Fixes for last commit.

cluster/ea_run_HMS_Orchestra_max.m

@@ -0,0 +1,13 @@
+function ea_run_HMS_Orchestra_max(options)
+
+% This is a function that runs code for each subject on a cluster. It needs
+% to be adapted to suit your needs. Then, you can "Export code" using
+% Lead-DBS and simply change the command ea_run to ea_run_cluster.
+
+
+jobID=ea_generate_guid;
+options.spmdir=spm('dir');
+save([options.root,options.patientname,filesep,'job_',jobID],'options')
+setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS','1')
+cmdstring=['cd ',options.earoot,' && bsub -q long -R "rusage[mem=20000]" -W 720:0 -o ',[options.root,options.patientname,filesep,'job_',jobID],'.out -e ',[options.root,options.patientname,filesep,'job_',jobID],'.err matlab -singleCompThread -nodisplay -r "ea_run runcluster ',[options.root,options.patientname,filesep,'job_',jobID],'"'];
+system(cmdstring);

connectomics/ea_convis.m

@@ -269,7 +269,7 @@ function ea_cvshowseedbasedresults(resultfig,directory,pV,pX,selectedparc,handle
     if ~ret % something has changed since last time.
         ea_deletePL(resultfig,'PL','mat');
 
-        [~,thresh]=ea_cvshowfiberconnectivities(resultfig,fibersfile,seed,targetsfile,thresh,1,options,'',changedstates,'mat');
+        [~,thresh]=ea_cvshowfiberconnectivities(resultfig,fibersfile,seed,targetsfile,thresh,1,options,'',changedstates,'mat',get(handles.vizmat_regs,'Value'),get(handles.vizmat_labs,'Value'));
         set(handles.matthreshis,'String',num2str(thresh));
 
     end

connectomics/ea_cvshowfiberconnectivities.m

@@ -1,4 +1,4 @@
-function [PL,thresh]=ea_cvshowfiberconnectivities(resultfig,fibersfile,seedfile,targetsfile,thresh,sides,options,stimparams,changedstates,mode)
+function [PL,thresh]=ea_cvshowfiberconnectivities(resultfig,fibersfile,seedfile,targetsfile,thresh,sides,options,stimparams,changedstates,mode,showregs,showlabs)
 % This function shows fiber-connectivity from a volume defined by a nx3
 % point-list (volume). If stimparams.showconnectivities is set, connected
 % areas to the volume are also visualized. To do so, the function uses
@@ -238,12 +238,8 @@
     % always show seed patch (i.e. VAT)
     PL.matseedsurf{side}=ea_showseedpatch(resultfig,seed{side},seed{side}.img,options);
 
-    if get(handles.vizvat_regs,'Value') || get(handles.vizvat_labs,'Value')
-        [PL.matsurf{side},PL.conlabels{side}]=ea_showconnectivitypatch(resultfig,targets,contargets,thresh,atlas_lgnd{2},tareas{side},[],get(handles.vizvat_regs,'Value'),get(handles.vizvat_labs,'Value'));
-    else
-        PL.matsurf{side}=[];
-        PL.conlabels{side}=[];
-    end
+        [PL.matsurf{side},PL.conlabels{side}]=ea_showconnectivitypatch(resultfig,targets,contargets,thresh,atlas_lgnd{2},tareas{side},[],showregs,showlabs);
+
     clear allcareas conareas
 %     %% now show areas
 %     targets.img=round(targets.img);

connectomics/ea_cvshowvatdmri.m

@@ -59,7 +59,7 @@ function ea_cvshowvatdmri(resultfig,directory,handles,selectedparc,options)
         if ~ret % something has changed since last time.
             ea_deletePL(resultfig,'PL','vat');
             if dimensionality % one of the vat checkboxes is active
-                [~,thresh]=ea_cvshowfiberconnectivities(resultfig,fibersfile,seedfile,targetsfile,thresh,sides,options,S,changedstates,'vat'); % 'vat' only used for storage of changes.
+                [~,thresh]=ea_cvshowfiberconnectivities(resultfig,fibersfile,seedfile,targetsfile,thresh,sides,options,S,changedstates,'vat',get(handles.vizvat_regs,'Value'),get(handles.vizvat_labs,'Value')); % 'vat' only used for storage of changes.
                 if isstruct(handles)
                     set(handles.vatthreshis,'String',num2str(thresh));
                 end

connectomics/ea_showconnectivitypatch.m

@@ -1,43 +1,43 @@
-function [matsurf,labels]=ea_showconnectivitypatch(resultfig,pV,mX,thresh,atlaslegend,atlasindices,showregs,showlabels)
+function [matsurf,labels]=ea_showconnectivitypatch(resultfig,pV,mX,thresh,atlaslegend,atlasindices,usecolormap,showregs,showlabels)
 
 
 
-
-tmX=mX>thresh;
-
-options.prefs=ea_prefs('');
-if options.prefs.hullsmooth
-   tmX=smooth3(tmX,'gaussian',options.prefs.hullsmooth); 
-end
-
-bb=[0,0,0;size(mX)];
-
-bb=map_coords_proxy(bb,pV);
-gv=cell(3,1);
-for dim=1:3
-    gv{dim}=linspace(bb(1,dim),bb(2,dim),size(mX,dim));
-end
-[X,Y,Z]=meshgrid(gv{1},gv{2},gv{3});
-fv=isosurface(X,Y,Z,permute(tmX,[2,1,3]),0.5); % graph_metric
-
-
-if ischar(options.prefs.hullsimplify)
-    % get to 1500 faces
-    simplify=1500;
-    fv=reducepatch(fv,simplify);
-else
-    if options.prefs.hullsimplify<1 && options.prefs.hullsimplify>0
-
-        fv=reducepatch(fv,options.prefs.hullsimplify);
-    elseif options.prefs.hullsimplify>1
-        simplify=options.prefs.hullsimplify/length(fv.faces);
+if showregs
+
+    tmX=mX>thresh;
+
+    options.prefs=ea_prefs('');
+    if options.prefs.hullsmooth
+        tmX=smooth3(tmX,'gaussian',options.prefs.hullsmooth);
+    end
+
+    bb=[0,0,0;size(mX)];
+
+    bb=map_coords_proxy(bb,pV);
+    gv=cell(3,1);
+    for dim=1:3
+        gv{dim}=linspace(bb(1,dim),bb(2,dim),size(mX,dim));
+    end
+    [X,Y,Z]=meshgrid(gv{1},gv{2},gv{3});
+    fv=isosurface(X,Y,Z,permute(tmX,[2,1,3]),0.5); % graph_metric
+
+
+    if ischar(options.prefs.hullsimplify)
+        % get to 1500 faces
+        simplify=1500;
         fv=reducepatch(fv,simplify);
+    else
+        if options.prefs.hullsimplify<1 && options.prefs.hullsimplify>0
+
+            fv=reducepatch(fv,options.prefs.hullsimplify);
+        elseif options.prefs.hullsimplify>1
+            simplify=options.prefs.hullsimplify/length(fv.faces);
+            fv=reducepatch(fv,simplify);
+        end
     end
-end
-
-
-set(0,'CurrentFigure',resultfig)
-if showregs
+
+
+    set(0,'CurrentFigure',resultfig)
     matsurf=patch(fv,'facealpha',0.7,'EdgeColor','none','facelighting','phong','FaceColor','interp');
 
     zidx=mX==0;
@@ -86,7 +86,7 @@
 
         [xx,yy,zz]=ind2sub(size(pV.img),find(pV.img==atlasindices(lab)));
         XYZ=[xx,yy,zz];
-        centr_vx=[mean(XYZ,1),1]';        
+        centr_vx=[mean(XYZ,1),1]';
         centr_mm=pV.mat*centr_vx;
 
         labels(lab)=text(centr_mm(1),centr_mm(2),centr_mm(3),sub2space(atlaslegend{atlasindices(lab)}));
@@ -103,39 +103,39 @@
 
 
 % %% old
-% 
+%
 % bb=[0,0,0;size(mX)];
-% 
+%
 % bb=map_coords_proxy(bb,pV);
 % gv=cell(3,1);
 % for dim=1:3
 %     gv{dim}=linspace(bb(1,dim),bb(2,dim),size(mX,dim));
 % end
 % [X,Y,Z]=meshgrid(gv{1},gv{2},gv{3});
-% 
-% 
+%
+%
 % fv=isosurface(X,Y,Z,permute(mX,[2,1,3]),thresh); % connected regions
-% 
+%
 % if ischar(options.prefs.lhullsimplify)
-%     
+%
 %     % get to certain number of faces
 %     simplify=10000/length(fv.faces);
 %     fv=reducepatch(fv,simplify);
-%     
+%
 % else
 %     if options.prefs.lhullsimplify<1 && options.prefs.lhullsimplify>0
 %         fv=reducepatch(fv,options.prefs.lhullsimplify);
 %     end
 % end
-% 
+%
 % set(0,'CurrentFigure',resultfig)
 % matsurf=patch(fv,'FaceColor','interp','facealpha',0.7,'EdgeColor','none','facelighting','phong');
-% 
+%
 % cmX=mX;
 % zidx=cmX==0;
 % zidx=logical(zidx+isnan(cmX));
 % cmX(isnan(cmX))=0;
-% 
+%
 % try % if not possible, connectivity is empty..
 % cmX=cmX-min(cmX(cmX~=0));
 % end
@@ -144,13 +144,13 @@
 % end
 % cmX(zidx)=0; % reset prior zero/nan values to zero
 % isocolors(X,Y,Z,permute(cmX,[2,1,3]),matsurf)
-% 
+%
 % set(matsurf,'DiffuseStrength',0.9)
 % set(matsurf,'SpecularStrength',0.1)
 % set(matsurf,'FaceAlpha',0.3);
 % %threshold seedcon
 % % seedcon=((seedcon-thresh)/(max(seedcon)-thresh))*255;
-% % 
+% %
 % % cX=pX;
 % % for i=1:length(seedcon)
 % %     cX(pX==i)=seedcon(i);

dbshub/ea_exportscore.m

@@ -0,0 +1,76 @@
+function score=ea_exportscore()
+
+% for now static sample export:
+
+score.studyOrigin='Earlystim'; % Tag label study name
+score.studyDoi='10.1056/NEJMoa1205158'; % Tag label study name
+score.metric='UPDRS-III'; % clinical score label
+score.dbsOff.vals=[1,2,0,0,0,0,0,0,0,0,0,0,0,0,2,3,2,2,3,3,1,1,1,2,2,2,2];
+score.dbsOff.mean=(mean(score.dbsOff.vals));
+score.dbsOn.vals=[0,2,0,0,0,0,0,2,2,0,0,0,0,0,3,3,1,2,1,3,0,2,1,2,2,2,2];
+score.dbsOn.mean=(mean(score.dbsOn.vals));
+score.patient.DOB='05-10-1951'; % date of birth
+score.patient.DOS='03-02-2014'; % date of surgery
+score.patient.disease='Parkinson''''s Disease';
+score.patient.diseaseSubtype='Tremor Dominant';
+score.version=1.0;
+
+ea_savejson('',score,ea_setjsopts('sample.json'));
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+function opt=ea_setjsopts(fname)
+
+
+   opt.FileName=fname;
+%        opt.FloatFormat ['%.10g'|string]: format to show each numeric element
+%                         of a 1D/2D array;
+%        opt.ArrayIndent [1|0]: if 1, output explicit data array with
+%                         precedent indentation; if 0, no indentation
+%        opt.ArrayToStruct[0|1]: when set to 0, savejson outputs 1D/2D
+%                         array in JSON array format; if sets to 1, an
+%                         array will be shown as a struct with fields
+%                         "_ArrayType_", "_ArraySize_" and "_ArrayData_"; for
+%                         sparse arrays, the non-zero elements will be
+%                         saved to _ArrayData_ field in triplet-format i.e.
+%                         (ix,iy,val) and "_ArrayIsSparse_" will be added
+%                         with a value of 1; for a complex array, the 
+%                         _ArrayData_ array will include two columns 
+%                         (4 for sparse) to record the real and imaginary 
+%                         parts, and also "_ArrayIsComplex_":1 is added. 
+%        opt.ParseLogical [0|1]: if this is set to 1, logical array elem
+%                         will use true/false rather than 1/0.
+%        opt.NoRowBracket [1|0]: if this is set to 1, arrays with a single
+%                         numerical element will be shown without a square
+%                         bracket, unless it is the root object; if 0, square
+%                         brackets are forced for any numerical arrays.
+%        opt.ForceRootName [0|1]: when set to 1 and rootname is empty, savejson
+%                         will use the name of the passed obj variable as the 
+%                         root object name; if obj is an expression and 
+%                         does not have a name, 'root' will be used; if this 
+%                         is set to 0 and rootname is empty, the root level 
+%                         will be merged down to the lower level.
+%        opt.Inf ['"$1_Inf_"'|string]: a customized regular expression pattern
+%                         to represent +/-Inf. The matched pattern is '([-+]*)Inf'
+%                         and $1 represents the sign. For those who want to use
+%                         1e999 to represent Inf, they can set opt.Inf to '$11e999'
+%        opt.NaN ['"_NaN_"'|string]: a customized regular expression pattern
+%                         to represent NaN
+%        opt.JSONP [''|string]: to generate a JSONP output (JSON with padding),
+%                         for example, if opt.JSON='foo', the JSON data is
+%                         wrapped inside a function call as 'foo(...);'
+%        opt.UnpackHex [1|0]: conver the 0x[hex code] output by loadjson 
+%                         back to the string form

ea_regressout.m

@@ -6,7 +6,7 @@
 nnanix=any(isnan(Cova),1);
 nnanix=nnanix+(isnan(S));
 nnanix=~nnanix;
-
+Cleaned=S;
 Cova=Cova(:,nnanix);
 
 S=S(nnanix);
@@ -15,4 +15,5 @@
 S=zscore(S);
 
 beta_hat = (Cova*Cova')\Cova*squeeze(S'); % ordinary least-squares estimator
-Cleaned=squeeze(S)'-Cova'*beta_hat; % regress out each covariate.
+Cleaned(nnanix)=squeeze(S)'-Cova'*beta_hat; % regress out each covariate.
+Cleaned=Cleaned';