abnormally long preprocessing time in Docker

[Dr-QingHe]

Hi guys,
I configured the TI-toolbox yesterday afternoon and then ran preprocessing on a subject's structural MRI (T1) in Docker. However, the process still hasn't finished as of now (11:30 am; more than 20 hours since the processing started). The software interface appears to be frozen, but there are no error messages (as shown in the screenshot). Is this situation normal?

Qing

[idossha]

Hi @Dr-QingHe,

Thanks for your post. It is best to describe your hardware, OS, and TI-Toolbox version when reporting a potential bug or weird behavior.

CHARM process should take about 1.0h to 1.5h depending on your hardware, whereas RECON-ALL could potentially take about 4h+.

Your screenshot did not show the latest output so I do not know what happened last. Also, you can look in the system monitor tab to see if the processes are still going on.

Thanks,
Ido

[Dr-QingHe]

Hi, Ido,

Thank you for your reply.

The information concerning my computer is listed below:

Processor 13th Gen Intel(R) Core(TM) i9-13900 (2.00 GHz)
Installed RAM 64.0 GB (63.7 GB usable)
Device ID 15153AD9-DA6E-4512-A820-EDA56D5D2F40
Product ID 00331-10000-00001-AA789
System type 64-bit operating system, x64-based processor
Pen and touch No pen or touch input is available for this display

Edition Windows 11 Pro
Version 25H2
Installed on ‎12/‎17/‎2024
OS build 26200.8246
Experience Windows Feature Experience Pack 1000.26100.297.0

And the version of the TI-toolbox is 2.3.0.

The last line of output is shown in the screenshot.

Thank you again.

Qing

[idossha]

Hi @Dr-QingHe,

It looks like the process is still running though I am not sure. What I meant is not the system Task Manager but the TI-Toolbox System Monitor tab.

Ido

[Dr-QingHe]

Hi @idossha
Here is the TI-Toolbox system monitor tab.

Qing

[idossha]

Okay. Very strange behavior and first time we are hearing about this.

I would suggest to look at the log files. If those are not insightful for you, please feel free to email the relevant log files and we will take a look to see if there is a possible explanation.

Ido

[Dr-QingHe]

Hi, @idossha, where are the log files in my Windows system computer?

[idossha]

The log files for the TI-Toolbox are always in /{your_project/derivatives/ti-toolbox/logs/*

[Dr-QingHe]

Here is the log file.
preprocess_20260421_052938.log

[idossha]

I would suggest testing the pre-process with a validated nifti file. It could be that your nifti, rather than the software, is the source of error. We shop ernie, which is validated to work well.

[idossha]

Hi @Dr-QingHe — thank you for the details and screenshots. A quick update: v2.3.1 includes GUI lifecycle and error-reporting improvements for long-running preprocessing jobs.

This does not fundamentally change expected CHARM / recon-all runtime, but it should make the GUI less ambiguous: preprocessing subprocess failures are now detected more reliably, dependent tabs refresh only after successful outputs, and failure messages point users toward the relevant logs and expected inputs.

These changes should be released with v2.3.1 in the coming days. If you still see a >20h preprocessing run after updating, please send the latest console output plus the log file under derivatives/ti-toolbox/logs/sub-{subject}/.