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Copy pathmm_writeEigImg.m
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mm_writeEigImg.m
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function varargout = mm_writeEigImg(varargin)
% Write Eigen Images
% Format varargout = mm_writeEigImg(varargin)
% see sub-functions for details.
%================================================================================
%- Copyright (C) 1997-2002 CEA
%- This software and supporting documentation were developed by
%- CEA/DSV/SHFJ/UNAF
%- 4 place du General Leclerc
%- 91401 Orsay cedex
%- France
%================================================================================
if nargin
typeAnal = varargin{1};
else
error('no input argument in mm_model')
end
switch typeAnal
case 'MLM'
Eig = sf_writeEigImg_mlm(varargin{2:nargin});
varargout = {Eig};
% varargin = {cwd, nbsub, Pimg, Res, Mask, NF, u, s, fname, h};
case 'SVD'
Eig = sf_writeEigImg_svd(varargin{2:nargin});
varargout = {Eig};
% varargin = {cwd, nbsub, Pimg, Res, Mask, NF, ...
% u, ds, fname, h, Filter, paramsAnal}
otherwise
error('unknown type of analysis')
end
%===================================================================
function Eig = sf_writeEigImg_mlm(cwd, nbsub, Pimg, Res, Mask, NF, u, ds, fname, h);
% write eigenimages.
%- Eig : filename of the eigen images.
% Yout output images data
% Yout = u' Z/sqrt(ds(i)), u eigen vector, ds eigen values.
% Yout = u' NF B/Res
%===================================================================
holds = 0; %- Interpolation method
[dimp tmp] = size(Pimg{1});
memchunk = 2^24;
sizeVox = ceil((memchunk/dimp/8)); % 8 = sizeof(double)
for sub=1:nbsub
V = spm_vol(Pimg{sub});
Vr = spm_vol(Res{sub});
dimx = V(1).dim(1);
dimy = V(1).dim(2);
Vm = spm_vol(Mask{sub});
nbp = sizeVox/prod(V(1).dim(1:2));
nbp = min(max(1,round(nbp)),V(1).dim(3));
Afname = [];
for U=1:size(u,2)
Afname = [Afname; fullfile(cwd{sub},sprintf('%s%03d.img',fname{sub},U))]; % Eigenimage filename
Veig=V(1);
Veig.fname= num2str(Afname(U,:));
% Veig.dim', [V(1).dim(1:3)],...
% 'mat', V(1).mat,...
Veig.pinfo=[1 0 0]';
Veig.descrip=sprintf('%s %d','eigenimage',U);
UMGS(U) = spm_create_vol(Veig); %- image structure.
end % for U=1:size(u,2)
Eig{sub} = Afname;
for p = 1:nbp:V(1).dim(3)
plank=length(p:min(p+nbp,V(1).dim(3)));
endpl = min(p+nbp-1,V(1).dim(3)); % position of last plane in bunch
nb_plan = endpl - p + 1;
plm = zeros(dimx*dimy,nb_plan);
idp = 1;
fprintf('\r%-20s: ',sprintf('Plane %3d/%-3d ',...
p,V(1).dim(3)))
fprintf('%20s',' Reading Mask ');
for n = p:endpl
fprintf('%-20s',sprintf('plank %3d/%-3d',...
idp,plank))
fprintf('%s',sprintf('\b')*ones(1,20))
Ma = spm_matrix([0 0 n]);
iplm = spm_slice_vol(Vm,Ma,Vm.dim(1:2),holds);
plm(:,idp) = iplm(:);idp=idp+1;
end
plm = plm(:) > 0;
nvox = sum(plm); % nombre de voxel
if nvox
BETAp = zeros(floor(nvox),dimp);
RES = zeros(floor(nvox),1);
fprintf('%s',sprintf('\b')*ones(1,20))
fprintf('%20s',' Reading data ')
for t = 1:dimp
plb = zeros(dimx*dimy,nb_plan);
plr = zeros(dimx*dimy,nb_plan);
idp = 1;
for n = p:endpl
fprintf('%-20s',sprintf('plank %3d/%-3d',...
idp,plank))
fprintf('%s',sprintf('\b')*ones(1,20))
Ma = spm_matrix([0 0 n]);
iplb = spm_slice_vol(V(t),Ma,V(t).dim(1:2),holds);
plb(:,idp) = iplb(:);
iplr = spm_slice_vol(Vr,Ma,Vr.dim(1:2),holds);
plr(:,idp) = iplr(:);
idp = idp + 1;
end
plb = plb(:);
BETAp(:,t) = plb(find(plm));
plr = plr(:);
RES = sqrt(plr(find(plm)));
end
end % if nvox
for U=1:size(u,2)
fprintf('%20s',sprintf(' writing Img %d',U));
Yout = zeros(dimx*dimy*nb_plan,1)*nan;
if nvox
Yout(plm)= ((NF*BETAp')./(ones(h,1)*RES'))'*u(:,U)/sqrt(ds(U));
end
i_plm = 0;
for ip = p:endpl
img = reshape(Yout([1:dimx*dimy] + i_plm*dimx*dimy), dimx, dimy);
spm_write_plane(UMGS(U),img,ip);
i_plm = i_plm + 1;
end
fprintf('%s',sprintf('\b')*ones(1,20))
end % for U=1:size(u,2)
end % for p = 1:nbp:V(1).dim(3)
end
% fprintf('%s',sprintf('\b')*ones(1,80))
% fprintf('%s\r',sprintf(' ')*ones(1,80))
%===================================================================
function Eig = sf_writeEigImg_svd(cwd, nbsub, Pimg, Res, Mask, NF, ...
u, ds, fname, h, Filter, paramsAnal,gsf);
%===================================================================
holds = 0; %- Interpolation method
[dimt tmp] = size(Pimg{1});
memchunk = 2^24;
sizeVox = ceil((memchunk/dimt/8)); % 8 = sizeof(double)
for sub=1:nbsub
V = spm_vol(Pimg{sub});
Vr = spm_vol(Res{sub});
dimx = V(1).dim(1);
dimy = V(1).dim(2);
Vm = spm_vol(Mask{sub});
nbp = sizeVox/prod(V(1).dim(1:2));
nbp = min(max(1,round(nbp)),V(1).dim(3));
Afname = [];
sf=gsf{sub}; %scaling factor for the subject sub
fprintf('\nworking on space domain : %d \n',sub);
for v=1:dimt
V(v,1).pinfo(1:2,:) = V(v,1).pinfo(1:2,:)*sf(v,1);
end
for U=1:size(u,2)
Afname = [Afname; fullfile(cwd{sub}, ...
sprintf('%s%03d.img',fname{sub},U))]; % Eigenimage filename
Veig = struct( ...
'fname', num2str(Afname(U,:)),...
'dim', [V(1).dim(1:3)],...
'mat', V(1).mat,...
'type', [spm_type('float') 0],...
'pinfo', [1 0 0]',...
'descrip', sprintf('%s %d','eigenimage',U) );
UMGS(U) = spm_create_vol(Veig); %- image structure.
end % for U=1:size(u,2)
Eig{sub} = Afname;
for p = 1:nbp:V(1).dim(3)
plank=length(p:min(p+nbp,V(1).dim(3)));
endpl = min(p+nbp-1,V(1).dim(3)); % position of last plane in bunch
nb_plan = endpl - p + 1;
plm = zeros(dimx*dimy,nb_plan);
idp = 1;
fprintf('\r%-20s: ',sprintf('Plane %3d/%-3d ',...
p,V(1).dim(3)))
fprintf('%20s',' Reading Mask ');
for n = p:endpl
fprintf('%-20s',sprintf('plank %3d/%-3d\n',idp,plank))
% fprintf('%s',sprintf('\b')*ones(1,20))
Ma = spm_matrix([0 0 n]);
iplm = spm_slice_vol(Vm,Ma,Vm.dim(1:2),holds);
plm(:,idp) = iplm(:);idp=idp+1;
end
plm = plm(:) > 0;
nvox = sum(plm); % nombre de voxel
if nvox
BETA = zeros(dimt, floor(nvox));
RES = zeros(floor(nvox),1);
% fprintf('%s',sprintf('\b')*ones(1,20))
fprintf('%20s',' Reading data ')
for t = 1:dimt
plb = zeros(dimx*dimy,nb_plan);
plr = zeros(dimx*dimy,nb_plan);
idp = 1;
for n = p:endpl
fprintf('%-20s',sprintf('plank %3d/%-3d',...
idp,plank))
fprintf('%s',sprintf('\b')*ones(1,20))
Ma = spm_matrix([0 0 n]);
iplb = spm_slice_vol(V(t),Ma,V(t).dim(1:2),holds);
plb(:,idp) = iplb(:);
iplr = spm_slice_vol(Vr,Ma,Vr.dim(1:2),holds);
plr(:,idp) = iplr(:);
idp = idp + 1;
end
plb = plb(:);
BETA(t,:) = plb(find(plm))';
plr = plr(:);
RES = sqrt(plr(find(plm)));
end
end % if nvox
for U=1:size(u,2)
fprintf('%20s',sprintf(' writing Img %d',U));
Yout = zeros(dimx*dimy*nb_plan,1);
if nvox
if paramsAnal.temporalFilter
BETA = spm_filter(Filter,BETA);
end
if paramsAnal.divideByRessd
%BETA = (NF*BETA)./(ones(h,1)*RES');
BETA = (BETA)./(ones(h,1)*RES');
end
Yout(plm) = u(:,U)'*BETA/sqrt(ds(U));
end
i_plm = 0;
for ip = p:endpl
img = reshape(Yout([1:dimx*dimy] + i_plm*dimx*dimy),dimx,dimy);
spm_write_plane(UMGS(U),img,ip);
i_plm = i_plm + 1;
end
fprintf('%s',char(sprintf('\b')*ones(1,20)))
end % for U=1:size(u,2)
end % for p = 1:nbp:V(1).dim(3)
end