nsub==1&&ncondition==1, x=zeros([size(temp,2),NdimsIn,CONN_x.Setup.nsubjects,nconditions]); end
if ~isempty(temp)
x(:,1:min(size(temp,1),NdimsIn),nsub,ncondition)=temp(1:min(size(temp,1),NdimsIn),:)';
end
end
end
c=zeros([Y1.size.Nv(slice),repmat([CONN_x.Setup.nsubjects,nconditions],[1,2])]);
for nsub=1:CONN_x.Setup.nsubjects
for ncondition=1:nconditions,
for nsub2=1:CONN_x.Setup.nsubjects
for ncondition2=1:nconditions,
c(:,nsub,ncondition,nsub2,ncondition2)=sum((x(:,:,nsub)*C(:,:,nsub,ncondition,nsub2,ncondition2)).*x(:,:,nsub2),2);
end
end
end
end
x=zeros([CONN_x.Setup.nsubjects*nconditions,NdimsOut,Y1.size.Nv(slice)]);
%nvox0=sum(Y1.size.Nv(1:slice-1));
for nvox=1:Y1.size.Nv(slice),
c1=reshape(c(nvox,:),CONN_x.Setup.nsubjects*nconditions*[1,1]);
c1=bsxfun(@minus,c1,mean(c1,1));
c1=bsxfun(@minus,c1,mean(c1,2));
[Q,D]=svd(c1);
d=diag(D);
Q=Q(:,1:NdimsOut);
d=sqrt(abs(d(1:NdimsOut)));
%doflip=sum(Q,1)<0;
%d(doflip)=-d(doflip);
Q=bsxfun(@times,Q,d');
x(:,:,nvox)=Q;
%conn_write_voxel(Yout,Q,nvox0+nvox);
end
conn_write_slice(Yout,reshape(x,[CONN_x.Setup.nsubjects*nconditions*NdimsOut,Y1.size.Nv(slice)]),slice);
conn_waitbar(slice/Y1.size.Ns,h2);
end
close(h2);
h2=conn_waitbar(0,['creating MVPA score volumes']);
for nsub=1:CONN_x.Setup.nsubjects
for ncondition=1:nconditions,
dsum=0;
for ndim=1:NdimsOut
x=conn_get_time(Yout,sub2ind([CONN_x.Setup.nsubjects,nconditions,NdimsOut],nsub,ncondition,ndim));
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(ndim,'%03d'),'.nii']);
a=struct('fname',filename,'mat',Yout.matdim.mat,'dim',Yout.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
spm_write_vol(a,x);
dsum=dsum+abs(x).^2;
end
filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(0,'%03d'),'.nii']);
a=struct('fname',filename,'mat',Yout.matdim.mat,'dim',Yout.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
spm_write_vol(a,sqrt(dsum));
end
conn_waitbar(nsub/CONN_x.Setup.nsubjects,h2);
end
close(h2);
% filename={fullfile(filepathresults,['TEMPORAL1_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']),...
% fullfile(filepathresults,['TEMPORAL2_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']),...
% fullfile(filepathresults,['TEMPORAL2_Measure',num2str(imeasure(nmeasure),'%03d'),'.matc'])};
% spm_unlink(filename{:});
end
n=n+1;
conn_waitbar(n/N,h);
end
else
n=n+nmeasures2;
conn_waitbar(n/N,h);
end
conn_waitbar('close',h);
end
% if nmeasures2>0,
% MAXDIMS=256;
% h=conn_waitbar(0,['Step ',num2str(sum(options<=13)),'/',num2str(length(options)),': connectome-level MVPA analyses']);
% N=nconditions*nmeasures2;
% n=0;
% for ncondition=1:nconditions,
% for nmeasure=nmeasures1+(1:nmeasures2),
% filename=fullfile(filepathresults,['BETA_Subject',num2str(CONN_x.Setup.nsubjects,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(1,'%03d'),'.nii']);
% isnew(nmeasure)=isnew(nmeasure)|isempty(dir(filename));
% end
% end
% if isempty(REDO)&&~all(isnew(nmeasures1+(1:nmeasures2))),
% if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
% end
% if strcmp(REDO,'Yes')||any(isnew(nmeasures1+(1:nmeasures2))),
% % filename_D1=fullfile(filepath,['vvPCcov_SubjectA',num2str(1,'%03d'),'_SubjectB',num2str(1,'%03d'),'_ConditionA',num2str(ncondition,'%03d'),'_ConditionB',num2str(ncondition,'%03d'),'.mat']);
% % D1=load(filename_D1,'D');
% % filename_B1=fullfile(filepath,['vvPC_Subject',num2str(1,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
% % Y1=spm_vol(filename_B1);
% % sA=prod(Y1(1).dim);
% % [gridx,gridy,gridz]=ndgrid(1:Y1(1).dim(1),1:Y1(1).dim(2),1:Y1(1).dim(3));xyz=[gridx(:),gridy(:),gridz(:),ones(numel(gridx),1)]';
% filename_B1=fullfile(filepath,['vvPC_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
% Y1=conn_vol(filename_B1);
% sA=prod(Y1.matdim.dim);
% for nmeasure=nmeasures1+(1:nmeasures2),
% if strcmp(REDO,'Yes')||isnew(nmeasure)
% opts=struct('issym',true,'isreal',true);
% [y,d]=eigs(@(x)conn_v2v('compute_Ax',x,CONN_x.folders.preprocessing,CONN_x.Setup.nsubjects,1:nconditions,measures.dimensions_in{nmeasure}),sA,measures.dimensions_out{nmeasure},'LM',opts);
%
% dsum=0;
% for ndim=1:measures.dimensions_out{nmeasure},
% filename=fullfile(filepathresults,['BETA_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(ndim,'%03d'),'.nii']);
% Yout=struct('fname',filename,'mat',Y1.matdim.mat,'dim',Y1.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
% %Yout=Y1(1);Yout.fname=filename;
% spm_write_vol(Yout,reshape(y(:,ndim),Y1.matdim.dim));
% dsum=dsum+abs(y(:,ndim)).^2;
% end
% filename=fullfile(filepathresults,['BETA_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(0,'%03d'),'.nii']);
% Yout=struct('fname',filename,'mat',Y1.matdim.mat,'dim',Y1.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
% %Yout=Y1(1);Yout.fname=filename;
% spm_write_vol(Yout,reshape(sqrt(dsum),Y1.matdim.dim));
% filename=fullfile(filepathresults,['BETAeig_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(0,'%03d'),'.mat']);
% D=d;Ndim=measures.dimensions_out{nmeasure};save(filename,'D','Ndim');
%
%
% filename=fullfile(filepathresults,['TEMPORAL1_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']);
% Y2=Y1; Y2.fname=filename;Y2.size.Nt=CONN_x.Setup.nsubjects*nconditions*measures.dimensions_out{nmeasure};
% Y2=conn_init_vol(Y2);
% for nsub=1:CONN_x.Setup.nsubjects
% disp([1,nsub])
% for ncondition=1:nconditions,
% % filename_B1=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
% % Y1=spm_vol(filename_B1);
% filename_B1=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
% Y1=conn_vol(filename_B1);
% dsum=0;
% for ndim=1:measures.dimensions_out{nmeasure},
% fprintf('.');
% z=0;
% for ncomp=1:measures.dimensions_in{nmeasure},
% x=conn_get_time(Y1,ncomp); %%%
% %x=spm_get_data(Y1(ncomp),xyz);
% z=z+x(:)*(x(:)'*y(:,ndim));
% end
% conn_write_time(Y2,z(Y2.voxels),sub2ind([CONN_x.Setup.nsubjects,nconditions,measures.dimensions_out{nmeasure}],nsub,ncondition,ndim));
% end
% fprintf('\n');
% end
% end
% filename=fullfile(filepathresults,['TEMPORAL2_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']);
% Ndims=min(MAXDIMS,min(CONN_x.Setup.nsubjects*nconditions,measures.dimensions_out{nmeasure}));
% Yout=Y1; Yout.fname=filename;Yout.size.Nt=CONN_x.Setup.nsubjects*nconditions*Ndims;
% Yout=conn_init_vol(Yout);
% for nvox=1:numel(Y2.voxels)
% x=reshape(conn_get_voxel(Y2,nvox),[CONN_x.Setup.nsubjects*nconditions,measures.dimensions_out{nmeasure}]);
% [Q,D]=svd(x);
% conn_write_voxel(Yout,Q*D,nvox);
% end
% for nsub=1:CONN_x.Setup.nsubjects
% disp([2,nsub])
% for ncondition=1:nconditions,
% dsum=0;
% for ndim=1:Ndims
% x=conn_get_time(Yout,sub2ind([CONN_x.Setup.nsubjects,nconditions,Ndims],nsub,ncondition,ndim));
% filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(ndim,'%03d'),'.nii']);
% Yout=struct('fname',filename,'mat',Yout.matdim.mat,'dim',Yout.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
% spm_write_vol(Yout,x);
% dsum=dsum+abs(x).^2;
% end
% filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(0,'%03d'),'.nii']);
% Yout=struct('fname',filename,'mat',Yout.matdim.mat,'dim',Yout.matdim.dim,'n',[1,1],'pinfo',[1;0;0],'dt',[spm_type('float32'),spm_platform('bigend')],'descrip',mfilename);
% spm_write_vol(Yout,sqrt(dsum));
% end
% end
% filename={fullfile(filepathresults,['TEMPORAL1_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']),...
% fullfile(filepathresults,['TEMPORAL1_Measure',num2str(imeasure(nmeasure),'%03d'),'.matc']),...
% fullfile(filepathresults,['TEMPORAL2_Measure',num2str(imeasure(nmeasure),'%03d'),'.mat']),...
% fullfile(filepathresults,['TEMPORAL2_Measure',num2str(imeasure(nmeasure),'%03d'),'.matc'])};
% spm_unlink(filename{:});
% end
% n=n+1;
% conn_waitbar(n/N,h);
% end
% else
% n=n+nmeasures2;
% conn_waitbar(n/N,h);
% end
% conn_waitbar('close',h);
% end
% if nmeasures3>0,
% h=conn_waitbar(0,['Step ',num2str(sum(options<=13)),'/',num2str(length(options)),': group-level MVPA analyses']);
% N=nconditions*nmeasures3;
% n=0;
% for ncondition=1:nconditions,
% for nmeasure=nmeasures1+(1:nmeasures3),
% filename=fullfile(filepathresults,['BETA_Subject',num2str(CONN_x.Setup.nsubjects,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(1,'%03d'),'.nii']);
% isnew(nmeasure)=isnew(nmeasure)|isempty(dir(filename));
% end
% end
% if isempty(REDO)&&~all(isnew(nmeasures1+(1:nmeasures3))),
% if isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite'), REDO=CONN_x.gui.overwrite; else, REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'Yes');end;
% end
% if strcmp(REDO,'Yes')||any(isnew(nmeasures1+(1:nmeasures3))),
% % filename_D1=fullfile(filepath,['vvPCcov_SubjectA',num2str(1,'%03d'),'_SubjectB',num2str(1,'%03d'),'_ConditionA',num2str(ncondition,'%03d'),'_ConditionB',num2str(ncondition,'%03d'),'.mat']);
% % D1=load(filename_D1,'D');
% filename_B1=fullfile(filepath,['vvPC_Subject',num2str(1,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
% Y1=spm_vol(filename_B1);
% sA=prod(Y1(1).dim);
% [gridx,gridy,gridz]=ndgrid(1:Y1(1).dim(1),1:Y1(1).dim(2),1:Y1(1).dim(3));xyz=[gridx(:),gridy(:),gridz(:),ones(numel(gridx),1)]';
% for nmeasure=nmeasures1+(1:nmeasures3),
% if strcmp(REDO,'Yes')||isnew(nmeasure)
%
% for nvoxel=1:numel(gridx),
% C=zeros([CONN_x.Setup.nsubjects,nconditions,CONN_x.Setup.nsubjects,nconditions]);
% for nsub=1:CONN_x.Setup.nsubjects
% for ncondition=1:nconditions,
% for nsub2=1:nsub
% for ncondition2=1:ncondition,
% C(nsub,ncondition,nsub2,ncondition2)
% end
% end
% end
% end
% end
%
% end
% opts=struct('issym',true,'isreal',true);
% [y,d]=eigs(@(x)conn_v2v('compute_Ax',x,CONN_x.folders.preprocessing,CONN_x.Setup.nsubjects,ncondition,measures.dimensions_in{nmeasure}),sA,measures.dimensions_out{nmeasure},'LM',opts);
%
% dsum=0;
% for ndim=1:measures.dimensions_out{nmeasure},
% filename=fullfile(filepathresults,['BETA_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(ndim,'%03d'),'.nii']);
% Yout=Y1(1);Yout.fname=filename;
% spm_write_vol(Yout,reshape(y(:,ndim),Y1(1).dim));
% dsum=dsum+abs(y(:,ndim)).^2;
% end
% filename=fullfile(filepathresults,['BETA_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(0,'%03d'),'.nii']);
% Yout=Y1(1);Yout.fname=filename;
% spm_write_vol(Yout,reshape(sqrt(dsum),Y1(1).dim));
% for nsub=1:CONN_x.Setup.nsubjects
% filename_B1=fullfile(filepath,['vvPC_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.nii']);
% Y1=spm_vol(filename_B1);
% dsum=0;
% for ndim=1:measures.dimensions_out{nmeasure},
% fprintf('.');
% z=0;
% for ncomp=1:measures.dimensions_in{nmeasure},
% x=spm_get_data(Y1(ndim),xyz);
% z=z+x*(x*y(:,ndim));
% end
% filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(ndim,'%03d'),'.nii']);
% Yout=Y1(1);Yout.fname=filename;
% spm_write_vol(Yout,reshape(z,Y1(1).dim));
% dsum=dsum+abs(z).^2;
% end
% fprintf('\n');
% end
% filename=fullfile(filepathresults,['BETA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(imeasure(nmeasure),'%03d'),'_Component',num2str(0,'%03d'),'.nii']);
% Yout=Y1(1);Yout.fname=filename;
% spm_write_vol(Yout,reshape(sqrt(dsum),Y1(1).dim));
%
%
%
% end
% n=n+1;
% conn_waitbar(n/N,h);
% end
% else
% n=n+nmeasures3;
% conn_waitbar(n/N,h);
% end
% end
% conn_waitbar('close',h);
% end
CONN_x.vvAnalyses.measures=conn_v2v('list_extended',CONN_x.vvAnalyses.regressors);
fileout=fullfile(filepathresults,'_list_measures.txt');
fh=fopen(fileout,'wt');
for n1=1:length(CONN_x.vvAnalyses.measurenames),fprintf(fh,'Measure%03d = %s\n',n1,CONN_x.vvAnalyses.measurenames{n1});end
fclose(fh);
fileout=fullfile(filepathresults,'_list_conditions.txt');
fh=fopen(fileout,'wt');
for n1=1:nconditions,fprintf(fh,'Condition%03d = %s\n',n1,CONN_x.Setup.conditions.names{n1});end
fclose(fh);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates resultsDATA_Condition###_Source###.mat files (combined first-level analyses)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0,%any(options==13) && any(CONN_x.Setup.steps([2])),
if ~isfield(CONN_x.Setup,'normalized'), CONN_x.Setup.normalized=1; end
if ~CONN_x.Setup.normalized,
disp(['Not spatially-normalized data. Skipping ROI-to-voxel second-level analyses']);
else,
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
if nargin>1,analyses=varargin{1}; % selected analysis only
else, analyses=1:length(CONN_x.Analyses); end;
h=conn_waitbar(0,['Step ',num2str(sum(options<=13)),'/',num2str(length(options)),': Preparing second-level analyses']);
analysisbak=CONN_x.Analysis;
for nanalyses=1:length(analyses),
ianalysis=analyses(nanalyses);
CONN_x.Analysis=ianalysis;
% ianalysis=CONN_x.Analysis;
filepathresults=fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(ianalysis).name);
nconditions=length(CONN_x.Setup.conditions.names)-1;
filename=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_12']); conn_waitbar('close',h);return; end
X1=load(filename);
[X,nill,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,X1,[]);
nrois=size(X,2)-1;
iroi=[];isnew=[];for nroi=1:nrois,[iroi(nroi),isnew(nroi)]=conn_sourcenames(names{nroi},'-');end
if any(isnew), error(['Non-existing ROI first-level data for ',names{find(isnew)},'. Please repeat first-level analyses']); return; end
if nanalyses==1, N=nconditions*nrois*length(analyses);n=0; nroisbak=nrois;
else N=N-nconditions*nroisbak+nconditions*nrois; end
for ncondition=1:nconditions,
for nroi=1:nrois,
clear Yin Yout;
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepathresults,['resultsDATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.mat']);
Yin(nsub)=conn_vol(filename);
end
filename=fullfile(filepathresults,['resultsDATA_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi(nroi),'%03d'),'.mat']);
Yout=Yin(1); Yout.fname=filename;
% Yout.size.Nt=CONN_x.Setup.nsubjects;
% Yout=conn_init_vol(Yout);
conn_write_combine(Yin,Yout);
n=n+1;
conn_waitbar(n/N,h);
end
clear Yin Yout;
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepathresults,['seDATA_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
Yin(nsub)=conn_vol(filename);
end
filename=fullfile(filepathresults,['seDATA_Condition',num2str(ncondition,'%03d'),'.mat']);
Yout=Yin(1); Yout.fname=filename;
Yout.DOF=cat(2,Yin(:).DOF);
% Yout.size.Nt=CONN_x.Setup.nsubjects;
% Yout=conn_init_vol(Yout);
conn_write_combine(Yin,Yout);
end
CONN_x.Analyses(ianalysis).sources=names;
end
CONN_x.Analysis=analysisbak;
conn_waitbar('close',h);
%CONN_x.Results.measure=CONN_x.Analyses(ianalysis).measure;
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates resultsROI_Condition###.mat files (combined first-level analyses)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==14) && any(CONN_x.Setup.steps([1])),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
if nargin>1,analyses=varargin{1}; % selected analysis only
else, analyses=1:length(CONN_x.Analyses); end;
doanalyses=false(1,numel(analyses));
for nanalyses=1:numel(analyses),if analyses(nanalyses)>0&&any(CONN_x.Analyses(analyses(nanalyses)).type==[1,3]), doanalyses(nanalyses)=true; end; end
analyses=analyses(doanalyses);
h=conn_waitbar(0,['Step ',num2str(sum(options<=14)),'/',num2str(length(options)),': Preparing second-level ROI analyses']);
analysisbak=CONN_x.Analysis;
for nanalyses=1:length(analyses),
ianalysis=analyses(nanalyses);
CONN_x.Analysis=ianalysis;
% ianalysis=CONN_x.Analysis;
filepathresults=fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(ianalysis).name);
nconditions=length(CONN_x.Setup.conditions.names)-1;
filename=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
if isempty(dir(filename)), disp(['Not ready to process step conn_process_13']); conn_waitbar('close',h);return; end
X1=load(filename);
[X,nill,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,X1,[]);
nrois=size(X,2)-1;
[X2,nill,names2,xyz2]=conn_designmatrix({CONN_x.Analyses(ianalysis).variables,CONN_x.Analyses(ianalysis).regressors},X1,[]);
nrois2=size(X2,2)-1;
idxroi1roi2=zeros(1,nrois);
for n1=1:nrois,temp=strmatch(names{n1},names2,'exact'); idxroi1roi2(n1)=temp(1);end
X2=cat(2,X2(:,1),X2(:,1+idxroi1roi2),X2(:,1+setdiff(1:nrois2,idxroi1roi2)));
names2=cat(2,{names2{idxroi1roi2}},{names2{setdiff(1:nrois2,idxroi1roi2)}});
xyz=cat(2,{xyz2{idxroi1roi2}},{xyz2{setdiff(1:nrois2,idxroi1roi2)}});
if nanalyses==1, n=0;N=CONN_x.Setup.nsubjects*nconditions*nrois*length(analyses); nroisbak=nrois;
else N=N-CONN_x.Setup.nsubjects*nconditions*nroisbak+CONN_x.Setup.nsubjects*nconditions*nrois; end
for ncondition=1:nconditions,
Z=zeros([nrois,nrois2,CONN_x.Setup.nsubjects]);
xyz={};
SE=zeros([CONN_x.Setup.nsubjects,nrois2]);
DOF=zeros([1,CONN_x.Setup.nsubjects]);
for nsub=1:CONN_x.Setup.nsubjects,
filename=fullfile(filepathresults,['resultsROI_Subject',num2str(nsub,'%03d'),'_Condition',num2str(ncondition,'%03d'),'.mat']);
t=load(filename,'Z','regressors','names','names2','xyz','SE','DOF');
IDX=[];IDX2=[];
for nroi=1:nrois,
idx=strmatch(names{nroi},t.names,'exact');
if isempty(idx), error(['Non-existing ROI first-level data for ',names{nroi},' subject ',num2str(nsub),'. Please repeat first-level analyses']); return; end
IDX(nroi)=idx(1);
n=n+1;
conn_waitbar(n/N,h);
end
for nroi=1:nrois2,
idx=strmatch(names2{nroi},t.names2,'exact');
if isempty(idx), error(['Non-existing ROI first-level data for ',names2{nroi},' subject ',num2str(nsub),'. Please repeat first-level analyses']); return; end
IDX2(nroi)=idx(1);
end
Z(:,:,nsub)=t.Z(IDX,IDX2);
xyz={t.xyz{IDX2}};
SE(nsub,:)=t.SE(IDX2);
DOF(nsub)=t.DOF;
end
regressors=CONN_x.Analyses(ianalysis).regressors;
filename=fullfile(filepathresults,['resultsROI_Condition',num2str(ncondition,'%03d'),'.mat']);
save(filename,'Z','regressors','names','names2','xyz','SE','DOF');
end
CONN_x.Analyses(ianalysis).sources=names;
end
CONN_x.Analysis=analysisbak;
conn_waitbar('close',h);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates nDATA_Condition###_Source###.mat files (normalized first-level analysis results)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0,%any(options==8.5),
[path,name,ext]=fileparts(CONN_x.filename);
filepath=CONN_x.folders.preprocessing;
nconditions=length(CONN_x.Setup.conditions.names)-1;
nrois=0;for n1=1:length(CONN_x.Analyses.regressors.names), nrois=nrois+CONN_x.Analyses.regressors.dimensions{n1}(1)*(CONN_x.Analyses.regressors.deriv{n1}+1); end;
h=conn_waitbar(0,['Step ',num2str(sum(options<=8)),'/',num2str(length(options)),': Processing functional data']);
fileref=fullfile(fileparts(which('spm')),'canonical','avg152T1.nii');
V0=spm_vol(fileref);
clear sfile;
for nsub=1:CONN_x.Setup.nsubjects,
[fpath,ffile,fext]=fileparts(deblank(CONN_x.Setup.structural{nsub}{1}));
sfile{nsub}=fullfile(fpath,[ffile,'_seg_inv_sn.mat']);
end
N=nconditions*nrois;
n=0;
for ncondition=1:nconditions,
for nroi=1:nrois,
filename=fullfile(filepath,['DATA_Condition',num2str(ncondition,'%03d'),'_Source',num2str(nroi,'%03d'),'.mat']);
fileout=fullfile(filepath,['nDATA_Condition',num2str(ncondition,'%03d'),'_Source',num2str(nroi,'%03d'),'.mat']);
Y0=conn_vol(filename);
conn_reslice(fileout,V0(1).mat,V0(1).dim,Y0,sfile,0*CONN_x.Setup.fwhm);
n=n+1;
conn_waitbar(n/N,h);
end
end
conn_waitbar('close',h); ;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates second-level SPM.mat results (second-level analysis results for SPM)
% CON_Subject### (source files for second-leve analyses)
% CON_Subject###_Source###.nii (source files for source-specific second-level analyses)
% between-subject contrasts of interest:
% T-contrast: "connectivity results": as specified in "between subject contrast"
% T-contrast: one per effect specified in "subject effects" (named as the corresponding second-level covariates)
% F-contrast: "effects of interest": F- test for all effects in second-levle model
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==15) && any(CONN_x.Setup.steps([2,3])),
if nargin>1, switch(lower(varargin{1})),
case 'dosingle',dosinglecontrast=1; % performs one specific analysis
case 'doall',dosinglecontrast=0; % one analysis per source
case 'readsingle', dosinglecontrast=2; % performs one speficic analysis (if it does not exist already)
otherwise, dosinglecontrast=0; end;
else, dosinglecontrast=0; end
state=2;
if nargin>2, switch(lower(varargin{2})),
case 'seed-to-voxel', state=2;
case 'voxel-to-voxel', state=3;
end
end
if ~isfield(CONN_x,'Results'), disp(['Not ready to process step conn_process_14']); return; end
if state==2
filepathresults1=fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(CONN_x.Analysis).name);
else
filepathresults1=CONN_x.folders.firstlevel;
end
filepathresults2=CONN_x.folders.secondlevel;
if state==2
nsources=CONN_x.Results.xX.nsources;
csources=CONN_x.Results.xX.csources;
sources=CONN_x.Analyses(CONN_x.Analysis).sources;
else
nsources=CONN_x.Results.xX.nmeasures;
csources=CONN_x.Results.xX.cmeasures;
sources=CONN_x.vvAnalyses.measures;
end
nconditions=CONN_x.Results.xX.nconditions;
cconditions=CONN_x.Results.xX.cconditions;
if ~isfield(CONN_x.Results.xX,'modeltype')||isempty(CONN_x.Results.xX.modeltype), CONN_x.Results.xX.modeltype=1; end; %note: obsolete 'modeltype=2' fixed-effect analyses option; remove in next release
modeltype=CONN_x.Results.xX.modeltype;
% if nargin>1&&varargin{1}>1, nsources=varargin{2}; csources=ones(1,length(nsources)); sources={sources{nsources}}; nsources=1:length(nsources); end
% if nargin>1, dosinglecontrast=(varargin{1}==1); else, dosinglecontrast=length(nsources)~=1; end; %~(length(nsources)>1 & all(csources==1/length(nsources))); end
if isfield(CONN_x.Results,'foldername')&&~isempty(CONN_x.Results.foldername),
[ok,nill]=mkdir(filepathresults2,CONN_x.Results.foldername);
filepathresults2=fullfile(filepathresults2,CONN_x.Results.foldername);
CONN_x.Results.foldername=[];
else,
if state==2
foldername={[CONN_x.Analyses(CONN_x.Analysis).name,'.']};
foldername{end+1}=['SUBJECT_EFFECTS_'];
else
foldername={'SUBJECT_EFFECTS_'};
end
for n1=1:length(CONN_x.Results.xX.nsubjecteffects),
if ~any(diff(CONN_x.Results.xX.csubjecteffects)),foldername{end+1}=[CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects(n1)},'.'];
else, foldername{end+1}=[CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects(n1)},'(',num2str(CONN_x.Results.xX.csubjecteffects(n1),'%2.1f'),')','.'];end
end
foldername{end+1}=['CONDITIONS_'];
for n1=1:length(nconditions),
if ~any(diff(cconditions(:))),foldername{end+1}=[CONN_x.Setup.conditions.names{nconditions(n1)},'.'];
else, foldername{end+1}=[CONN_x.Setup.conditions.names{nconditions(n1)},'(',num2str(cconditions(:,n1)','%2.1f'),')','.'];end
end
foldername=strcat(foldername{:});
foldername(foldername==' '|foldername==filesep)='_';
[ok,nill]=mkdir(filepathresults2,foldername);
if ok,filepathresults2=fullfile(filepathresults2,foldername);
else,filepathresults2=uigetdir(filepathresults2,'Select a directory to write the results');end
end
if ~ischar(filepathresults2), return; end;
% disp(['Second-level results stored in ',filepathresults2]);
X=zeros(CONN_x.Setup.nsubjects,length(CONN_x.Setup.l2covariates.names)-1);
for nsub=1:CONN_x.Setup.nsubjects,
for ncovariate=1:length(CONN_x.Setup.l2covariates.names)-1;
X(nsub,ncovariate)=CONN_x.Setup.l2covariates.values{nsub}{ncovariate};
end
end
nsubjects=find(any(X(:,CONN_x.Results.xX.nsubjecteffects)~=0,2));
clear SPMall;
cwd=pwd;
cd(filepathresults2);
REDUCENAMES=(state==2);
if dosinglecontrast>0,
foldername={};
if state==3
txttmp={};for n2=1:length(nsources),txttmp{end+1}=conn_v2v('pcleartext',sources{nsources(n2)}); end
[nill,idxcharstart]=max(any(diff(double(char(txttmp)),1,1),1));
else
[nill,idxcharstart]=max(any(diff(double(char(sources(nsources))),1,1),1));
end
for n2=1:length(nsources),
txttmp=sources{nsources(n2)};
if state==3,txttmp=conn_v2v('pcleartext',txttmp); end
if REDUCENAMES&&length(txttmp)>2&&strcmp(txttmp(1:3),'BA.'),
idxtxttmp=find(txttmp=='.');idxtxttmp2=find(txttmp=='_');
if length(idxtxttmp)>1&&length(idxtxttmp2)>1&&idxtxttmp(end)-1<idxtxttmp2(end-1),
txttmp=txttmp([1:idxtxttmp(end)-1,idxtxttmp2(end-1):end]);
end;
elseif n2>1&&idxcharstart>1
txttmp=txttmp(idxcharstart:end);
end
if ~any(diff(csources(:))),foldername{end+1}=[txttmp,'.'];
else, foldername{end+1}=[txttmp,'(',num2str(csources(:,n2)','%2.1f'),')','.'];end
end
foldername=strcat(foldername{:});foldername(foldername==' '|foldername==filesep|foldername=='*')='_';
[ok,nill]=mkdir(filepathresults2,foldername);
if ok,filepathresults3{1}=fullfile(filepathresults2,foldername);
else,filepathresults3{1}=uigetdir(filepathresults2,'Select a directory to write the results');dosinglecontrast=1;end
if dosinglecontrast==2,
if isempty(dir(fullfile(filepathresults3{1},'SPM.mat'))), dosinglecontrast=1;
elseif ~(isfield(CONN_x,'gui')&&isstruct(CONN_x.gui)&&isfield(CONN_x.gui,'overwrite')), REDO=questdlg('Overwrite existing subject results?','','Yes', 'No', 'No'); if strcmp(REDO,'Yes'),dosinglecontrast=1; end; end
end
if dosinglecontrast==1,
h=conn_waitbar(0,['Step ',num2str(sum(options<=15)),'/',num2str(length(options)),': Functional data second-level analyses']);
clear SE Y;
altestsmooth=false;
for nsub=1:length(nsubjects),%CONN_x.Setup.nsubjects,
if 0,%modeltype==2||((length(nsources)>1||length(nconditions)>1)&&size(csources,1)==1&&size(cconditions,1)==1),%||any(csources(:)~=1)||any(cconditions(:)~=1)),
% bb=0;
% for n1=1:length(nsources),
% nroi=nsources(n1);
% roiname=sources{nroi};
% if state==2
% [iroi,isnew]=conn_sourcenames(roiname,'-');
% if isnew, error(['Non-existing ROI first-level data for ',roiname,' subject ',num2str(nsubjects(nsub)),'. Please repeat first-level analyses']); return; end
% else
% [iroi,isnew,ncomp]=conn_v2v('match_extended',roiname);
% %[iroi,isnew]=conn_v2v('match_measures',CONN_x.vvAnalyses.regressors,nroi,'-');
% if isnew, error(['Non-existing voxel-to-voxel first-level data for ',roiname,' subject ',num2str(nsubjects(nsub)),'. Please repeat first-level analyses']); return; end
% end
% b=0;
% for n0=1:length(nconditions),
% ncondition=nconditions(n0);
% if state==2
% filename=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub)),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi,'%03d'),'.nii']);
% else
% filename=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub),'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(iroi,'%03d'),'_Component',num2str(ncomp,'%03d'),'.nii']);
% end
% a=spm_vol(filename);
% if n0==1&&n1==1&&nsub==1
% [gridx,gridy,gridz]=ndgrid(1:a.dim(1),1:a.dim(2),1:a.dim(3));xyz=a.mat*[gridx(:),gridy(:),gridz(:),ones(numel(gridx),1)]'; adim=a.dim(1:3);
% end
% b=b+cconditions(n0)*reshape(spm_get_data(a,pinv(a.mat)*xyz),adim);%spm_read_vols(a);
% if state==2&&modeltype==2&&nsub==1,
% filename=fullfile(filepathresults1,['resultsDATA_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi,'%03d'),'.mat']);
% Y(n1,n0)=conn_vol(filename);
% if n1==1,
% filename=fullfile(filepathresults1,['seDATA_Condition',num2str(ncondition,'%03d'),'.mat']);
% SE(n0)=conn_vol(filename);
% end
% end
% end
% bb=bb+csources(n1)*b;
% end
% filename=fullfile(filepathresults3{1},['CON_Subject',num2str(nsubjects(nsub),'%03d'),'.nii']);
% a.fname=filename;
% spm_write_vol(a,bb);
% filename={filename};
% contrast=1;
else
filename={};
for n0=1:numel(nconditions)
for n1=1:numel(nsources)
nroi=nsources(n1);
roiname=sources{nroi};
ncondition=nconditions(n0);
if state==2
[iroi,isnew]=conn_sourcenames(roiname,'-');
if isnew, error(['Non-existing seed-to-voxel first-level data for ',roiname,' subject ',num2str(nsubjects(nsub)),'. Please repeat first-level analyses']); return; end
tfilename=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub)),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi,'%03d'),'.nii']);
else
altestsmooth=altestsmooth|~isempty(strmatch('connectome',roiname));
[iroi,isnew,ncomp]=conn_v2v('match_extended',roiname);
%[iroi,isnew]=conn_v2v('match_measures',CONN_x.vvAnalyses.regressors,nroi,'-');
if isnew, error(['Non-existing voxel-to-voxel first-level data for ',roiname,' subject ',num2str(nsubjects(nsub)),'. Please repeat first-level analyses']); return; end
tfilename=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub),'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(iroi,'%03d'),'_Component',num2str(ncomp,'%03d'),'.nii']);
end
filename{n1,n0}=tfilename;
end
end
if numel(nconditions)>1&&size(cconditions,1)==1
for n1=1:numel(nsources)
b=0;
for n0=1:numel(nconditions)
a=spm_vol(filename{n1,n0});
b=b+spm_read_vols(a)*cconditions(n0);
end
tfilename=fullfile(filepathresults3{1},['CON_Subject',num2str(nsubjects(nsub),'%03d'),'_compA',num2str(n1,'%03d'),'.nii']);
a.fname=tfilename;
spm_write_vol(a,b);
filename{n1,numel(nconditions)+1}=tfilename;
end
filename=filename(:,end);
new_cconditions=1;
else
new_cconditions=cconditions;
end
if numel(nsources)>1&&size(csources,1)==1
for n0=1:numel(nconditions)
b=0;
for n1=1:numel(nsources)
a=spm_vol(filename{n1,n0});
b=b+spm_read_vols(a)*csources(n1);
end
tfilename=fullfile(filepathresults3{1},['CON_Subject',num2str(nsubjects(nsub),'%03d'),'_compB',num2str(n1,'%03d'),'.nii']);
a.fname=tfilename;
spm_write_vol(a,b);
filename{numel(nsources)+1,n0}=tfilename;
end
filename=filename(end,:);
new_csources=1;
else
new_csources=csources;
end
filename=filename(:);
contrast=kron(new_cconditions,new_csources);
end
SPMall(1).xY.VY(nsub,:)=spm_vol(char(filename))';
SPMall(1).altestsmooth=altestsmooth;
for n1=1:numel(filename),SPMall(1).xY.VY(nsub,n1).fname=filename{n1}; end
if modeltype==2&&nsub==1, SPMall(1).connvols.Y=Y;SPMall(1).connvols.SE=SE;SPMall(1).connvols.cconditions=cconditions;SPMall(1).connvols.csources=csources;end
conn_waitbar(2/4*(nsub/length(nsubjects)),h);
end
nrepeated=size(SPMall(1).xY.VY,2);
SPMall(1).xX.X=kron(eye(nrepeated),X(nsubjects,CONN_x.Results.xX.nsubjecteffects));%CONN_x.Results.xX.X;
SPMall(1).xX.name=repmat({CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects}},[1,nrepeated]);%CONN_x.Results.xX.name;
SPMall(1).xX.iH = [];
SPMall(1).xX.iC = 1:size(SPMall(1).xX.X,2);
SPMall(1).xX.iB = [];
SPMall(1).xX.iG = [];
SPMall(1).xGX = [];
if nrepeated>1
xVi=struct('I',[repmat((1:size(SPMall(1).xY.VY,1))',[nrepeated,1]),reshape(repmat(1:nrepeated,[size(SPMall(1).xY.VY,1),1]),[],1)],'var',[0,1],'dep',[1,0]);
SPMall(1).xVi=spm_non_sphericity(xVi);
end
end
else,
h=conn_waitbar(0,['Step ',num2str(sum(options<=15)),'/',num2str(length(options)),': Functional data second-level analyses']);
for n1=1:length(sources),
txttmp=sources{n1};
if state==3,txttmp=conn_v2v('pcleartext',txttmp); end
if REDUCENAMES&&length(txttmp)>2&&strcmp(txttmp(1:3),'BA.'),
idxtxttmp=find(txttmp=='.');idxtxttmp2=find(txttmp=='_');
if length(idxtxttmp)>1&&length(idxtxttmp2)>1&&idxtxttmp(end)-1<idxtxttmp2(end-1),
txttmp=txttmp([1:idxtxttmp(end)-1,idxtxttmp2(end-1):end]);
end;
end
foldername=[txttmp,'.'];
foldername(foldername==' '|foldername==filesep|foldername=='*')='_';
[ok,nill]=mkdir(filepathresults2,foldername);
if ok,filepathresults3{n1}=fullfile(filepathresults2,foldername);
else,filepathresults3{n1}=uigetdir(filepathresults2,'Select a directory to write the results');end
end
clear SE Y;
for nsub=1:length(nsubjects),%CONN_x.Setup.nsubjects,
for n1=1:length(sources),
altestsmooth=false;
nroi=n1;
roiname=sources{n1};
if state==2
[iroi,isnew]=conn_sourcenames(roiname,'-');
if isnew, error(['Non-existing ROI first-level data for ',roiname,' subject ',num2str(nsubjects(nsub)),'. Please repeat first-level analyses']); return; end
else
altestsmooth=altestsmooth|~isempty(strmatch('connectome',roiname));
[iroi,isnew,ncomp]=conn_v2v('match_extended',roiname);
% [iroi,isnew]=conn_v2v('match_measures',CONN_x.vvAnalyses.regressors,nroi,'-');
if isnew, error(['Non-existing voxel-to-voxel first-level data for ',roiname,' subject ',num2str(nsubjects(nsub)),'. Please repeat first-level analyses']); return; end
end
if modeltype==2||(length(nconditions)>1&&size(cconditions,1)==1),%||any(cconditions~=1),
b=0;
for n0=1:length(nconditions),
ncondition=nconditions(n0);
if state==2
filename=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub)),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi,'%03d'),'.nii']);
else
filename=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub),'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(iroi,'%03d'),'_Component',num2str(ncomp,'%03d'),'.nii']);
end
a=spm_vol(filename);
b=b+cconditions(n0)*spm_read_vols(a);
% if n0==1&&n1==1&&nsub==1
% [gridx,gridy,gridz]=ndgrid(1:a.dim(1),1:a.dim(2),1:a.dim(3));xyz=a.mat*[gridx(:),gridy(:),gridz(:),ones(numel(gridx),1)]'; adim=a.dim(1:3);
% end
% b=b+cconditions(n0)*reshape(spm_get_data(a,pinv(a.mat)*xyz),adim);%spm_read_vols(a);
% if state==2&&modeltype==2&&nsub==1,
% filename=fullfile(filepathresults1,['resultsDATA_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi,'%03d'),'.mat']);
% Y(n1,n0)=conn_vol(filename);
% if n1==1,
% filename=fullfile(filepathresults1,['seDATA_Condition',num2str(ncondition,'%03d'),'.mat']);
% SE(n0)=conn_vol(filename);
% end
% end
end
filename=fullfile(filepathresults3{n1},['CON_Subject',num2str(nsubjects(nsub),'%03d'),'.nii']);
%filename=fullfile(filepathresults2,['CON_Subject',num2str(nsubjects(nsub)),'_Source',num2str(iroi,'%03d'),'.nii']);
a.fname=filename;
spm_write_vol(a,b);
filename={filename};
contrast=1;
else
filename={};
for n0=1:numel(nconditions)
ncondition=nconditions(n0);
if state==2
filename{end+1}=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub)),'_Condition',num2str(ncondition,'%03d'),'_Source',num2str(iroi,'%03d'),'.nii']);
else
filename{end+1}=fullfile(filepathresults1,['BETA_Subject',num2str(nsubjects(nsub),'%03d'),'_Condition',num2str(ncondition,'%03d'),'_Measure',num2str(iroi,'%03d'),'_Component',num2str(ncomp,'%03d'),'.nii']);
end
end
contrast=cconditions;
end
SPMall(n1).xY.VY(nsub,:)=spm_vol(char(filename))';
SPMall(n1).altestsmooth=altestsmooth;
if state==2&&modeltype==2&&nsub==1, SPMall(n1).connvols.Y=Y(n1,:);SPMall(n1).connvols.SE=SE;SPMall(1).connvols.cconditions=cconditions;SPMall(1).connvols.csources=1;end
end
conn_waitbar(2/4*(nsub/length(nsubjects)),h);
end
for n1=1:length(sources),
nrepeated=size(SPMall(n1).xY.VY,2);
SPMall(n1).xX.X=kron(eye(nrepeated),X(nsubjects,CONN_x.Results.xX.nsubjecteffects));%CONN_x.Results.xX.X;
SPMall(n1).xX.name=repmat({CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects}},[1,nrepeated]);%CONN_x.Results.xX.name;
SPMall(n1).xX.iH = [];
SPMall(n1).xX.iC = 1:size(SPMall(n1).xX.X,2);
SPMall(n1).xX.iB = [];
SPMall(n1).xX.iG = [];
SPMall(n1).xGX = [];
if nrepeated>1
xVi=struct('I',[repmat((1:size(SPMall(n1).xY.VY,1))',[nrepeated,1]),reshape(repmat(1:nrepeated,[size(SPMall(n1).xY.VY,1),1]),[],1)],'var',[0,1],'dep',[1,0]);
SPMall(n1).xVi=spm_non_sphericity(xVi);
end
end
end
if dosinglecontrast==2,
cd(filepathresults3{1});
if isfield(CONN_x,'gui')&&isnumeric(CONN_x.gui)&&CONN_x.gui, conn_display('SPM.mat',1); end
cd(cwd);
else,
switch(modeltype),
case 1, % random-effects
for n1=1:length(SPMall),
cd(filepathresults3{n1});
SPM=SPMall(n1);
save('SPM.mat','SPM');
spm('Defaults','fmri');
spm_unlink('mask.img');
SPM=spm_spm(SPM);
c=kron(contrast,CONN_x.Results.xX.csubjecteffects); %CONN_x.Results.xX.C;
cname='connectivity result';
if size(c,1)==1, Statname='T'; else Statname='F'; end
SPM.xCon = spm_FcUtil('Set',cname,Statname,'c',c',SPM.xX.xKXs);
if 0,%adds other contrasts (one T-test per regressor, and one "effects of interest" F-test)
C=eye(length(CONN_x.Results.xX.nsubjecteffects));
if size(C,1)>1,
for n2=1:size(C,1),
c=C(n2,:);
cname=CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects(n2)}; %CONN_x.Results.xX.name{n2};
SPM.xCon(end+1) = spm_FcUtil('Set',cname,'T','c',c',SPM.xX.xKXs);
end
cname='effects of interest';
SPM.xCon(end+1) = spm_FcUtil('Set',cname,'F','c',C,SPM.xX.xKXs);
end
end
if isfield(SPM,'altestsmooth')&&SPM.altestsmooth, % modified smoothness estimation
SPM=conn_est_smoothness(SPM);
save('SPM.mat','SPM');
end
SPM=spm_contrasts(SPM,1:length(SPM.xCon));
save('SPM.mat','SPM');
if state==2&&~isempty(dir('con_0001.img')),
switch(CONN_x.Analyses(CONN_x.Analysis).measure),
case {1,2}, %correlation
V=spm_vol('con_0001.img');
t=spm_read_vols(V);
V.fname='corr_0001.img';
spm_write_vol(V,tanh(t));
end
end
conn_waitbar(1/2+1/2*(n1/(length(SPMall))),h);
if isfield(CONN_x,'gui')&&isnumeric(CONN_x.gui)&&CONN_x.gui, conn_display('SPM.mat',1); end
end
conn_waitbar('close',h);
cd(cwd);
case 2, % fixed-effects
for n1=1:length(SPMall),
cd(filepathresults3{n1});
csources=SPMall(n1).connvols.csources;
cconditions=SPMall(n1).connvols.cconditions;
Y=SPMall(n1).connvols.Y;
SE=SPMall(n1).connvols.SE;
xf=SPMall(n1).xX.X;
filename='CON_spmT_0001.mat';
Yout=Y(1); Yout.fname=filename;
Yout.size.Nt=1;
Yout.DOF=sum([SE(:).DOF]);
Yout=conn_init_vol(Yout);
for slice=1:Y(1).matdim.dim(3),
yf=0;
se.data=0;
se.dof=0;
for ncondition=1:size(Y,2),
for nsource=1:size(Y,1),
[temp,y.idx]=conn_get_slice(Y(nsource,ncondition),slice);
yf=yf+temp*csources(nsource)*cconditions(ncondition);
end;
[temp,nill]=conn_get_slice(SE(ncondition),slice);
se.data=se.data+sum(csources.^2)*(cconditions(ncondition)*temp).^2;
se.dof=se.dof+SE(ncondition).DOF;
end
se.data=sqrt(se.data);
[B,opt]=conn_glmunivariate('estimatefixed',xf,yf,se);
[H,F,p,dof,R]=conn_glmunivariate('evaluatefixed',opt,[],CONN_x.Results.xX.csubjecteffects);
conn_write_slice(Yout,F,slice);
conn_waitbar(1/2+1/2*((n1-1+slice/Y(1).matdim.dim(3))/(length(SPMall))),h);
end
t=nan+zeros(Yout.matdim.dim);
y=conn_get_time(Yout,1,[],false);
%V=spm_vol(deblank(CONN_x.Setup.structural{nsub}{1})); V=V(1);
V=CONN_x.Setup.structural{1}{3}; V=V(1);
t(Yout.voxels)=y;
V.fname='spmT_0001.img';
if isfield(V,'dt'), V.dt=[spm_type('float32') spm_platform('bigend')];
elseif length(V.dim)>3, V.dim(4)=spm_type('float32'); end
spm_write_vol(V,t);
clear SPM;
SPM.xCon(1).Vspm=V;
SPM.xCon(1).eidf=inf;
SPM.xX.erdf=Yout.DOF;
SPM.xVol.R=[];
SPM.xVol.S=[];
save('SPM.mat','SPM');
if isfield(CONN_x,'gui')&&isnumeric(CONN_x.gui)&&CONN_x.gui, conn_display('SPM.mat',1); end
end
conn_waitbar('close',h);
cd(cwd);
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates second-level ROI.mat results
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==16) && any(CONN_x.Setup.steps([1])),
filepathresults1=fullfile(CONN_x.folders.firstlevel,CONN_x.Analyses(CONN_x.Analysis).name);
filepathresults2=CONN_x.folders.secondlevel;
sources=CONN_x.Analyses(CONN_x.Analysis).sources;
nconditions=CONN_x.Results.xX.nconditions;
cconditions=CONN_x.Results.xX.cconditions;
if nargin<=1,
dosinglecontrast=0;
nsources=1:length(sources);
csources=ones(1,length(nsources));
else
dosinglecontrast=1;
nsources=varargin{1};
csources=varargin{2};
end
if ~nargout,
if isfield(CONN_x.Results,'foldername')&&~isempty(CONN_x.Results.foldername),
[ok,nill]=mkdir(filepathresults2,CONN_x.Results.foldername);
filepathresults2=fullfile(filepathresults2,CONN_x.Results.foldername);
CONN_x.Results.foldername=[];
else,
foldername={[CONN_x.Analyses(CONN_x.Analysis).name,'.']};
foldername{end+1}=['SUBJECT_EFFECTS_'];
for n1=1:length(CONN_x.Results.xX.nsubjecteffects),
if ~any(diff(CONN_x.Results.xX.csubjecteffects)),foldername{end+1}=[CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects(n1)},'.'];
else, foldername{end+1}=[CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects(n1)},'(',num2str(CONN_x.Results.xX.csubjecteffects(n1),'%2.1f'),')','.'];end
end
foldername{end+1}=['CONDITIONS_'];
for n1=1:length(nconditions),
if ~any(diff(cconditions(:))),foldername{end+1}=[CONN_x.Setup.conditions.names{nconditions(n1)},'.'];
else, foldername{end+1}=[CONN_x.Setup.conditions.names{nconditions(n1)},'(',num2str(cconditions(:,n1)','%2.1f'),')','.'];end
end
foldername=strcat(foldername{:});
foldername(foldername==' '|foldername==filesep)='_';
[ok,nill]=mkdir(filepathresults2,foldername);
if ok,filepathresults2=fullfile(filepathresults2,foldername);
else,filepathresults2=uigetdir(filepathresults2,'Select a directory to write the results');end
% if isfield(CONN_x.Results,'foldername')&&~isempty(CONN_x.Results.foldername),
% [ok,nill]=mkdir(filepathresults2,CONN_x.Results.foldername);
% filepathresults2=fullfile(filepathresults2,CONN_x.Results.foldername);
% else,
% filepathresults2=CONN_x.folders.secondlevel;
% filepathresults2=uigetdir(filepathresults2,'Select a directory to write the results');
% end
end
if ~ischar(filepathresults2), return; end;
end
X=zeros(CONN_x.Setup.nsubjects,length(CONN_x.Setup.l2covariates.names)-1);
for nsub=1:CONN_x.Setup.nsubjects,
for ncovariate=1:length(CONN_x.Setup.l2covariates.names)-1;
X(nsub,ncovariate)=CONN_x.Setup.l2covariates.values{nsub}{ncovariate};
end
end
nsubjects=find(any(X(:,CONN_x.Results.xX.nsubjecteffects)~=0,2));
%h=conn_waitbar(0,['Step ',num2str(sum(options<=16)),'/',num2str(length(options)),': ROI data second-level analyses']);
se.data=0;
se.dof=0;
y=0;
Y=repmat({0},[1,length(nsources)]);
for n0=1:length(nconditions),
ncondition=nconditions(n0);
filename=fullfile(filepathresults1,['resultsROI_Condition',num2str(ncondition,'%03d'),'.mat']);
if isempty(dir(filename)),
Ransw=questdlg('First-level ROI analyses have not completed. Perform now?','warning','Yes','No','Yes');
if strcmp(Ransw,'Yes'), conn_process('analyses_roi'); end
end
load(filename,'Z','names','names2','xyz','SE','DOF');
iroi=[];clear ixyz; for nroi=1:length(sources),
roiname=sources{nroi};
tiroi=strmatch(roiname,names,'exact');
if isempty(tiroi), error(['Non-existing ROI first-level data for ',roiname,'. Please repeat first-level analyses']); return; end
iroi(nroi)=tiroi(1);
ixyz{nroi}=xyz{tiroi(1)};
end
for n1=1:length(nsources),
nroi=nsources(n1);
yt=permute(Z(iroi(nroi),:,:),[3,2,1]);
if n0==1&&n1==1, y=zeros([size(yt,1),size(yt,2),length(nsources),length(nconditions)]); end
if n0==1, Y{n1}=zeros([size(yt,1),size(yt,2),length(nconditions)]); end
y(:,:,n1,n0)=yt;% subjects x rois x nsources x nconditions
Y{n1}(:,:,n0)=yt;% subjects x rois x nconditions
%y=y+bsxfun(@times,yt,shiftdim(csources(:,n1)*cconditions(:,n0)',-2)); % subjects x rois x sourcecontrasts x conditioncontrasts
%Y{n1}=Y{n1}+bsxfun(@times,yt,shiftdim(cconditions(:,n0),-2)); % subjects x rois x conditioncontrasts
end
% se.data=se.data+(cconditions(n0)*SE).^2;
% se.dof=se.dof+DOF;
end
% se.data=sqrt(se.data);
%if nargin>1, dosinglecontrast=(varargin{1}==1); else, dosinglecontrast=~(length(nsources)>1 & all(csources==1/length(nsources))); end
clear SPMall filepathresults3;
if dosinglecontrast,
ROIall.xX.X=X(nsubjects,CONN_x.Results.xX.nsubjecteffects);%CONN_x.Results.xX.X;
ROIall.xX.name={CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects}};%CONN_x.Results.xX.name;
% if ~nargout, filepathresults3{n1}=filepathresults2; end
ROIall.y=y(nsubjects,:,:,:);
ROIall.c2=kron(cconditions,csources);
% ROIall.se=se;
% ROIall.se.data=sqrt(sum(csources.^2))*ROIall.se.data;
% ROIall.se.data=ROIall.se.data(nsubjects,:);
% ROIall.se.dof=ROIall.se.dof(nsubjects);
else
for n1=1:length(nsources),
ROIall(n1).xX.X=X(nsubjects,CONN_x.Results.xX.nsubjecteffects);%CONN_x.Results.xX.X;
ROIall(n1).xX.name={CONN_x.Setup.l2covariates.names{CONN_x.Results.xX.nsubjecteffects}};%CONN_x.Results.xX.name;
nroi=nsources(n1);
roiname=sources{nroi};
% if ~nargout,[ok,nill]=mkdir(filepathresults2,roiname); filepathresults3{n1}=fullfile(filepathresults2,roiname); end
ROIall(n1).y=Y{n1}(nsubjects,:,:);
ROIall(n1).c2=cconditions;
% ROIall(n1).se=se;
% ROIall(n1).se.data=ROIall(n1).se.data(nsubjects,:);
% ROIall(n1).se.dof=ROIall(n1).se.dof(nsubjects);
end
end
clear ROIout;
for n1=1:length(ROIall),
ROI=ROIall(n1);
ROI.names=sources;
ROI.xyz=ixyz;
ROI.names2=names2;
ROI.xyz2=xyz;
ROI.cname='connectivity result';
ROI.c=CONN_x.Results.xX.csubjecteffects;%CONN_x.Results.xX.C;
if ~isfield(CONN_x.Results.xX,'modeltype')||isempty(CONN_x.Results.xX.modeltype), CONN_x.Results.xX.modeltype=1; end
if CONN_x.Results.xX.modeltype==1,
[ROI.h,ROI.F,ROI.p,ROI.dof,ROI.statsname]=conn_glm(ROI.xX.X,permute(ROI.y(:,:,:),[1,3,2]),ROI.c,ROI.c2);
ROI.h=reshape(ROI.h,[size(ROI.h,1)*size(ROI.h,2),size(ROI.h,3)]);
if size(ROI.h,1)>1, ROI.h=sqrt(sum(abs(ROI.h).^2,1)); end
ROI.F=reshape(ROI.F,[size(ROI.F,1)*size(ROI.F,2),size(ROI.F,3)]);
ROI.p=reshape(ROI.p,[size(ROI.p,1)*size(ROI.p,2),size(ROI.p,3)]);
%[b,opt]=conn_glmunivariate('estimate',ROI.xX.X,ROI.y);
%[ROI.h,ROI.F,ROI.p,ROI.dof,nill,ROI.statsname]=conn_glmunivariate('evaluate',opt,[],ROI.c);
else,
[b,opt]=conn_glmunivariate('estimatefixed',ROI.xX.X,ROI.y,ROI.se);
[ROI.h,ROI.F,ROI.p,ROI.dof,nill,ROI.statsname]=conn_glmunivariate('evaluatefixed',opt,[],ROI.c);
end
ROIout(n1)=ROI;
% if ~(nargin>1), save(fullfile(filepathresults3{n1},'ROI.mat'),'ROI');
% elseif dosinglecontrast, varargout{1}=ROI;
% elseif n1<=length(nsources), varargout{1}(n1)=ROI; end
%conn_waitbar(1/2+1/2*(n1/(length(nsources)+1)),h);
end
varargout{1}=ROIout;
if ~nargout, ROI=ROIout;save(fullfile(filepathresults2,'ROI.mat'),'ROI'); end
%conn_waitbar('close',h); ;
%cd(cwd);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Displays second-level SPM.mat results
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if any(options==17) && any(CONN_x.Setup.steps([2])),
conn_display;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% additional version-update step
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0,%any(options==18),
[path,name,ext]=fileparts(CONN_x.filename);
% filepath=fullfile(path,name,'data');
filepath=CONN_x.folders.preprocessing;
filename=fullfile(filepath,['ROI_Subject',num2str(1,'%03d'),'_Condition',num2str(1,'%03d'),'.mat']);
X1=load(filename);
[X,nill,names]=conn_designmatrix(CONN_x.Analyses.regressors,X1,[]);
CONN_x.Analyses(CONN_x.Analysis).sources=names;
% CONN_x.Results.measure=CONN_x.Analyses.measure;
end
return;
% from SPM5
function savefields(fnam,p)
if length(p)>1, error('Can''t save fields.'); end;
fn = fieldnames(p);
if numel(fn)==0, return; end;
for i=1:length(fn),
eval([fn{i} '= p.' fn{i} ';']);
end;
if spm_matlab_version_chk('7') >= 0
save(fnam,'-V6',fn{:});
else
save(fnam,fn{:});
end;
function h=conn_waitbar(varargin);
global CONN_x;
h=[];
if isfield(CONN_x,'gui')&&isnumeric(CONN_x.gui)&&CONN_x.gui,
if ischar(varargin{1}), h=varargin{2}; close(h);
else, h=conn_timedwaitbar(varargin{:}); end
else,
if ischar(varargin{1}), conn_cumdisp;
elseif ~varargin{1}, conn_cumdisp;disp(varargin{2});
else, conn_cumdisp([num2str(100*varargin{1},'%3.1f'),'% ']); end
end
function conn_cumdisp(txt);
% CUMDISP persistent disp
% cumdisp; initializes persistent display
% cumdisp(text); displays persistent text
%
persistent oldtxt;
if nargin<1,
oldtxt='';
fprintf(1,'\n');
else,
fprintf(1,[repmat('\b',[1,length(oldtxt)]),'%s'],txt);
oldtxt=sprintf('%s',txt);
end