[Windows/Docker] FreeSurfer container fails to start: "nu_correct: Command not found" & Restarting loop

[garamlee-25742]

Hello,
I am trying to run TI-Toolbox on Windows 11 (WSL 2 backend) using Docker Desktop.
While the simnibs_container starts and runs correctly (Green status), the freesurfer_container gets stuck in a "Restarting" loop immediately after launch.

Upon checking the logs, the primary error seems to be related to nu_correct not being found or executed properly within the container environment. Consequently, the TI-Toolbox launcher eventually fails with a "Command timed out" error because the FreeSurfer container never becomes ready.

System Information

• OS: Windows 11 (WSL 2 enabled)
• Hardware: CPU (High-end), RAM 64GB, GPU RTX 5090
• Docker Desktop: Latest version (Memory allocated: 32GB+)
• TI-Toolbox Version: Latest (Launcher)
• Docker Images:
  • idossha/simnibs:v2.2.3 (Status: Running OK)
  • idossha/ti-toolbox_freesurfer:v7.4.1 (Status: Restarting / Failed)

Steps to Reproduce

1. Clean installation of TI-Toolbox Launcher.
2. Set Resources > Memory to 32GB in Docker Desktop.
3. Select project directory (Tried both external D: drive and C:\Users\Desktop to rule out permission issues).
4. Click "Launch".
5. The freesurfer_container continuously restarts and eventually fails.

Error Logs
The specific error observed in the FreeSurfer container logs:
...
nu_correct: Command not found
...
(Or sometimes immediate exit with code 127/126 related to path/permissions)

And the launcher eventually displays
Failed to launch: Command timed out after 300000 milliseconds: docker compose ... up --build -d Timed out

What I have tried (Troubleshooting)

• Memory Allocation: Increased Docker memory limit to 32GB (and Swap to 4GB).
• Manual Pull: Manually ran docker pull idossha/ti-toolbox_freesurfer:v7.4.1 to ensure the image is not corrupted. (Status: Up to date).
• Storage Location: Moved the sourcedata folder from an external drive (D:) to the system drive (C:\Users\username\Desktop\TI_Work) to avoid WSL2 mount/permission issues.
• Full Reset: Deleted all containers, images, and volumes, then re-downloaded everything.
• Manual Run: Tried docker run ... tail -f /dev/null manually. The container stays alive, but once the Launcher takes over or setup scripts run, it fails again.
• Suspected Cause It seems like the environment setup script inside the ti-toolbox_freesurfer:v7.4.1 image is failing to locate nu_correct or has path configuration issues specifically on Windows Docker mounts.

Any guidance for this issue would be greatly appreciated.

[idossha]

Hi @garamlee-25742

Thanks for working on debugging it and sharing your finding. Have you tried using the loader.sh in combination with docker-compose.yml. It could be there is an edge case I have not considered using the desktop app.

If that does not work, I would assume it is in the docker-WSL configuration.

Please let me know how is goes with the bash entry. I will think of possible solutions in the meantime.

Thanks,
Ido

[garamlee-25742]

Hello, @idossha

Thank you for the quick response! I followed your suggestion and tried the bash entry method using loader.sh and docker-compose.yml on my Windows/WSL2 environment before launch the ti-toolbox.

Unfortunately, I am still encountering the same issues as shown in the attached screenshots:

Container Loop: While simnibs_container is running fine, the freesurfer_container enters a constant "Restarting" loop immediately after services start.

Example Data Failure: The terminal reports Failed to set up example data during the initialization process.

Thanks,
Garam

[idossha]

Hi @garamlee-25742 ,

I am not sure what problem here, as you are successfully inside the toolbox. Only thing remaining is for you to hit GUI or type some of the CLI commands.

Regarding the data error, this seems to be a bug in the toolbox initialization step. However this only copies some nifti files to your local directory. It is not a critical step.

However, I just released an updated loader.sh which is a more robust and efficient version. It should handle that step correctly.

To implement it please re download the loader.sh and docker-compose.yml and it should be behaving as expected.

[garamlee-25742]

Hi, @idossha

Thank you for your kind request.
The CLI commands successfully installed and executed program.

Best,
Garam

[idossha]

Hi @garamlee-25742 — glad to hear the CLI route worked for you. A quick update for completeness: v2.3.1 includes launcher/config documentation cleanup and more robust GUI process/error reporting, which should make Docker/GUI startup issues easier to diagnose.

Some Windows/WSL/FreeSurfer container behavior can still depend on local Docker Desktop configuration, but any relevant launcher-side updates will be included in v2.3.1 in the coming days.