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mm_writeData.m
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mm_writeData.m
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function varargout = mm_writeData(varargin)
%====================================================================
% This package was developped by Ferath Kherif primarily
% with some help from Jean-Baptiste Poline.
%
% Please do not distribute and redirect requests for the toolbox to
% us. For bugs, remarks, additions, etc, please contact jb at
%====================================================================
% WARNING : THIS SOFTWARE IS DISTRIBUTED FREE WITHOUT ANY GUARANTY !
%====================================================================
if nargin
typeAnal = varargin{1}
else
error('no input argument in mm_model')
end
switch typeAnal
case 'MLM'
Eig = sf_writeData_mlm(varargin{2:nargin});
varargout = {Eig};
% varargin = {cwd, nbsub, Nvox, Pimg, Res, Mask, NF, u, s, fname, h};
case 'SVD'
Eig = sf_writeData_svd(varargin{2:nargin});
varargout = {Eig};
% varargin = {cwd, nbsub, Nvox, Pimg, Res, Mask, NF, ...
% u, ds, fname, h, Filter, paramsAnal}
otherwise
error('unknown type of analysis')
end
%===================================================================
function Eig = sf_writeData_mlm(cwd, nbsub, Nvox, Pimg, Res, Mask, NF, u, s, 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
% FORMAT Eig = tt_writeData(cwd,nbsub, Nvox,Pimg, Res,Mask,NF,u,s,fname,h);
%===================================================================
cwd
2
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
UMGS(U) = struct( 'fname',...
num2str(Afname(U,:)),...
'dim', [V(sub).dim(1:3),spm_type('float')],...
'mat', V(sub).mat,...
'pinfo', V(sub).pinfo',...
'descrip', sprintf('%s %d','eigenimage',U) );
UMGS(U) = spm_create_image(UMGS(U)); %- image structure.
end % for U=1:size(u,2)
Eig{sub} = Afname;
for p = 1: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;
for n = p:endpl
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
Nvox(sub) = Nvox(sub) + nvox;
if nvox
BETAp = zeros(floor(nvox),dimp);
RES = zeros(floor(nvox),1);
for t = 1:dimp
plb = zeros(dimx*dimy,nb_plan);
plr = zeros(dimx*dimy,nb_plan);
idp = 1;
for n = p:endpl
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)
Yout = zeros(dimx*dimy*nb_plan,1);
if nvox
Yout(plm)= ((NF*BETAp')./(ones(h,1)*RES'))'*u(:,U)/sqrt(s(U,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
end % for U=1:size(u,2)
end % for p = 1:nbp:V(1).dim(3)
end
%===================================================================
function Eig = sf_writeData_svd(cwd, nbsub, Nvox, Pimg, Res, Mask, NF, ...
u, ds, fname, h, Filter, paramsAnal);
%===================================================================
holds = 0; %- Interpolation method
[dimp tmp] = size(Pimg);
memchunk = 2^24;
sizeVox = ceil((memchunk/dimp/8)) % 8 = sizeof(double)
V = spm_vol(Pimg);
Vr = spm_vol(Res);
dimx = V(1).dim(1);
dimy = V(1).dim(2);
Vm = spm_vol(Mask);
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, ...
sprintf('%s%03d.img',fname,U))]; % Eigenimage filename
UMGS(U) = struct( ...
'fname', num2str(Afname(U,:)),...
'dim', [V(1).dim(1:3),spm_type('float')],...
'mat', V(1).mat,...
'pinfo', V(1).pinfo',...
'descrip', sprintf('%s %d','eigenimage',U) );
UMGS(U) = spm_create_image(UMGS(U)); %- image structure.
end % for U=1:size(u,2)
Eig = Afname;
for p = 1: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;
for n = p:endpl
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
Nvox = Nvox + nvox;
if nvox
BETAp = zeros(floor(nvox),dimp);
RES = zeros(floor(nvox),1);
for t = 1:dimp
plb = zeros(dimx*dimy,nb_plan);
plr = zeros(dimx*dimy,nb_plan);
idp = 1;
for n = p:endpl
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)
Yout = zeros(dimx*dimy*nb_plan,1);
if nvox
if paramsAnal.temporalFilter
BETA = spm_filter('apply',Filter,BETAp');
end
if paramsAnal.divideByRessd
BETA = ((NF*BETA)./(ones(h,1)*RES'))';
end
Yout(plm) = BETA*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
end % for U=1:size(u,2)
end % for p = 1:nbp:V(1).dim(3)