CemrgApp crashes during segmentation (Scar quantification tool)

[leokrueger]

Hey, I'm working with the CemrgApp for about 8 months now, especially with the scar quantification tool (Scar quantification in the left atrium). By now I finished about 80 cases, more or less without any problems. But recently the programm crashes everytime after converting the DICOMS into Niftis at the beginning of my segmentation. Most of the times I don't even get to segment one slice before the programm crashes. Has anybody experienced this kind of problem or knows how to solve it? I'd be happy for any help.

[alonsoJASL]

Hello, thank you for using our application and for reporting this. A few follow up questions to help narrow down the potential problem:

1. What operating system are you using?
2. Which version of CemrgApp are you using? You can check this on the splash screen when opening the app.
3. From your description, it seems to me that this is happening when you press the Convert to Nifti button, which is part of Step2: Process Images. Is this correct or is your problem before, like when loading the DICOM image in the data manager?
4. Has anything changed in your work environment, setup or data? Examples are change of computer, upgrading of operating system, the acquisition of the DICOMs was different in anyway or they come from a different dataset?

Suggestions: Consider trying the following:

• Take one of the 80 cases you have already processed successfully, save a backup copy and try processing it again from the beginning. Does the problem persist?
• If available, try using a different computer.
• Convert the DICOMs using a different tool (for example: https://pypi.org/project/dicom2nifti/). Then drag the file to the data manager and press the Convert to Nifti button.
• Find the log and attach it here after a crash. Depending on the operating system, the way you can find where it is.

Finally, I would encourage you to use our issue template and check our bug reporting guidelines. These are really helpful to minimise the follow up questions from us and resolving the issue sooner.

[leokrueger]

Hey, thank you very much for your help!

Put an X between the brackets (without spaces [X]) on the following lines if you have done all of the following:

• [X] Checked the wiki board for common solutions: https://github.com/CemrgAppDevelopers/CemrgApp/wiki
• [X] Checked that your issue isn't already filed: https://github.com/search?q=+is%3Aissue+user%3ACemrgAppDevelopers
• [X] Are you providing the log? https://github.com/CemrgAppDevelopers/CemrgApp/wiki/Troubleshooting

Description

According to your questions:

1. Operating system: Windows 10 Enterprise 22H2
2. CemrgApp Version: CemrgApp v2.2 v2018.04.02
3. Pressing the "convert to Nifti" button still works and I still get the converted images. I can also click the "Scar analysis" and "segment image" button. As soon as I start the segmentation, the program crashes while scrolling through the slices.

Steps to Reproduce

1. Loading the DICOMs into CemrgApp
2. Converting the DICOMs into Niftis by clicking "Convert to Nifti"
3. Click "Scar analysis" -> answer question with "no"
4. Click "Segment Image" -> answer both questions with "no"
5. now the right hand panel shows the segmentation window -> click "New" and name the Segmentation
6. scroll through the slices in the axial plane

Expected behaviour:

The program should run smoothly while scrolling through the slices

Actual behavior:

The program stops working and crashes

Reproduces how often:

In the last 8 months this problem almost never occurred but during the last two weeks the app crashed in about 95% of the times while scrolling through the slices.

Additional Information

No changes happened, at least non that I know of. I didn't change computers nor did I upgrade the operating system. The acquisition and data set are also the same as before. I also installed the CemrgApp again.

regarding your suggestions:

• I tried using one of the previous cases, the problem still persists
• another computer wasn't available yet, but I will definitely look into that
• I will also look into converting the DICOMS using the mentioned tool
• I can't access the log as soon as the program crashes. I'll happily attach what the log says after restarting the program.

Again, thank you very much for the help and suggestions.

Kind regards

[alonsoJASL]

Hi @leokrueger,

I understand your problem much better now. I thought the problem was with the conversion from DICOM to NIFTI, but it is not. The problem is with the manual segmentation. I can think of two more tests you can run:

Get the log

First, do one of the cases that you know crashes the application, only this time as soon as you open CemrgApp, open the LOG as I showed you before and look for an entry that looks like below

Info Logfile: C:/Users/USER/.../KCL/CemrgApp v2.2_1495662208/data/7/mitk-0.log

The values change, and the path too. Nonetheless, that is the log file, you can navigate on Windows Explorer and retrieve it after the application crashes. Then send it over. I do not have a Windows computer with me, otherwise I would have checked for you exactly where that is.

Remove previous saved files

CemrgApp saves things in a hidden folder to help loading certain things, it does so every time you open the application. This is helpful in some ways, but if there is an error in something, it will replicate over and over, which could be what is happening to you. It would also explain why re-installing CemrgApp did not work, since uninstalling it does not remove these folders.

Since you did the previous step to find the log, you have done most of the job. If you notice, the path arrives at a folder called KCL/CemrgApp v2.2_<some random numbers>. What you need to do is delete the parent folder called KCL, and try again. CemrgApp will take slightly longer to start and might need you to start it twice, but that is all normal.

Have a go and let us know.

[leokrueger]

Hey @alonsoJASL,

I followed your instructions and deleted the "KCL" folder. Afterwards I did two cases without the program crashing. On the third case it crashed again but after retrying it a few times the program worked smoothly again. Hopefully deleting the folder resolved the problem. I'll try out a couple of more cases and will let you know if anything changes.

Thank you a lot for the very helpful suggestion.

Kind regards