ea_coregmr_flirt.m

function ea_coregmr_flirt(options)
% uses FLIRT instead of SPM to coregister MRIs.

if exist([options.root,options.patientname,filesep,options.prefs.tranii_unnormalized],'file') &&...
        ~ea_coreglocked(options,[options.root,options.patientname,filesep,options.prefs.tranii_unnormalized]) % file has already been locked and approved by used
    disp('Coregistering postop MR tra to preop MRI...');
    ea_flirt([options.root,options.patientname,filesep,options.prefs.prenii_unnormalized],...
            [options.root,options.patientname,filesep,options.prefs.tranii_unnormalized],...
            [options.root,options.patientname,filesep,options.prefs.tranii_unnormalized],...
            options.prefs.mrcoreg.writeoutcoreg);
    disp('Coregistration done.');
end

if exist([options.root,options.patientname,filesep,options.prefs.cornii_unnormalized],'file') &&...
        ~ea_coreglocked(options,[options.root,options.patientname,filesep,options.prefs.cornii_unnormalized]) % file has already been locked and approved by used
    disp('Coregistering postop MR cor to preop MRI...');
    ea_flirt([options.root,options.patientname,filesep,options.prefs.prenii_unnormalized],...
            [options.root,options.patientname,filesep,options.prefs.cornii_unnormalized],...
            [options.root,options.patientname,filesep,options.prefs.cornii_unnormalized],...
            options.prefs.mrcoreg.writeoutcoreg);
    disp('Coregistration done.');
end

if exist([options.root,options.patientname,filesep,options.prefs.sagnii_unnormalized],'file') &&...
        ~ea_coreglocked(options,[options.root,options.patientname,filesep,options.prefs.sagnii_unnormalized]) % file has already been locked and approved by used
    disp('Coregistering postop MR sag to preop MRI...');
    ea_flirt([options.root,options.patientname,filesep,options.prefs.prenii_unnormalized],...
            [options.root,options.patientname,filesep,options.prefs.sagnii_unnormalized],...
            [options.root,options.patientname,filesep,options.prefs.sagnii_unnormalized],...
            options.prefs.mrcoreg.writeoutcoreg);
    disp('Coregistration done.');
end