cat_batch_long.m

function cat_batch_long(namefile,output_surface,long_model,cat_defaults,export_dartel,printlong)
% wrapper for using batch mode (see cat_batch_long.sh)
%
% namefile       - array of file names
% output_surface - enable surface estimation
% long_model     - 0: use model for large developmental changes (i.i with brain/head growth)
%                  1: use model for (small) plasticity changes
%                  2: use model for (large) ageing/developmental changes
%                  3: use both models 1 and 2
% cat_defaults   - use this default file instead of cat_defaults.m
% export_dartel  - export affine registered segmentations for Dartel
% ______________________________________________________________________
%
% Christian Gaser, Robert Dahnke
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% ______________________________________________________________________
% $Id$

if nargin < 1
  fprintf('Syntax: cat_batch_long(namefile)\n');
  exit
end

if nargin < 2
  output_surface = 1;
else
  % string argument has to be converted 
  if isstr(output_surface)
    output_surface = str2num(output_surface);
  end
end

if nargin < 3
  long_model = 1;
else
  % string argument has to be converted 
  if isstr(long_model)
    long_model = str2num(long_model);
  end
end

fid = fopen(namefile,'r');
names = textscan(fid,'%s');
names = names{:};
fclose(fid);

n = length(names);

if n == 0, error('No file found in %s.\n',namefile); end

global defaults cat matlabbatch

spm_get_defaults;

if nargin < 4
    cat_get_defaults;
else
  if isempty(cat_defaults)
    cat_get_defaults;
  else
    fprintf('Use defaults in %s.\n',cat_defaults);
    [pp, name] = spm_fileparts(cat_defaults);
    global cat;

    addpath(pp);
    eval(name);
    rmpath(pp);
    
  end
end

if nargin < 5
  export_dartel = 0;
else
  % string argument has to be converted 
  if isstr(export_dartel)
    export_dartel = str2num(export_dartel);
  end
end

if nargin < 6
  printlong = 2;
else
  % string argument has to be converted 
  if isstr(printlong)
    printlong = str2num(printlong);
  end
end

matlabbatch{1}.spm.tools.cat.long.datalong.subjects{1} = names;
matlabbatch{1}.spm.tools.cat.long.nproc = 0;
matlabbatch{1}.spm.tools.cat.long.modulate = 1;

% update parameters
matlabbatch{1}.spm.tools.cat.long.output.surface = output_surface;
matlabbatch{1}.spm.tools.cat.long.longmodel = long_model;
matlabbatch{1}.spm.tools.cat.long.printlong = printlong; 
matlabbatch{1}.spm.tools.cat.long.dartel = 2*export_dartel; % affine registered data

warning off
try
  % use expert mode for long. batch
  cat12('expert')
  spm_jobman('initcfg');
  spm_jobman('run',matlabbatch);
catch %#ok<CTCH> % catch with lasterror is necessary for old matlab versions
  caterr = lasterror;  %#ok<LERR>
  fprintf('\n%s\nCAT Preprocessing error: %s:\n%s\n', repmat('-',1,72),caterr.identifier,caterr.message,repmat('-',1,72));
  for si=1:numel(caterr.stack), cat_io_cprintf('err',sprintf('%5d - %s\n',caterr.stack(si).line,caterr.stack(si).name)); end;
  cat_io_cprintf('err',sprintf('%s\\n',repmat('-',1,72)));  
  error('Batch failed.');
end

spm_unlink(char(namefile))

warning off
exit