gin_list_dlabels.m

function varargout = gin_list_dlabels(varargin)
% Display and analysis of SPM{.}
% FORMAT TabDat = spm_list('List',SPM,hReg,[Num,Dis,Str])
% Summary list of local maxima for entire volume of interest
% FORMAT TabDat = spm_list('ListCluster',SPM,hReg,[Num,Dis,Str])
% List of local maxima for a single suprathreshold cluster
%
% SPM    - structure containing SPM, distribution & filtering details
%        - spm2
%
% (see spm_getSPM for further details of xSPM structures)
%
% hReg   - Handle of results section XYZ registry (see spm_results_ui.m)
%
% Num    - number of maxima per cluster
% Dis    - distance among clusters (mm)
% Str    - header string
%
% TabDat - Structure containing table data
%        - fields are
% .tit   - table Title (string)
% .hdr   - table header (2x3 cell array)
% .fmt   - fprintf format strings for table data (1x3 cell array)
% .str   - table filtering note (string)
% .ftr   - table footnote information (4x2 cell array)
% .dat   - table data (Nx3 cell array)
%
%                           ----------------
% See spm_list.m for more details
%
%                           ----------------
% FORMAT spm_list('TxtList',TabDat,c)
% Prints a tab-delimited text version of the table
% TabDat - Structure containing table data (format as above)
% c      - Column of table data to start text table at
%          (E.g. c=3 doesn't print set-level results contained in columns 1 & 2)
%
%                           ----------------
% This function loads the labelised atlas, MNI VOIs & Labels, and the distances
% between VOIs and Labels.
% For each local maximum (Minimum distance between maxima 8mm) of a cluster, 
% this function search for nearest regions 
% and displays the table :
%		- local maxima of cluster
%		- the nearest regions (labels)
%		- distances between regions and local maxima.
% To Compute Labels & Distances we use the 'gin_det_dlabels'
% routine. 
% ______________________________________________________________________
%
% gin_list_dlabels.m		B Landeau 26/01/2006
% ______________________________________________________________________
% 
%


% satellite figure global variable
%-----------------------------------------------------------------------
global SatWindow


%=======================================================================
switch lower(varargin{1}), case 'list'                            %-List
%=======================================================================
% FORMAT TabDat = spm_list('list',SPM,hReg)

%-Tolerance for p-value underflow, when computing equivalent Z's
%-----------------------------------------------------------------------
tol = eps*10;

%-Parse arguments and set maxima number and separation
%-----------------------------------------------------------------------

if nargin < 2,	error('insufficient arguments'),     end
if nargin < 3,  hReg = []; else, hReg = varargin{3}; end
%In case the file is used in batch mode (from toolbox)
if length(varargin) > 2 ,	hReg = [];  atlas = char(varargin{3}); pr= varargin{4}; end

spm_figure('Clear','Graphics');
%-Get current location (to highlight selected voxel in table)
%-----------------------------------------------------------------------
%xyzmm     = spm_results_ui('GetCoords');

%-Extract data from xSPM
%-----------------------------------------------------------------------
S     = varargin{2}.S;
R     = varargin{2}.R;
FWHM  = varargin{2}.FWHM;
VOX   = varargin{2}.VOX;
n     = varargin{2}.n;
STAT  = varargin{2}.STAT;
df    = varargin{2}.df;
u     = varargin{2}.u;
M     = varargin{2}.M;
v2r   = 1/prod(FWHM(~isinf(FWHM)));			%-voxels to resels
k     = varargin{2}.k*v2r;
try
  QPs   = varargin{2}.Ps;					% Needed for FDR
  QPs   = sort(QPs(:));
catch
end


%-get number and separation for maxima to be reported
%-----------------------------------------------------------------------
if length(varargin) > 4

	Num    = varargin{5};		% number of maxima per cluster
	Dis    = varargin{6};		% distance among clusters (mm)
else
	Num    = 3;
	Dis    = 8;
end
if length(varargin) > 6

	Title  = varargin{7};
else
	Title  = ['volume summary',...
			' (labels and distances for entire volume)'];
end


%-Setup graphics panel
%-----------------------------------------------------------------------
spm('Pointer','Watch')
if SatWindow
	Fgraph = SatWindow;
	figure(Fgraph);
else
	Fgraph = spm_figure('GetWin','Graphics');
end
spm_results_ui('Clear',Fgraph)
FS    = spm('FontSizes');			%-Scaled font sizes
PF    = spm_platform('fonts');			%-Font names (for this platform)


%-Table header & footer
%=======================================================================

%-Table axes & Title
%----------------------------------------------------------------------
if SatWindow, ht = 0.85; bot = .14; else, ht = 0.4; bot = .1; end;
ht = 0.85; 
bot = .14;
%if STAT == 'P'
%	Title = 'Posterior Probabilities';
%end
	
hAx   = axes('Position',[0.025 bot 0.9 ht],...
	'DefaultTextFontSize',FS(8),...
	'DefaultTextInterpreter','Tex',...
	'DefaultTextVerticalAlignment','Baseline',...
	'Units','points',...
	'Visible','off');

AxPos = get(hAx,'Position'); set(hAx,'YLim',[0,AxPos(4)])
dy    = FS(9);
y     = floor(AxPos(4)) - dy;

text(0,y,['Working Dir : ',varargin{2}.swd],'FontSize',FS(11),'FontWeight','Bold','Editing','on');	
y = y - 1.5*dy;
text(0,y,varargin{2}.title,'FontSize',FS(11),'FontWeight','Bold');	
y = y - 1.5*dy;
text(0,y,['Labels :  \it\fontsize{',num2str(FS(9)),'}',Title],...
	'FontSize',FS(11),'FontWeight','Bold');	
y = y - dy/2;
line([0 1],[y y],'LineWidth',3,'Color','r');
y = y - 9*dy/8;


%-Construct table header
%-----------------------------------------------------------------------
set(gca,'DefaultTextFontName',PF.helvetica,'DefaultTextFontSize',FS(8))

Hc = [];

text(0.01,y - dy/2,'x,y,z {mm}','FontSize',FS(9));
text(0.14,y - dy/2,'label','FontSize',FS(9))
text(0.38,y - dy/2,'dist {mm}','FontSize',FS(9));

label='label name';



%-Headers for text table...
%-----------------------------------------------------------------------
TabDat.tit = Title;

TabDat.hdr = {	'',		'x,y,z {mm}';...
				'',		label;...
				'',		'dist {mm}'}';

TabDat.fmt = { '%3.0f %3.0f %3.0f','%s','%3.2f'};


%-Column Locations
%-----------------------------------------------------------------------
%tCol       = [  0.00      0.07 ...				%-Set
%	        0.16      0.26      0.34 ...			%-Cluster
%	        0.46      0.55      0.62      0.71      0.80 ...%-Voxel
 %               0.92];						%-XYZ

% move to next vertial postion marker
%-----------------------------------------------------------------------
y     = y - 7*dy/4;
line([0 1],[y y],'LineWidth',1,'Color','r')
y     = y - 5*dy/4;
y0    = y;


%-Table filtering note
%-----------------------------------------------------------------------
if isinf(Num)
	TabDat.str = sprintf('table shows all local maxima > %.1fmm apart',Dis);
else
	TabDat.str = sprintf(['table shows at most %d local maxima ',...
		'> %.1fmm apart per cluster'],Num,Dis);
end
text(0.5,4,TabDat.str,'HorizontalAlignment','Center','FontName',PF.helvetica,...
    'FontSize',FS(8),'FontAngle','Italic')


%-Volume, resels and smoothness (if classical inference)
%-----------------------------------------------------------------------
%if STAT ~= 'P'
%-----------------------------------------------------------------------
FWHMmm          = FWHM.*VOX; 				% FWHM {mm}
Pz              = spm_P(1,0,u,df,STAT,1,n,S);
Pu              = spm_P(1,0,u,df,STAT,R,n,S);
try
  Qu              = spm_P_FDR(u,df,STAT,n,QPs);
catch
  Qu = NaN;
end

 [P Pn Em En] = spm_P(1,k,u,df,STAT,R,n,S);


%-Footnote with SPM parameters
%-----------------------------------------------------------------------
line([0 1],[0 0],'LineWidth',1,'Color','r')
set(gca,'DefaultTextFontName',PF.helvetica,...
	'DefaultTextInterpreter','None','DefaultTextFontSize',FS(8))
TabDat.ftr    = cell(5,2);
TabDat.ftr{1} = ...
	sprintf('Height threshold: %c = %0.2f, p = %0.3f (%0.3f)',...
		 STAT,u,Pz,Pu);
TabDat.ftr{2} = ...
	sprintf('Extent threshold: k = %0.0f voxels, p = %0.3f (%0.3f)',...
	         k/v2r,Pn,P);
TabDat.ftr{3} = ...
	sprintf('Expected voxels per cluster, <k> = %0.3f',En/v2r);
TabDat.ftr{4} = ...
	sprintf('Expected number of clusters, <c> = %0.2f',Em*Pn);
TabDat.ftr{5} = ...
	sprintf('Expected false discovery rate, <= %0.2f',Qu);
TabDat.ftr{6} = ...
	sprintf('Degrees of freedom = [%0.1f, %0.1f]',df);
TabDat.ftr{7} = ...
	sprintf(['Smoothness FWHM = %0.1f %0.1f %0.1f {mm} ',...
		 ' = %0.1f %0.1f %0.1f {voxels}'],FWHMmm,FWHM);
TabDat.ftr{8} = ...
	sprintf('Search vol: %0.0f cmm; %0.0f voxels; %0.1f resels',S*prod(VOX),S,R(end));
TabDat.ftr{9} = ...
	sprintf(['Voxel size: [%0.1f, %0.1f, %0.1f] mm ',...
		' (1 resel = %0.2f voxels)'],VOX,prod(FWHM));

text(0.0,-1*dy,TabDat.ftr{1},...
	'UserData',[u,Pz,Pu,Qu],'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.0,-2*dy,TabDat.ftr{2},...
	'UserData',[k/v2r,Pn,P],'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.0,-3*dy,TabDat.ftr{3},...
	'UserData',En/v2r,'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.0,-4*dy,TabDat.ftr{4},...
	'UserData',Em*Pn,'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.0,-5*dy,TabDat.ftr{5},...
	'UserData',Qu,'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.5,-1*dy,TabDat.ftr{6},...
	'UserData',df,'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.5,-2*dy,TabDat.ftr{7},...
	'UserData',FWHMmm,'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.5,-3*dy,TabDat.ftr{8},...
	'UserData',[S*prod(VOX),S,R(end)],...
	'ButtonDownFcn','get(gcbo,''UserData'')')
text(0.5,-4*dy,TabDat.ftr{9},...
	'UserData',[VOX,prod(FWHM)],...
	'ButtonDownFcn','get(gcbo,''UserData'')')

%end % Classical


%-Characterize excursion set in terms of maxima
% (sorted on Z values and grouped by regions)
%=======================================================================
if ~length(varargin{2}.Z)
	text(0.5,y-6*dy,'no suprathreshold clusters',...
		'HorizontalAlignment','Center',...
		'FontAngle','Italic','FontWeight','Bold',...
		'FontSize',FS(16),'Color',[1,1,1]*.5);
	TabDat.dat = cell(0,3);
	varargout  = {TabDat};
	spm('Pointer','Arrow')
	return
end

% Includes Darren Gitelman's code for working around
% spm_max for conjunctions with negative thresholds
%-----------------------------------------------------------------------
minz        = abs(min(min(varargin{2}.Z)));
zscores     = 1 + minz + varargin{2}.Z;
[N Z XYZ A] = spm_max(zscores,varargin{2}.XYZ);
Z           = Z - minz - 1;

%-Convert cluster sizes from voxels to resels
%-----------------------------------------------------------------------
if isfield(varargin{2},'VRvp')
	V2R = spm_get_data(varargin{2}.VRvp,XYZ);
else
	V2R = v2r;
end
N           = N.*V2R;

%-Convert maxima locations from voxels to mm
%-----------------------------------------------------------------------
XYZmm = M(1:3,:)*[XYZ; ones(1,size(XYZ,2))];

% load MNI ROIs & Labels
%-----------------------------------------------------------------------

spm_defaults;
global defaults

flag_flip = 0;	% Modif BL 4/10/03
% defaults = L/R -> MNI = L/L
%	if defaults.analyze.flip 
%		defaults.analyze.flip = 0;
%		flag_flip = 1;
%	end

	%MNI=spm_get(1,'.img','select an labelised atlas');
		
    if exist('atlas')
        MNI = atlas;
    else 
        MNI = spm_select(1,'image','Select an labelised atlas');
    end
    
    
	MNID=spm_vol(MNI);
	eval(['load ''',strrep(MNI,'.nii','_List.mat''')]);
	%ROI.ID
	%ROI.Nom_C
	%ROI.Nom_L
	eval(['load ''',strrep(MNI,'.nii','_Border.mat''')]);
	BORDER_XYZ(1,:)=MNID.mat(1,4)-BORDER_XYZ(1,:);
	%BORDER_V

%	if flag_flip 
%		defaults.analyze.flip = 1;
%		flag_flip = 0;
%	end
		


%-Table proper (& note all data in cell array)
%=======================================================================

%-Pagination variables
%-----------------------------------------------------------------------
hPage = [];
set(gca,'DefaultTextFontName',PF.courier,'DefaultTextFontSize',FS(7))


%-Set-level p values {c} - do not display if reporting a single cluster
%-----------------------------------------------------------------------
c     = max(A);					%-Number of clusters
TabLin     = 1;					%-Table data line


%-Local maxima p-values & statistics
%-----------------------------------------------------------------------
HlistXYZ = [];
while sum(~isnan(Z)),

	% Paginate if necessary
	%---------------------------------------------------------------
	if y < min(Num + 1,3)*dy

		% added Fgraph term to paginate on Satellite window
		%-------------------------------------------------------
		h     = text(0.5,-5*dy,...
			sprintf('Page %d',spm_figure('#page',Fgraph)),...
			'FontName',PF.helvetica,'FontAngle','Italic',...
			'FontSize',FS(8));

		spm_figure('NewPage',[hPage,h])
		hPage = [];
		y     = y0;
	end

    	%-Find largest remaining local maximum
    	%---------------------------------------------------------------
	[U,i]   = max(Z);			% largest maxima
	j       = find(A == A(i));		% maxima in cluster



	%-Compute Labels & Distances
    %---------------------------------------------------------------
	[Label,Dist] = gin_det_dlabels(XYZmm(:,i), MNID, ROI, BORDER_XYZ, BORDER_V);
    %---------------------------------------------------------------

	h     = text(0.00,y,sprintf(TabDat.fmt{1},XYZmm(:,i)),...
		'FontWeight','Bold',...
		'Tag','ListXYZ',...
		'ButtonDownFcn',...
		'spm_mip_ui(''SetCoords'',get(gcbo,''UserData''));',...
		'Interruptible','off','BusyAction','Cancel',...
		'UserData',XYZmm(:,i));
	HlistXYZ = [HlistXYZ, h];
	hPage = [hPage, h];
	
 	x=0.14;
 	for kkk=1:size(Dist,2),
			if y < 2*dy
				h = text(0.5,-5*dy,sprintf('Page %d',...
					spm_figure('#page')),...
					'FontName',PF.helvetica,...
					'FontAngle','Italic',...
					'FontSize',FS(8));
				spm_figure('NewPage',[hPage,h])
				hPage = [];
				y     = y0;
			end
			h     = text(x,y,sprintf(TabDat.fmt{2},Label(kkk).Nom),	'FontWeight','Bold',...
				'UserData',label,'ButtonDownFcn','get(gcbo,''UserData'')');
			hPage = [hPage, h];
			x=x+0.24;

			h     = text(x,y,sprintf(TabDat.fmt{3},Dist(kkk)),	'FontWeight','Bold',...
				'UserData',Dist(kkk),'ButtonDownFcn','get(gcbo,''UserData'')');
			hPage = [hPage, h];
			x=x+0.07;
			[TabDat.dat{TabLin,1:3}] = deal(XYZmm(:,i),Label(kkk).Nom,Dist(kkk));
			TabLin = TabLin + 1;
	end
	
	y = y - dy;

	%-Print Num secondary maxima (> Dis mm apart)
    	%---------------------------------------------------------------
	[l q] = sort(-Z(j));				% sort on Z value
	D     = i;
	for i = 1:length(q),
	    d = j(q(i)); % ----- a voir
	    if min(sqrt(sum((XYZmm(:,D)-XYZmm(:,d)*ones(1,size(D,2))).^2)))>Dis

		if length(D) < Num
			
			% Paginate if necessary
			%-----------------------------------------------
			if y < dy
				h = text(0.5,-5*dy,sprintf('Page %d',...
					spm_figure('#page')),...
					'FontName',PF.helvetica,...
					'FontAngle','Italic',...
					'FontSize',FS(8));
				spm_figure('NewPage',[hPage,h])
				hPage = [];
				y     = y0;
			end

			% Compute Labels & Distances
			%-----------------------------------------------
			[Label,Dist] = gin_det_dlabels(XYZmm(:,d), MNID, ROI, BORDER_XYZ, BORDER_V);

			h     = text(0.0,y,...
				sprintf(TabDat.fmt{1},XYZmm(:,d)),...
				'Tag','ListXYZ',...
				'ButtonDownFcn',[...
					'spm_mip_ui(''SetCoords'',',...
					'get(gcbo,''UserData''));'],...
				'Interruptible','off','BusyAction','Cancel',...
				'UserData',XYZmm(:,d));
			HlistXYZ = [HlistXYZ, h];
			hPage = [hPage, h];
			
			x=0.14;
			for kkk=1:size(Dist,2),
				if y < 2*dy
					h = text(0.5,-5*dy,sprintf('Page %d',...
						spm_figure('#page')),...
						'FontName',PF.helvetica,...
						'FontAngle','Italic',...
						'FontSize',FS(8));
					spm_figure('NewPage',[hPage,h])
					hPage = [];
					y     = y0;
				end
				h     = text(x,y,sprintf(TabDat.fmt{2},Label(kkk).Nom),...
					'UserData',label,...
					'ButtonDownFcn','get(gcbo,''UserData'')');
				hPage = [hPage, h];
				x=x+0.24;

				h     = text(x,y,sprintf(TabDat.fmt{3},Dist(kkk)),...
					'UserData',Dist(kkk),...
					'ButtonDownFcn','get(gcbo,''UserData'')');
				hPage = [hPage, h];
				x=x+0.07;
				[TabDat.dat{TabLin,1:3}] = deal(XYZmm(:,d),Label(kkk).Nom,Dist(kkk));
				TabLin = TabLin + 1;

			end
			y = y - dy;
			D = [D d];
			
		end % if length(D) < Num
	    end % if min(sqrt(sum((XYZmm(:,D)-XYZmm(:,d)*ones(1,size(D,2))).^2)))>Dis
	end % for i = 1:length(q),
	Z(j) = NaN;		% Set local maxima to NaN
end 				% end region

% for printing the results in batch mode
if spm_figure('#page',Fgraph)==1
if exist('pr')
    if pr == 3 || pr == 4
      spm_figure('Print');
    end
end
end
a=2
save('TabDat.dat')
%-Number and register last page (if paginated)
%-Changed to use Fgraph for numbering
%-----------------------------------------------------------------------
if spm_figure('#page',Fgraph)>1
	h = text(0.5,-5*dy,sprintf('Page %d/%d',spm_figure('#page',Fgraph)*[1,1]),...
		'FontName',PF.helvetica,'FontSize',FS(8),'FontAngle','Italic');
	spm_figure('NewPage',[hPage,h])
    
    % for printing the results in batch mode
    if exist('pr')
        if pr == 3 || pr == 4
      spm_figure('Print');
        end
    end
end

if spm_figure('#page',Fgraph)>1 

end

%-End: Store TabDat in UserData of axes & reset pointer
%=======================================================================
h      = uicontextmenu('Tag','TabDat',...
		'UserData',TabDat);
set(gca,'UIContextMenu',h,...
	'Visible','on',...
	'XColor','w','YColor','w')
uimenu(h,'Label','Table')
uimenu(h,'Separator','on','Label','Print text table',...
	'Tag','TD_TxtTab',...
	'CallBack',...
	'gin_list_dlabels(''txtlist'',get(get(gcbo,''Parent''),''UserData''),3)',...
	'Interruptible','off','BusyAction','Cancel');
uimenu(h,'Separator','off','Label','Extract table data structure',...
	'Tag','TD_Xdat',...
	'CallBack','get(get(gcbo,''Parent''),''UserData'')',...
	'Interruptible','off','BusyAction','Cancel');
uimenu(h,'Separator','on','Label','help',...
	'Tag','TD_Xdat',...
	'CallBack','spm_help(''gin_list_dlabels'')',...
	'Interruptible','off','BusyAction','Cancel');

%-Setup registry
%-----------------------------------------------------------------------
set(hAx,'UserData',struct('hReg',hReg,'HlistXYZ',HlistXYZ))
%spm_XYZreg('Add2Reg',hReg,hAx,'spm_list');

%-Return TabDat structure & reset pointer
%-----------------------------------------------------------------------
varargout = {TabDat};
spm('Pointer','Arrow');




%=======================================================================
case 'txtlist'                                  %-Print ASCII text table
%=======================================================================
% FORMAT spm_list('TxtList',TabDat,c)

if nargin<2, error('Insufficient arguments'), end
if nargin<3, c=1; else, c=varargin{3}; end
TabDat = varargin{2};

%-Table Title
%-----------------------------------------------------------------------
fprintf('\n\nSTATISTICS: %s\n',TabDat.tit)
fprintf('%c','='*ones(1,80)), fprintf('\n')

%-Table header
%-----------------------------------------------------------------------
fprintf('%s\t',TabDat.hdr{1,c:end-1}), fprintf('%s\n',TabDat.hdr{1,end})
fprintf('%s\t',TabDat.hdr{2,c:end-1}), fprintf('%s\n',TabDat.hdr{2,end})
fprintf('%c','-'*ones(1,80)), fprintf('\n')

%-Table data
%-----------------------------------------------------------------------
for i = 1:size(TabDat.dat,1)
	for j=c:size(TabDat.dat,2)
		fprintf(TabDat.fmt{j},TabDat.dat{i,j})
		fprintf('\t')
    end
    TabDat.dat
	fprintf('\n')
    
end
for i=1:max(1,11-size(TabDat.dat,1)), fprintf('\n'), end
fprintf('%s\n',TabDat.str)
fprintf('%c','-'*ones(1,80)), fprintf('\n')

%-Table footer
%-----------------------------------------------------------------------
fprintf('%s\n',TabDat.ftr{:})
fprintf('%c','='*ones(1,80)), fprintf('\n\n')

save('TabDat.mat');
%=======================================================================
otherwise                                        %-Unknown action string
%=======================================================================
error('Unknown action string')


%=======================================================================
end
%=======================================================================