cat_batch_spm.m

function cat_batch_spm(batchname,varargin)
% wrapper for using spm8 batch mode (see cat_batch_cat12.sh)
% ______________________________________________________________________
%
% 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_spm(batchname)\n');
    exit
end
if nargin > 1
% initialize variables given by the shell script to adapt batches

    if mod(numel(varargin),2) ~= 0
        fprintf('Syntax: cat_batch_spm(batchname,''var1name'',var1,...)\n');
        exit
    end
    for vi = 1:2:numel(varargin)-1
        try
            eval(sprintf('%s = varargin{vi+1};', varargin{vi} )); 
        catch
            fprintf('Cannot evaluate variable %0.0f "%s = varargin{%0.0f+1}; " \n', (vi+1)/2, varargin{vi}, (vi+1)/2 );
            fprintf('Syntax: cat_batch_spm(batchname,''var1name'',var1,...)\n');
            exit
        end 
    end
    clear vi; 
    
    % show result    
end


% set up SPM enviroment (the batch may need SPM variables/functions)
spm_get_defaults;
global defaults
spm_jobman('initcfg'); 

if ~exist(batchname,'file')
    fprintf('Batchfile %s not found\n',batchname);
    exit
end

eval(batchname)

if ~exist('matlabbatch','var')
    fprintf('Batchfile %s did not returned variable matlabbatch.\n', batchname);
    exit
end

warning off
try
    spm_jobman('run',matlabbatch);
catch
    fprintf('Batchfile %s was not running successfully.\n', batchname);

    exit
end 
warning off
exit