Error running Osprey Process

dina_satriawan · February 27, 2023, 9:56am

Hi!

I’m using Osprey for the first time on Ubuntu 20.04 and I’m running into this error message while running Process:

I tried again on a Windows computer and instead got this error message:

Unrecognized function or variable ‘whitespacePattern’.

Error in OspreyJob (line 230)
str = replace(str, whitespacePattern + ‘"’, ‘"’);

Error in CreateOspreyJob_app/CREATEJOBButtonPushed (line 472)
MRSCont = OspreyJob(jobm,1);

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 335)
Error while evaluating DestroyedObject PrivateButtonPushedFcn.

What could be the cause and how can I fix this?

Thank you!

Kind regards,
Dina

Helge · February 27, 2023, 4:25pm

Hi @dina_satriawan,

Thank you for reaching out!

About your two issues:

Can you post the PDF of OspreyLoad just so that I can see what your data looks like. And could you also post the jobfile?
whitespace is Matlab function that was introduced in R2020b (Match whitespace characters - MATLAB whitespacePattern). Which MATLAB version are you using?

Best,
Helge

dina_satriawan · February 28, 2023, 10:03am

Hi @Helge,

Thanks for your response!

Here is the OspreyLoad pdf for when I was running on Linux (MATLAB version R2021a):
DBIEX_6_2_raw_act_Voxel_1_Exp_1_OspreyLoad_mets.pdf (16.7 KB)

Here is the jobfile:
OspreyJob_sub-PILOT01.txt (855 Bytes)

Apparently the MATLAB version I was using on Windows was version R2019.

Please let me know if you need any further information. Thank you!

Kind regards,
Dina

Helge · March 9, 2023, 4:48pm

Hi @dina_satriawan,

I don’t see any obvious issues in the jobfile and the also looks high quality.

Any chance that you can share the data so that I can figure out where the processing is going wrong?

Best,
Helge

dina_satriawan · March 27, 2023, 8:09pm

Hi @Helge,

Thank you for the reply!

Please find the data here: https://drive.google.com/drive/folders/1hMWVD0HSXwa2cM7Ck6qASltT762tF432?usp=sharing

I tried analyzing the same data again on my Windows computer ( MATLAB R2023a), and it worked fine. However, I will need to run it on my lab’s Linux server (MATLAB R2021a), and this is when the problem occurs.

Thank you,
Dina

Helge · April 11, 2023, 11:20pm

Hi @dina_satriawan,

I’ve looked into your data. I was able to fully analyze the data using your jobfile in a Ubuntu 22.04.1 virtual machine and Matlab 2023a. I am still a bit puzzled about the error you are reporting as the function that results in the crash is called several times before without any failure.

Are you running this in the Matlab GUI on the server or are you running nosplash nodesktop mode?

Could you download the latest version 2.5.0 from GitHub and try again? If it is still not working I will download MATLAB R2021a and see if I can reproduce the error.

Best,
Helge

dina_satriawan · April 12, 2023, 10:39am

Hi @Helge,

We are running this on Matlab GUI and Ubuntu 20.04. Do we need to pull the develop branch (default) or master? We currently have develop.

Thanks,
Dina

Helge · April 12, 2023, 7:44pm

Hi @dina_satriawan,

both the develop and the master branch are currently equivalent. Or you can download the source code from the release page (Release Osprey v2.5.0 · schorschinho/osprey · GitHub).

If you are interested in running the OspreyGUI only you can also try installing Osprey using the Ubuntu.zip on the release page.

Best,
Helge

dina_satriawan · April 14, 2023, 10:25am

Hi @Helge,

We tried again with develop v2.5.0 from GitHub and the same error remains:

The logical indices contain a true value outside of the array bounds.

Error in osp_XReferencing (line 85)
[max_value,max_ind] = max(r(limits));

Error in OspreyProcess (line 675)
[refShift, ~] = osp_XReferencing(raw,[3.03 3.22],[1 1],[1.85 4.2]);% determine frequency shift

Error in osp_onProc (line 37)
MRSCont = OspreyProcess(MRSCont);

Error while evaluating UIControl Callback.

Helge · April 19, 2023, 3:29pm

Hi @dina_satriawan,

Ok. I’ll implement additional error handling into this function to avoid this. However, it is still unclear to me why this is happening.

I’ll let you know when it is done.

Best,
Helge

gauthami.nair · October 31, 2023, 11:22am

Hi,

So I was recently running Osprey and I came across the same error.

Is there any solution to fix this error now? I installed Version 2.5 first and then tried it again with Version 2.0 and 2.2 but I got the same error on all the versions. Tried using different subjects as well. My matlab version is 2021b

dina_satriawan · January 31, 2024, 3:55pm

Hi @gauthami.nair,

We still don’t have a solution to this. We tried pulling the latest version of Osprey and still encountered the same issue.

Are there possibly any updates regarding this matter @Helge?

Thank you!

dina_satriawan · February 8, 2024, 9:49am

Hi @Helge and @gauthami.nair

We managed to solve the issue (running Matlab 2021b on our Ubuntu 20.04 OS server) by moving Osprey with its subfolders to the top of the Matlab path, i.e. BEFORE the Matlab built-in functions.

Hence, the problem is likely due to calling a Matlab built-in rather than an Osprey function if the former is higher up on the path?!

Hopefully this helps!

Best wishes,

Dina et al

alex · February 8, 2024, 4:07pm

Hi @dina_satriawan,

Do you have the econometrics toolbox installed? If so, I’m fairly sure the crosscorr function from that toolbox is the culprit (I started investigating this the other day, but didn’t get quite far enough to confirm my suspicions – looks like you’ve figured it out in the meantime)