cg_mantis_ws_csf_run.m

function res = cg_mantis_ws_csf_run( job )
%cfg_mantis_ws_run Watershed segmentation of csf using phase1 tissue maps
%   Calls external ITK code

% job contains the GM map from phase1 and the name of the subfolder
% that phase1 results were put in. We use that information to construct 
% an external call. 
% We use this messy method as the structural scan isn't available
% as a dependency

exedir = char(cg_mantis_get_defaults('opts.itk'));
% Do we need to do something for windows?
exe = fullfile(exedir, 'segCSF'); 
exeprefix = char(cg_mantis_get_defaults('opts.externalcommandprefix'));
exe = [exeprefix exe];

%Phase2Dir = char(cg_mantis_get_defaults('opts.phase2'));
% Suffix used by segCSF
SUFF='_csfmask'; 
% We need to be able to process multiple structural scans
for k=1:numel(job.vols)
    Phase1Dir = job.parent{k};
    Phase2Dir = job.target{k};
    structfile=char(job.vols{k});
    [srcdir, corename, ext]=fileparts(structfile);
    ext=regexprep(ext, ',\d$','');
    T2=fullfile( srcdir, [corename ext]);
    CSF=fullfile( Phase1Dir, ['c3' corename ext]);
    GM=fullfile( Phase1Dir, ['c1' corename ext]);
    OUTPREF=fullfile(Phase2Dir, corename);
    command=[exe ' --input ' T2 ' --csf ' CSF ' --grey ' GM ' --outputprefix ' OUTPREF];
    system(command);
    outnames{k}=fullfile(Phase2Dir, [corename SUFF ext]);
    mantisCopyHeader(CSF, outnames{k});
    T2names{k}=T2;
end



% result is the segmented csf. We need to return a structure containing
% this filename
res.csfseg = outnames;
res.structural=T2names;
end