ea_coregpostopct.m

function done = ea_coregpostopct(options)
% Entry function to coregister post-op CT to pre-op MRI

done = 0;

if ~ea_reglocked(options, options.subj.postopAnat.CT.coreg)
    % Setup log
    if options.prefs.diary
        ea_mkdir(fileparts(options.subj.coreg.log.logBaseName));
        diary([options.subj.coreg.log.logBaseName, 'CT', datestr(now, 'yyyymmddTHHMMss'), '.log']);
    end

    % Do coregistration
    switch lower(options.coregct.method)
        case lower({'ANTs (Avants 2008)', 'ANTs'})
            ea_coregpostopct_ants(options);
        case lower({'ANTs (Avants 2008) multiple runs', 'ANTsMulti'})
            ea_coregpostopct_ants_multiple(options);
        case lower({'BRAINSFit (Johnson 2007)', 'BRAINSFit'})
            ea_coregpostopct_brainsfit(options);
        case lower({'FLIRT (Jenkinson 2001 & 2002)', 'FLIRT'})
            ea_coregpostopct_fsl(options);
        case lower({'FLIRT (Jenkinson 2001 & 2002) multiple runs', 'FLIRTMulti'})
            ea_coregpostopct_fsl_multiple(options);
        otherwise
            warning('Coregistrion method not recognized...');
            diary off;
            return;
    end

    % Dump method
    ea_dumpmethod(options, 'coreg', 'CT');

    % Compute tone-mapped coregistered CT
    if strcmp(options.subj.postopModality, 'CT')
        ea_tonemapct(options, 'native');
    end

    if options.prefs.diary
        diary off;
    end

    if options.overwriteapproved && isfolder(options.subj.brainshiftDir)
        ea_delete(options.subj.brainshiftDir);
        ea_cprintf('CmdWinWarnings', 'CT coregistration has been rerun. Please also rerun brain shift correction!\n');
    end

    done = 1;
end