ea_coreg_all_mri.m

function ea_coreg_all_mri(options,usebrainmask)

% __________________________________________________________________________________
% Copyright (C) 2015 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn

if ~exist('usefa','var')
    usefa=1;
end

[options,presentfiles]=ea_assignpretra(options);
directory=[options.root,options.patientname,filesep];

for coregfi=2:length(presentfiles)
    if ~ea_coreglocked(options,presentfiles{coregfi}) % file has already been locked and approved by used
        ea_coreg2images(options,[directory,presentfiles{coregfi}],[directory,presentfiles{1}],[directory,presentfiles{coregfi}]);

        % reslice images if needed
        V1=ea_open_vol([directory,presentfiles{1}]);
        V2=ea_open_vol([directory,presentfiles{coregfi}]);
        if ~isequal(V1.mat,V2.mat)
            ea_conformspaceto([directory,presentfiles{1}],[directory,presentfiles{coregfi}],1);
        end
        % better slab support:
        nii=ea_load_nii(V2.fname);
        nii.img(abs(nii.img)<0.0001)=0;
        ea_write_nii(nii);
    end
end


function masks=segmentall(from,options)
directory=[fileparts(from{1}),filesep];
for fr=1:length(from)
    [~,fn,ext]=fileparts(from{fr});
    switch [fn,ext]
        case options.prefs.fa2anat
            if ~exist([directory,'tc2',options.prefs.prenii_unnormalized],'file')
            	ea_newseg(directory,options.prefs.prenii_unnormalized,0,options);
                % assume that tc2 doesn't exist
                nii=ea_load_nii([directory,'c2',options.prefs.prenii_unnormalized]);
                nii.img=nii.img>0.7;
                nii.fname=[directory,'tc2',options.prefs.prenii_unnormalized];
                spm_write_vol(nii,nii.img);
            end
            masks{fr,1}=[ea_space(options),'c2mask.nii'];
            masks{fr,2}=[directory,'tc2',options.prefs.prenii_unnormalized];

        otherwise
            if ~exist([directory,'tc1',options.prefs.prenii_unnormalized],'file')
                ea_newseg(directory,options.prefs.prenii_unnormalized,0,options);
                % assume that tc1 doesn't exist
                nii=ea_load_nii([directory,'c1',options.prefs.prenii_unnormalized]);
                nii.img=nii.img>0.3;
                nii.fname=[directory,'tc1',options.prefs.prenii_unnormalized];
                spm_write_vol(nii,nii.img);
            end
            masks{fr,1}=[ea_space(options),'c1mask.nii'];
            masks{fr,2}=[directory,'tc1',options.prefs.prenii_unnormalized];
    end
end

if ~exist([directory,'tc1c2',options.prefs.prenii_unnormalized],'file')
    Vc1=ea_load_nii([directory,'tc1',options.prefs.prenii_unnormalized]);
    Vc2=ea_load_nii([directory,'tc2',options.prefs.prenii_unnormalized]);
    Vc1.img=Vc1.img+Vc2.img;
    Vc1.fname=[directory,'tc1c2',options.prefs.prenii_unnormalized];
    spm_write_vol(Vc1,Vc1.img);
end


function ea_genbrainmask(options)
directory=[options.root,options.patientname,filesep];
ea_newseg(directory,options.prefs.prenii_unnormalized,0,options);
c1=ea_load_nii([directory,'c1',options.prefs.prenii_unnormalized]);
c2=ea_load_nii([directory,'c2',options.prefs.prenii_unnormalized]);
c3=ea_load_nii([directory,'c3',options.prefs.prenii_unnormalized]);
bm=c1;
bm.img=c1.img+c2.img+c3.img;
bm.fname=[directory,'brainmask.nii'];
bm.img=bm.img>0.5;
spm_write_vol(bm,bm.img);


function ea_maskimg(options,file,prefix)
directory=[options.root,options.patientname,filesep];
if ~exist([directory,'brainmask.nii'],'file')
	ea_genbrainmask(options);
end
[pth,fn,ext]=fileparts(file);
if ~exist([pth,filesep,prefix,fn,ext],'file')
    nii=ea_load_nii(file);
    bm=ea_load_nii([directory,'brainmask.nii']);
    nii.img=nii.img.*double(bm.img);
    nii.fname=[pth,filesep,prefix,fn,ext];
    spm_write_vol(nii,nii.img);
end