Neurocommand for windows. No interface

[B8017913]

Dear professor,

I’m trying to set up Neurocommand on my laptop, but I’ve encountered some issues.

After following the excellent guidance in your document, I've successfully connected to my remote Linux desktop environment. However, there is nothing on the desktop, like this:

I tried to open a terminal, but the window closes immediately after opening.

Other applications seem to work fine, but I’m unable to access the terminal.

Is there something wrong with my setup? Or is there another way I can access the CLI?

Thank you very much.

BR,
Cecilia

[stebo85]

Can you describe the exactly what you did?

[B8017913]

Of course!
Here’s what I did to open an LXDE Linux desktop environment:

After entering my WSL username and password to get connected to the Linux desktop:

I see the following interface:

However, there doesn’t seem to be anything I can do in this environment. When I right-click, I see the following menu:

Among the options, only “Applications” contains any items. When I try to open the Zutty terminal, the window flashes for a second and then closes immediately. The other menu options are unresponsive when clicked.

Thank you for helping!!!

[stebo85]

i assume you are running this on a windows computer. Can you please try our Neurodesk app ? That has everything correctly configured: https://neurodesk.org/docs/getting-started/local/neurodeskapp/ Thank you Steffen

…

-- W: https://mri.sbollmann.net<https://mri.sbollmann.net/> | W: https://www.neurodesk.org<https://www.neurodesk.org/> | T: https://twitter.com/sbollmann_MRI | G: https://github.com/stebo85 Book meeting: https://calendly.com/s-bollmann/meeting

________________________________ From: B8017913 ***@***.***> Sent: Tuesday, August 5, 2025 7:31:04 PM To: neurodesk/neurodesk.github.io ***@***.***> Cc: Steffen Bollmann ***@***.***>; Comment ***@***.***> Subject: Re: [neurodesk/neurodesk.github.io] Neurocommand for windows. No interface (Discussion #561) Of course! Here’s what I did to open an LXDE Linux desktop environment: image.png (view on web)<https://github.com/user-attachments/assets/dc5184fd-8a8a-4f83-9296-e97feabcc300> After entering my WSL username and password to get connected to the Linux desktop: image.png (view on web)<https://github.com/user-attachments/assets/97b2f07c-038f-4a37-9761-c96c5e801dc3> I see the following interface: image.png (view on web)<https://github.com/user-attachments/assets/e9da47da-cfa0-4585-81fc-2242aeb40d76> However, there doesn’t seem to be anything I can do in this environment. When I right-click, I see the following menu: image.png (view on web)<https://github.com/user-attachments/assets/3d5dddef-494b-4ca3-be98-feaf1cb9ca15> Among the options, only “Applications” contains any items. When I try to open the Zutty terminal, the window flashes for a second and then closes immediately. The other menu options are unresponsive when clicked. Thank you for helping!!! — Reply to this email directly, view it on GitHub<#561 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA6V2W4JSHHOPV6PFV3Z5F33MB2VRAVCNFSM6AAAAACDEK4ZHKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMBQGMYTMMQ>. You are receiving this because you commented.Message ID: ***@***.***>

[B8017913]

Thank you very much for suggestion. I've been using the app for several days and it's truly amazing — it has been a great help in my research.

However, my computer doesn't have strong computing power, and mounting some of the larger tools often takes several hours. Even though I’ve tried using CVMFS to speed things up, it still hasn’t worked smoothly. I don't want to have to reload the container every time I reopen it. That’s why I’m hoping to try a more direct way of using containers.

Perhaps using Neurocommand directly on Windows is not the best approach in my case. I really appreciate your advice — I’ll continue with the Neurodesk Play you recommended. My data and pipelines are running well on the server side.

Best Regards,

Cecilia

[stebo85]

Dear Cecilia, The containers are automatically cached after opening them for the first time. Another option you can try in the NeurodeskApp: switch it from streaming to download mode in the settings - then it will download the containers you open and disable cvmfs. the play service is a cloud service and is not running in your computer. The Neurodesk app will give you access to both. If you can describe your problem in more detail we can help find a good solution. Thank you Steffen

…

-- W: https://mri.sbollmann.net<https://mri.sbollmann.net/> | W: https://www.neurodesk.org<https://www.neurodesk.org/> | T: https://twitter.com/sbollmann_MRI | G: https://github.com/stebo85 Book meeting: https://calendly.com/s-bollmann/meeting

________________________________ From: B8017913 ***@***.***> Sent: Tuesday, August 5, 2025 7:57:03 PM To: neurodesk/neurodesk.github.io ***@***.***> Cc: Steffen Bollmann ***@***.***>; Comment ***@***.***> Subject: Re: [neurodesk/neurodesk.github.io] Neurocommand for windows. No interface (Discussion #561) Thank you very much for suggestion. I've been using the app for several days and it's truly amazing — it has been a great help in my research. However, my computer doesn't have strong computing power, and mounting some of the larger tools often takes several hours. Even though I’ve tried using CVMFS to speed things up, it still hasn’t worked smoothly. I don't want to have to reload the container every time I reopen it. That’s why I’m hoping to try a more direct way of using containers. Perhaps using Neurocommand directly on Windows is not the best approach in my case. I really appreciate your advice — I’ll continue with the Neurodesk Play you recommended. My data and pipelines are running well on the server side. Best Regards, Cecilia — Reply to this email directly, view it on GitHub<#561 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA6V2W3VJ3VKXQ45E63FMV33MB5W7AVCNFSM6AAAAACDEK4ZHKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMBQGM3DGOA>. You are receiving this because you commented.Message ID: ***@***.***>

[B8017913]

Dear Professor,

Thanks！

I’m wondering if the download mode also works with notebooks. Can I directly use the containers I previously downloaded within a notebook?

I’ve noticed during use that different cases seem to be isolated from each other — they don’t share the containers loaded in other sessions. I’m really curious how this is achieved, but it also makes me a bit concerned about this approach.

Thank you for your help — I’d greatly appreciate it if you could clarify this for me.

Thank you

Cecilia

[stebo85]

Dear @B8017913 - yes that works: You can use a downloaded container from a notebook. Can you please share more details about your use case, what exactly you are doing and what problems you experience specifically?

[B8017913]

Dear Professor,

The issue I encountered was that the initial startup of containers was extremely slow on my personal computer. So I followed your suggestion and switched to download mode, which indeed helped — by skipping the container loading step, data processing became much faster.

From your previous presentation, I understood that in stream mode, after running module load, lmod works with CVMFS to modify the PATH and automatically distribute the necessary parts of the container to enable tool usage.

I’m really curious about how tool version switching is handled technically in download mode. For example, if I download version 6.0.7 of FSL, will it overwrite version 6.0.4, or can both versions coexist so that I can switch between them freely?

When I specify module load('fsl/6.0.7.16') in a notebook, will it automatically switch to and use the corresponding container version?
Or are the tools made directly available once downloaded, without needing to explicitly run module load?

Thank you very much for your generous sharing. The issues I previously experienced have already been resolved — I’m just genuinely curious about the inner workings of this impressive project.

Best regards,
Cecilia

[stebo85]

Dear @B8017913

multiple versions of containers can co-exist and you can switch between them freely using the module load command.

yes, when you run this in a notebook it will load the correct container. It will use downloaded offline containers first and only if they are not downloaded will switch to cvmfs:

import module
await module.purge()
await module.load('afni/21.2.00')
await module.load('mriqc/24.0.2')
await module.load('ants/2.6.0')
await module.load('bidscoin/4.3.3')
await module.load('freesurfer/7.3.2')
await module.load('mrtrix3/3.0.4')
await module.load('fsl/6.0.7.16')
await module.list()

The tools have to be loaded explicitly via module load - they will not be made available automatically.

[B8017913]

Dear Professor,

I’ve encountered a strange issue. After switching to download mode and trying to run my notebook, I noticed that the list of available modules in the sidebar was reduced to just four:

When I run await module.load(), it fails with the following error:

Lmod has detected the following error: The following module(s) are unknown: 
"mriqc/24.0.2"

Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
  $ module --ignore_cache load "mriqc/24.0.2"

Also make sure that all modulefiles written in TCL start with the string
#%Module

Interestingly, in the GUI interface, I can still load and use all types of containers without any issues.

I’ve checked the official documentation but couldn’t find anything related to this behavior. Is there any configuration I need to apply to make Lmod recognize all tools again, so that I can use them properly within the notebook?

Best regards,
Cecilia

[stebo85]

The notebook system will only show the notebooks that are downloaded. To get them downloaded go through the menu system in the desktop and start them from there - that will trigger the download. After that they will show up in the notebook system. Thank you Steffen

…

-- W: https://mri.sbollmann.net<https://mri.sbollmann.net/> | W: https://www.neurodesk.org<https://www.neurodesk.org/> | T: https://twitter.com/sbollmann_MRI | G: https://github.com/stebo85 Book meeting: https://calendly.com/s-bollmann/meeting

________________________________ From: B8017913 ***@***.***> Sent: Wednesday, August 6, 2025 12:45:10 PM To: neurodesk/neurodesk.github.io ***@***.***> Cc: Steffen Bollmann ***@***.***>; Comment ***@***.***> Subject: Re: [neurodesk/neurodesk.github.io] Neurocommand for windows. No interface (Discussion #561) Dear Professor, I’ve encountered a strange issue. After switching to download mode and trying to run my notebook, I noticed that the list of available modules in the sidebar was reduced to just four: image.png (view on web)<https://github.com/user-attachments/assets/3b26070d-59af-4fda-8132-eb315e68fe2f> When I run await module.load(), it fails with the following error: Lmod has detected the following error: The following module(s) are unknown: "mriqc/24.0.2" Please check the spelling or version number. Also try "module spider ..." It is also possible your cache file is out-of-date; it may help to try: $ module --ignore_cache load "mriqc/24.0.2" Also make sure that all modulefiles written in TCL start with the string #%Module Interestingly, in the GUI interface, I can still load and use all types of containers without any issues. I’ve checked the official documentation but couldn’t find anything related to this behavior. Is there any configuration I need to apply to make Lmod recognize all tools again, so that I can use them properly within the notebook? Best regards, Cecilia — Reply to this email directly, view it on GitHub<#561 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA6V2W2UBZZQAPYCRCJVYAL3MFXL5AVCNFSM6AAAAACDEK4ZHKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMBRGM3DQMA>. You are receiving this because you commented.Message ID: ***@***.***>