Error running Osprey Process

MRS Software Osprey
#1

Hi!

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

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image945×540 122 KB

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

#2

Hi @dina_satriawan,

Thank you for reaching out!

About your two issues:

  1. 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?
  2. whitespace is Matlab function that was introduced in R2020b (Match whitespace characters - MATLAB whitespacePattern). Which MATLAB version are you using?

Best,
Helge

#3

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

#4

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

#5

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

#6

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

#7

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

#8

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

#9

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.

#10

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