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Hi Paul,

I did the same as you suggested,
1. Configured MATLAB; 
2. copy+paste the full FSL matlab configuration directly into a matlab session. 

However, it still doesn’t work and I still got the same error
——————————————————————————————————
/bin/bash: slices_summary: command not found
Error using imread>get_full_filename (line 516)
File "/private/var/folders/xn/xqzh0j0x4hbcd23hn9q0kysc0000gn/T/tpfbdfa343_54a2_4a67_adf4_e6c0b538df55.png" does not exist.

Error in imread (line 340)
    fullname = get_full_filename(filename);

Error in nets_nodepics (line 16)
 pic=imread(sprintf('%s.png',grot));
——————————————————————————————————

Any suggestions are appreciated!

Thank you,

Xiao

On Jul 24, 2018, at 10:59, Xiao Yang <[log in to unmask]> wrote:

Hi Paul,

I just saw your email and tried it. Unfortunately, it still doesn’t work.

Thanks,

Xiao

On Tue, Jul 24, 2018 at 10:40 XIAO YANG <[log in to unmask]> wrote:
Dear FSL experts,

I still couldn’t be able to run FSL_Nets. The same error “slices_summary: command not found”.

Any help is appreciated!

All the best,

Xiao


On Jul 18, 2018, at 10:00, XIAO YANG <[log in to unmask]> wrote:

Hi Paul,

Thank you for your suggestion. 

I just tried to modified the startup.m file from the page you shared with me,
leledeMacBook-Pro:matlab lele$ pwd
/Users/lele/matlab
leledeMacBook-Pro:matlab lele$ ls
startup.m
leledeMacBook-Pro:matlab lele$ cat startup.m 
%------------ FreeSurfer -----------------------------%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
    addpath(genpath(fsmatlab));
end
clear fshome fsmatlab;
%-----------------------------------------------------%

%------------ FreeSurfer FAST ------------------------%
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
    path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-----------------------------------------------------%
setenv( 'FSLDIR', '/usr/local/fsl');
fsldir = getenv('FSLDIR');
fsldirmpath = sprintf('%s/etc/matlab',fsldir);
path(path, fsldirmpath);
clear fsldir fsldirmpath;
leledeMacBook-Pro:matlab lele$ 



Unfortunately, I still got the same error when I ran the FSL_Nets. Even failed after I restarted the computer again.

I think I already configured MATLAB before since we had this following command in Fsl_nets:
addpath(sprintf('%s/etc/matlab',getenv('FSLDIR')))    % you don't need to edit this if FSL is setup already

And I also setup the FSL as  you can see this: 
leledeMacBook-Pro:resting_state_FSLNets lele$ cd ${FSLDIR}
leledeMacBook-Pro:fsl lele$ pwd
/usr/local/fsl
leledeMacBook-Pro:fsl lele$ 

I also tried to configured MATLAB by using following command which still didn’t work:
addpath([getenv('FSLDIR') '/usr/local/fsl/etc/matlab’])


Can you give me some advice?

Thank you,

Xiao

On Jul 18, 2018, at 03:57, paul mccarthy <[log in to unmask]> wrote:

Hi Xiao,

Have you configured MATLAB so that it knows about FSL?


Cheers,

Paul

On 17 July 2018 at 16:09, Xiao Yang <[log in to unmask]> wrote:
Dear FSL_Nets experts,

I came across the similar error two days ago. I went through the FSL Archive and found some answers. I tried but it still showed the same error when I ran fsl_nets.

First, I located the slices_summary:
leledeMacBook-Pro:resting_state_FSLNets lele$ which slices_summary
/usr/local/fsl/bin/slices_summary

I tried to check the slices_summary executable and it worked. I can also use slices_summary to do the following command outside the matlab:
slices_summary /Users/lele/Desktop/resting_state_FSLNets/group_melodic/melodic_IC.nii.gz 4 $FSLDIR/data/standard/MNI152_T1_2mm /Users/lele/Desktop/resting_state_FSLNets/group_melodic/melodic_IC.nii.gz.sum

It still showed the same error when I ran fsl_nets.

Second, I copy this file to the current folder where I ran fsl_nets and make it executable by doing this:
cp /usr/local/fsl/bin/slices_summary /Users/lele/Desktop/resting_state_FSLNets/
chmod +x /Users/lele/Desktop/resting_state_FSLNets/slices_summary

Also the same error when I ran fsl_nets.

Here is the error information in matlab when I ran fsl_nets:
--------------------------------------------------------------------------------------------------------------------------------------------
/bin/bash: slices_summary: command not found
Error using imread>get_full_filename (line 516)
File "/private/var/folders/xn/xqzh0j0x4hbcd23hn9q0kysc0000gn/T/tp1b5af7dc_2ca5_413f_96e3_ddee7340464d.png" does
not exist.

Error in imread (line 340)
    fullname = get_full_filename(filename);

Error in nets_nodepics (line 16)
 pic=imread(sprintf('%s.png',grot));

Error in nets_examples_xiao (line 42)
nets_nodepics(ts,group_maps);            % quick views of the good and bad components

--------------------------------------------------------------------------------------------------------------------------------------------
Any help is appreciated!

All the best,

Xiao

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