Can not run system commands from matlab -MAC OSX

Question

Hasan 2013-11-21

1
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/107068-can-not-run-system-commands-from-matlab-mac-osx

评论： Cristiana Dinea 2023-3-8

I am trying to run a image processing software called Flirt through matlab. When I try

system'flirt', I get a /bin/bash: flirt: command not found error.

If I try system('/usr/local/fsl/bin/flirt'); then it works fine. Typing just flirt in terminal also launches the program.

Is there a way of setting matlab to find this program in path and running it without giving its full address?

Thanks

Hasan

0 个评论
显示 -2更早的评论隐藏 -2更早的评论

请先登录，再进行评论。

请先登录，再回答此问题。

Answer 1

Matthias Fripp 2017-10-8

3
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/107068-can-not-run-system-commands-from-matlab-mac-osx#answer_284740

在 MATLAB Online 中打开

For some reason, Matlab on a Mac doesn't see the whole search path you normally get in a terminal. So you need to add the directory to the $PATH environment variable within Matlab. You can do that temporarily by running

setenv('PATH', [getenv('PATH') ':/usr/local/fsl/bin']);

You can make this permanent by adding the command to a startup.m file somewhere in your Matlab path (as shown by Matlab's "path" command).

10 个评论
显示 8更早的评论隐藏 8更早的评论

Walter Roberson 2017-10-8

在 MATLAB Online 中打开

"For some reason, Matlab on a Mac doesn't see the whole search path you normally get in a terminal."

That is misleading.

Oni:358789 roberson$ echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/MacGPG2/bin
Oni:358789 roberson$ matlab -nodesktop -nojvm
                                                         < M A T L A B (R) >
                                               Copyright 1984-2017 The MathWorks, Inc.
                                                R2017a (9.2.0.538062) 64-bit (maci64)
  [...]
>> getenv('PATH')
ans =
    '/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/MacGPG2/bin'

So if you start MATLAB from a terminal, you will get the PATH inherited from the shell.

The issue is that when you click on the icon in MacOS or OS-X, you are not running at the terminal: the program is run by launcher, which does not go through a shell login session. You get the system default PATH environment variable.

I have posted more detailed explanations before, including information about which shell initialization files are or are not executed when you system() on OS-X / MacOS / Linux systems, and I have posted links to information on how to permanently modify the system default PATH .

Cristiana Dinea 2023-2-25

在 MATLAB Online 中打开

@Walter Roberson thank you for the reply.

I am runnign this script fro converting dicom to nifti

function par = dicom2nii(src, outfile)
%% Converting DICOM to NIFTI for 4D data
%
% Syntax:
%   [filename, par] = dicom2nii(src, [options])
%
% Description:
%   This function is an extension of the DICOM-to_NIFTI converter
%   'dicm2nii'. It converts a set of DICOM files to NIFTI format 
%   for 4D data. It supports the automatic conversion to a 4D NIFTI 
%   file.
%
% Input Arguments:
%   src     - the directory where DICOM files are located.
%   outfile - the output NIFTI file.
%
% Output Arguments:
%   par     - a structure of DICOM parameters.
%
% Examples:
%   dicom2nii('dcm','out.nii.gz'); 
%
% See also 
%
% References:
%
% Notes:
% 1. This function requires the DICOM-to_NIFTI converter dicm2nii.
%    https://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter--nifti-tool-and-viewer
% 2. This function requires FSL, and works on Linux.
%
% History:
%   07/14/2016 - initial script.
%
%__________________________________________________________________________
% Wonsang You(wsgyou@gmail.com)
% 07/14/2016
% Copyright (c) 2016 Wonsang You.
%% converting DCM to NIFTI for each volume
path_str = fileparts('out.nii.gz');
niidir   = fullfile(path_str,'nii');
subject  = dicm2nii('/Users/cdinea/Downloads', niidir, '3D.nii.gz');
data     = load(fullfile(niidir,'dcmHeaders.mat'));
prefix   = fieldnames(data.h);
%% concatenating 3D volumes into a 4D NIFTI files
system(sprintf('full_list=`imglob %s_?????.*`;fslmerge -t %s $full_list',fullfile(niidir,prefix{1}),'out.nii.gz'),'-echo');
system(sprintf('rm -f %s',niidir));

Walter Roberson 2023-2-25

What steps did you take to put imglob and fslmerge onto your shell PATH? And what is the path to each of those executables?

Cristiana Dinea 2023-3-8

在 MATLAB Online 中打开

@Walter Roberson I set

>> setenv('PATH', [getenv('PATH') ':/Users/cdinea/fsl/bin']);

and on my Mac fsl and imglob are recognized

cdinea@cdinea-mlt bin % imglob
Usage: imglob [-extension/extensions] <list of names>
       -extension for one image with full extension
       -extensions for image list with full extensions

请先登录，再进行评论。

Can not run system commands from matlab -MAC OSX

0 个评论
显示 -2更早的评论隐藏 -2更早的评论

回答（1 个）

10 个评论
显示 8更早的评论隐藏 8更早的评论

另请参阅

类别

标签

Community Treasure Hunt

Can not run system commands from matlab -MAC OSX

0 个评论 显示 -2更早的评论隐藏 -2更早的评论

回答（1 个）

10 个评论 显示 8更早的评论隐藏 8更早的评论

另请参阅

类别

标签

Community Treasure Hunt

0 个评论
显示 -2更早的评论隐藏 -2更早的评论

10 个评论
显示 8更早的评论隐藏 8更早的评论