ea_coregmr.m

function ea_coregmr(options)
% wrapper for coreg routines

% in CT imaging, coregistration is done elsewhere.
% also ignore when there is no tra/cor/sag existing (normal conn study)
if options.modality == 2 || ~isfield(options.prefs,'tranii_unnormalized')
    return
end

directory=[options.root,options.patientname,filesep];

    doreslice=1;

    % restore raw files -> postop files from prior attempts. & make backups
    % from original files in any case.
    try
        if  ~ea_coreglocked(options,[directory,options.prefs.tranii_unnormalized]) % file has already been locked and approved by used
            if exist([directory,'raw_',options.prefs.tranii_unnormalized],'file')
                copyfile([directory,'raw_',options.prefs.tranii_unnormalized],[directory,options.prefs.tranii_unnormalized]);
            else
                copyfile([directory,options.prefs.tranii_unnormalized],[directory,'raw_',options.prefs.tranii_unnormalized]);
            end
        end
    end
    try
        if  ~ea_coreglocked(options,[directory,options.prefs.cornii_unnormalized]) % file has already been locked and approved by used
            if exist([directory,'raw_',options.prefs.cornii_unnormalized],'file')
                copyfile([directory,'raw_',options.prefs.cornii_unnormalized],[directory,options.prefs.cornii_unnormalized]);
            else
                copyfile([directory,options.prefs.cornii_unnormalized],[directory,'raw_',options.prefs.cornii_unnormalized]);
            end
        end
    end
    try
        if  ~ea_coreglocked(options,[directory,options.prefs.sagnii_unnormalized]) % file has already been locked and approved by used
            if exist([directory,'raw_',options.prefs.sagnii_unnormalized],'file')
                copyfile([directory,'raw_',options.prefs.sagnii_unnormalized],[directory,options.prefs.sagnii_unnormalized]);
            else
                copyfile([directory,options.prefs.sagnii_unnormalized],[directory,'raw_',options.prefs.sagnii_unnormalized]);
            end
        end
    end

    
    switch options.coregmr.method
        case 'SPM' % SPM
            ea_coregmr_spm(options,doreslice);
        case 'FSL' % FSL
            ea_coregmr_flirt(options);
        case 'ANTs' % ANTs
            ea_coregmr_ants(options,0);
        case 'BRAINSFIT' % BRAINSFit
            ea_coregmr_brainsfit(options);
        case 'Hybrid SPM & ANTs' % Hybrid SPM -> ANTs
            ea_coregmr_spm(options,0); % dont use doreslice here to refrain for doing two interpolations.
            ea_coregmr_ants(options);
        case 'Hybrid SPM & BRAINSFIT' % Hybrid SPM -> Brainsfit
            ea_coregmr_spm(options,0); % dont use doreslice here to refrain for doing two interpolations.
            ea_coregmr_brainsfit(options);     
    end
    ea_dumpnormmethod(options,options.coregmr.method,'coregmrmethod');