Using matlab "system" to use fsl function: zsh:1: command not found

Hi, I am currently using nets_glm.m to analyze timeseries data. When I run:

system('randomise -i /private/var/folders/_t/nh0js0wn4pn2qvrpzc3_p6th0000gn/T/tpdd6495da_b958_4230_a49e_a51b1baf05c9 -o /private/var/folders/_t/nh0js0wn4pn2qvrpzc3_p6th0000gn/T/tpdd6495da_b958_4230_a49e_a51b1baf05c9 -d design/design.mat -t design/design.con -x -n 5000')

it will return: zsh:1: command not found: randomise.

However, when I run "randomise" function directly in zsh, it works well.

Could you please help me figure out the probelm?

Thanks

Answer 1

[Nazirah Mohd Khairi]

I've used this solution, it works for me:

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

Basically add the path where the command is (usually in /usr/local/bin or where you install it).

[Cristiana Dinea]

this does not seem to work for me.

Any other WAR?

[Walter Roberson]

@Cristiana Dinea

Setting the environment variables correctly has to do with what executables can be found when you use system() or the ! command in MATLAB. It does not provide a way for MATLAB to find .m or .mdl or .slx or similar -- use pathtool for that. It also does not provide a way to be able to execute external programs such as randomize or imglob from the MATLAB command line -- you have to system() or ! to run those.

[Cristiana Dinea]

@Walter Roberson I am still unable to run a command

"imglob" 

commnad with system() in the following script

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([e-mail])
% 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);
system(imglob)
%% 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));

I get the following erros when running the script

>> dicom2nii
Xiangrui Li's dicm2nii.m 20230223 (feedback to [e-mail])
Validating 30800 files ... (1615 valid)
Converting 1 series (GE) into 3-D .nii.gz: subject '***'
 x5_95_5_1_25MM             512x512x85x19
 Please install pigz for fast compression: http://macappstore.org/pigz/
Elapsed time by dicm2nii is 212.6 seconds

Unrecognized function or variable 'imglob'.

Error in dicom2nii (line 47)
system(imglob)

[Walter Roberson]

Still waiting for your reply https://www.mathworks.com/matlabcentral/answers/170268-how-do-i-set-environment-variables-on-mac-os-x#comment_2632570

[Cristiana Dinea]

@Walter Roberson thank you for the reply.Sorry for the double post.

Re: https://www.mathworks.com/matlabcentral/answers/170268-how-do-i-set-environment-variables-on-mac-os-x#comment_2632570 I added my reply.

I am using this converter to convert from 4D DICOM to 4D nifti data. The are some issues though and I get these errors

Image Exception : #63 :: No image files match: /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00001 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00002 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00003 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00004 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00005 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00006 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00007 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00008 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00009 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00010 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00011 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00012 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00013 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00014 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00015 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00016 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00017 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00018 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00019

libc++abi: terminating with uncaught exception of type std::runtime_error: No image files match: /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00001 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00002 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00003 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00004 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00005 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00006 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00007 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00008 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00009 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00010 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00011 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00012 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00013 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00014 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00015 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00016 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00017 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00018 /Users/cdinea/Downloads/nii/x5_95_5_1_25MM_00019

/Users/cdinea/fsl/bin/fslmerge -t /Users/cdinea/Downloads/out.nii.gz $full_list: Aborted

rm: /Users/cdinea/Downloads/nii/: is a directory