Hi,
when taking a look at the code of nntraintool you will see:
function [result,result2] = nntraintool(command,varargin)
%NNTRAINTOOL Neural network training tool
%
% Syntax
%
% nntraintool
% nntraintool('close')
%
% Description
%
% NNTRAINTOOL opens the training window GUI. This is launched
% automatically when TRAIN is called.
%
% To disable the training window set the following network training
% property.
%
% net.<matlab:doc nnproperty.net_trainParam trainParam>.<matlab:doc nnparam.showWindow showWindow> = false;
%
% To enable command line training instead.
%
% net.<matlab:doc nnproperty.net_trainParam trainParam>.<matlab:doc nnparam.showCommandLine showCommandLine> = true;
%
% NNTRAINTOOL('close') closes the window.
% Copyright 2007-2012 The MathWorks, Inc.
So call a to this
YourNet.trainParam.showWindow = false;
should do it.
