How to correct this error in Matlab

Question

I have customized part of function feature_select.m below to use my own generated masks whole_brain_mask_1,whole_brain_mask_2,…,whole_brain_mask_10 into subj.

function [subj] = feature_select(subj,data_patin,regsname,selsgroup,varargin)

% No-peeking feature selection
%
% [SUBJ] = FEATURE_SELECT(SUBJ,DATA_PATIN,REGSNAME,SELSGROUP,...)
%
% Calls a statmap generation function multiple times, using
% a different selector each time. This creates a group of
% statmaps, which are then thresholded to create a group of
% boolean masks, ready for use in no-peeking
% cross-validation classification.
%
% Adds the following objects:
% - pattern group of statmaps called NEW_MAP_PATNAME
% - mask group based on the statmaps called
%   sprintf('%s%i',NEW_MASKSTEM,THRESH)
%
% DATA_PATIN should be the name of the pattern object that
% contains voxel (or other feature) values that you want to
% create a mask of. If DATA_PATIN is a group_name, then this
% will use a different member of the group for each
% iteration.
%
% REGSNAME should be a binary nConds x nTimepoints 1-of-n matrix
%
% SELSGROUP should be the name of a selectors group, such as
% created by create_xvalid_indices
%
% For each iteration: call the ANOVA on the DATA_PATIN data,
% which will produce a statmap, employing only the TRs
% labelled with a 1 in the selector for that iteration
%
% NEW_MAP_PATNAME (optional, default = DATA_PATIN +
% STRIPPED_NAME). The name of the new statmap pattern group
% to be created. By default, this will be 'anova' if
% STATMAP_FUNCT = 'statmap_anova' etc.
%
% NEW_MASKSTEM (optional, default = DATA_PATIN +
% 'anovathresh'). The name of the new thresholded boolean
% mask group to be created from the ANOVA statmap. You'll
% need to create multiple mask groups if you want to try out
% multiple thresholds, so adding the threshold to the name
% is a good idea
%
% THRESH (optional, default = 0.05). Voxels that don't meet
% this criterion value don't get included in the boolean
% mask that gets created from the ANOVA statmap. If THRESH =
% [], the thresholding doesn't get run
%
% STATMAP_FUNCT (optional, default = 'statmap_anova'). Feed
% in a function name and this will create a function handle
% to that and use it to create the statmaps instead of
% statmap_anova
%
% STATMAP_ARG (optional, default = []). If you're using an
% alternative voxel selection method, you can feed it a
% single argument through this
%
% Need to implement a THRESH_TYPE argument (for p vs F
% values), which would also set the toggle differently xxx
%
% e.g. subj = feature_select( ...
%         subj,'epi_z','conds','runs_nmo_xvalid','thresh',0.001)

% License:
%=====================================================================
%
% This is part of the Princeton MVPA toolbox, released under
% the GPL. See http://www.csbmb.princeton.edu/mvpa for more
% information.
% 
% The Princeton MVPA toolbox is available free and
% unsupported to those who might find it useful. We do not
% take any responsibility whatsoever for any problems that
% you have related to the use of the MVPA toolbox.
%
% ======================================================================


defaults.new_map_patname = '';
defaults.new_maskstem = sprintf('%s_thresh',data_patin);
defaults.thresh = 0.05;
defaults.statmap_funct = 'statmap_anova';
defaults.statmap_arg = struct([]);
args = propval(varargin,defaults);

if isempty(args.new_map_patname)
  % get the name of the function being run, e.g. 'statmap_anova' -> 'anova'
  stripped_name = strrep(args.statmap_funct,'statmap_','');
  args.new_map_patname = sprintf('%s_%s',data_patin,stripped_name);
end

% append the thresh to the end of the name
args.new_maskstem = sprintf( ...
    '%s%s',args.new_maskstem,num2str(args.thresh));

% Find the selectors within the specified group
selnames = find_group(subj,'selector',selsgroup);
nIterations = length(selnames);

[data_patnames isgroup] = find_group_single(subj,'pattern',data_patin,'repmat_times',nIterations);

if length(data_patnames) ~= length(selnames)
  error('Different number of patterns and selectors');
end

if nIterations == 0
  error('No selectors in %s group',selsgroup);
end

% % this warning used to be here to remind people of the
% % existence of peek_feature_select, but since there are good
% % reasons why one might want to have just one selector
% % without using peek_feature_select, i took it out
% if nIterations == 1
%   warning('You''re only calling the anova once because you have one selector - use peek_feature_select instead?');
% end

if ~ischar(args.statmap_funct)
  error('The statmap function name has to be a string');
end

disp( sprintf('Starting %i %s iterations',nIterations,args.statmap_funct) );

for n=1:nIterations
  fprintf('  %i',n);

  % Get the pattern for this iteration
  cur_data_patname = data_patnames{n};

  % Get the selector name for this iteration
  cur_selname = selnames{n};

  % Name the new statmap pattern and thresholded mask that will be created
  cur_maskname = sprintf('%s_%i',args.new_maskstem,n);
  cur_map_patname = sprintf('%s_%i',args.new_map_patname,n);

  % if a pattern with the same name already exists, it
  % will trigger an error later in init_object, but we
  % want to catch it here to save running the entire
  % statmap first
  if exist_object(subj,'pattern',cur_map_patname)
    error('A pattern called %s already exists',cur_map_patname);
  end

  if ~isempty(args.statmap_arg) && ~isstruct(args.statmap_arg)
    warning('Statmap_arg is supposed to be a struct');
  end

  % Add the current iteration number to the extra_arg, just in case
  % it's useful
  args.statmap_arg(1).cur_iteration = n;

  % Create a handle for the statmap function handle and then run it
  % to generate the statmaps
  statmap_fh = str2func(args.statmap_funct);
  subj = statmap_fh(subj,cur_data_patname,regsname,cur_selname,cur_map_patname,args.statmap_arg);
  subj = set_objfield(subj,'pattern',cur_map_patname,'group_name',args.new_map_patname);

  if ~isempty(args.thresh)
    % Now, create a new thresholded binary mask from the p-values
    % statmap pattern returned by the anova
    subj = create_thresh_mask(subj,cur_map_patname,cur_maskname,args.thresh);
    subj = set_objfield(subj,'mask',cur_maskname,'group_name',args.new_maskstem);
  end

end % i nIterations

disp(' ');
disp( sprintf('Pattern statmap group ''%s'' and mask group ''%s'' created by feature_select', ...
          args.new_map_patname,args.new_maskstem) );

This is the piece of the function above that I have adapted to use my own masks:

dirIn_Mask = ['/D disk/my_fold/My_generated_Mask'];

data_patin = subj.patterns{1,2}.name;  

defaults.new_maskstem = sprintf(‘whole_brain_mask’); 

defaults.statmap_arg = struct([]);

args = propval(varargin,defaults);

args.new_maskstem = sprintf( '%s',args.new_maskstem );

for n = 1:1:10

fprintf('  %i', n );

inputFile_mask = ['whole_brain_mask_',num2str(n)];

load(fullfile(dirIn_Mask,inputFile_mask)); 

    cur_maskname = sprintf('%s_%i',args.new_maskstem,n );

    subj.masks{1,(runID+1)}.mat = whole_brain_new_1; 


    subj = set_objfield(subj,'mask',cur_maskname,'group_name',new_maskstem);
end

And this is the error I'm getting:

Attempt to execute SCRIPT varargin as a function:
C:\D disk\MATLAB\R2014a\toolbox\matlab\lang\varargin.m
Error in MVPA (line 89)
args = propval(varargin,defaults);

Can anyone help me fix the problem?

Answer 1

You are using varargin as an argument of propval, but varargin is not defined anywhere in your code. In that case, varargin rolls back to Matlab script varargin. As a result, the interpreter assumes you want to run it as a function that returns values to propval and given that scripts are not supposed to return values, you get the error message.

Just as a side note: varargin is usually set as the last argument of a function to allow programmers to declare functions with variable number of arguments.

Answer 2

Remove the varargin from your code. varargin is a special keyword that is only available when you run the code as a function. varargin allows for a variable number of inputs to be placed into your function. These inputs are hashed into a cell array.

Because this is a script file, that variable does not exist. This is also apparent from the MATLAB error you received. FWIW, MATLAB error messages are very verbose. It would be hard to misinterpret or misunderstand what they're trying to say.

Therefore, do this:

args = propval(defaults);

If that doesn't work, then I'm not sure how propval takes in inputs, but perhaps fool it with putting in an empty cell array:

args = propval(cell(1,1), defaults);

Because the function propval relies on a variable number of inputs, it should handle the case where varargin doesn't exist, and so we can simulate varargin having no additional parameters by using an empty cell array.