tbx_scfg_Utils_FxICVmsk.m

function FxICVmsk = tbx_scfg_Utils_FxICVmsk
% MATLABBATCH sub-configuration file.
% Small tool to fix an ICV mask
%_______________________________________________________________________
% Copyright (C) 2015 Cyclotron Research Centre

% Written by C. Phillips.
% Cyclotron Research Centre, University of Liege, Belgium

% ---------------------------------------------------------------------
% fnICVmsk Filename of ICV mask to be fixed
% ---------------------------------------------------------------------
fnICVmsk         = cfg_files;
fnICVmsk.tag     = 'fnICVmsk';
fnICVmsk.name    = 'ICV mask image to be fixed';
fnICVmsk.help    = {'ICV (intracranial volume) mask image to be fixed.', ...
    'If multiple images are selected, they are processed one by one.'};
fnICVmsk.filter = 'image';
fnICVmsk.num     = [1 Inf];

%--------------------------------------------------------------------------
% SzThr Size threshold
%--------------------------------------------------------------------------
SzThr         = cfg_entry;
SzThr.tag     = 'SzThr';
SzThr.name    = 'Size threshold of small blob (mm^3)';
SzThr.help    = {'Maximum size (mm^3) of small blobs that can be filled up.'};
SzThr.strtype = 'r';
SzThr.num     = [1 1];
SzThr.val     = {1000};

% ---------------------------------------------------------------------
% options Options
% ---------------------------------------------------------------------
options         = cfg_branch;
options.tag     = 'options';
options.name    = 'Options';
options.val     = {SzThr};
options.help    = {'Some processing options.'};

%% EXEC function
%----------------------------------------------------------------------
% FxICVmsk Fixing some mask image(s)
% ---------------------------------------------------------------------
FxICVmsk        = cfg_exbranch;
FxICVmsk.tag    = 'FxICVmsk';
FxICVmsk.name   = 'Fixing ICV mask image';
FxICVmsk.val    = {fnICVmsk options};
FxICVmsk.help   = {'Fixing an ICV (intracranial volume) mask image by', ...
    '1/ filling small holes, based on #voxel threshold (1000mm^3 by def.)', ...
    '2/ removing blobs outside brain, i.e. the biggest blob'};
FxICVmsk.prog   = @crc_run_FxICVmsk;
FxICVmsk.vout   = @vout_FxICVmsk;

end

%% OUTPUT function
%_______________________________________________________________________
function dep = vout_FxICVmsk(job) %#ok<*INUSD>

cdep(1) = cfg_dep;
cdep(1).sname = 'Fixed mask image(s)';
cdep(1).src_output = substruct('.','files');
cdep(1).tgt_spec   = cfg_findspec({{'filter','image'}});

% nMsk = size(job.fnICVmsk,1);
% for ii=1:nMsk
%     dep(ii) = cfg_dep; %#ok<*AGROW>
%     
% end
% img_c = 0;
% for ii=1:numel(job.wMPM)
%     for jj=1:numel(job.wcImg)
%         img_c = img_c+1;
%         cdep(img_c) = cfg_dep; %#ok<*AGROW>
%         cdep(img_c).sname  = sprintf('fin%d_c%d image',[ii jj]);
%         cdep(img_c).src_output =  ...
%             substruct('.','fn','{}',{ii},'()',{jj});
% %         cdep(img_c).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
%         cdep(img_c).tgt_spec = cfg_findspec({{'filter','nifti'}});
%     end
% end

dep = cdep;
end
%_______________________________________________________________________
%% RUN function
%_______________________________________________________________________
function out = crc_run_FxICVmsk(job)

nMsk = size(job.fnICVmsk,1);
fn = cell(nMsk,1);
for ii=1:nMsk
    fn{ii} = crc_fix_ICV(job.fnICVmsk{ii},job.options);
end

% out.files = {cellstr(char(fn))};
out.files = cellstr(char(fn));

end