Freesurfer terminal and quit.

[grojasy]

In a terminal window, I started processing a volumetric analysis using FreeSurfer. How can I close the terminal window so that FreeSurfer can continue processing? Is there any documentation on this topic?

[stebo85]

Dear @grojasy,

To keep an analysis running we recommend running it in a jupyter notebook: https://neurodesk.org/example-notebooks/structural_imaging/freesurfer.html

[grojasy]

If I begin a FreeSurfer processing run in a Jupyter notebook, how can I exit Neurodesk while continuing the FreeSurfer processing?

[stebo85]

are you running neurodesk locally in docker or remote in a cloud or on an HPC?

[grojasy]

I am using Neurodeskapp remote....

[stebo85]

Ok, are you using your own cloud setup or our play service? If you are using you own remote setup how did you set it up?

[grojasy]

I am using your play service... El sáb, 23 de ago de 2025, 18:40, Steffen Bollmann ***@***.***> escribió:

…

Ok, are you using your own cloud setup or our play service? If you are using you own remote setup how did you set it up? — Reply to this email directly, view it on GitHub <#570 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADBUG2ERF6N55QOJYG2PDY33PDUWXAVCNFSM6AAAAACETM5T66VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJZHEZDEMA> . You are receiving this because you were mentioned.Message ID: <neurodesk/neurodesk.github.io/repo-discussions/570/comments/14199220@ github.com>

[stebo85]

Ok, then you can just close your browser window and it will keep running. If the analysis doesn't finish, check if you are running out of memory- our free play service have tight restrictions on storage and RAM usage.

[grojasy]

How much storage and RAM size is the limit? El sáb, 23 de ago de 2025, 18:59, Steffen Bollmann ***@***.***> escribió:

…

Ok, then you can just close your browser window and it will keep running. If the analysis doesn't finish, check if you are running out of memory- our free play service have tight restrictions on storage and RAM usage. — Reply to this email directly, view it on GitHub <#570 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADBUG2AW7GMXTGYDSMYWGLD3PDW5TAVCNFSM6AAAAACETM5T66VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJZHEZDSMY> . You are receiving this because you were mentioned.Message ID: <neurodesk/neurodesk.github.io/repo-discussions/570/comments/14199293@ github.com>

[stebo85]

The limits depend on the server you are on . Which play server are you using? There is also the possibility of increasing the limits. Let us know what exactly you are doing , what errors you get and what you need.

[grojasy]

I tried to keep a freesurfer analysis running in a jupyter notebook. I close Neurodesk app window, and then freesurfer analysis stop. Why? El sáb, 23 de ago de 2025, 18:59, Steffen Bollmann ***@***.***> escribió:

…

Ok, then you can just close your browser window and it will keep running. If the analysis doesn't finish, check if you are running out of memory- our free play service have tight restrictions on storage and RAM usage. — Reply to this email directly, view it on GitHub <#570 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADBUG2AW7GMXTGYDSMYWGLD3PDW5TAVCNFSM6AAAAACETM5T66VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJZHEZDSMY> . You are receiving this because you were mentioned.Message ID: <neurodesk/neurodesk.github.io/repo-discussions/570/comments/14199293@ github.com>

[grojasy]

Ok. Thank you very much..

[grojasy]

Please don't interfere with the processing right now until we found the bug

Please tell me when you have found the bug.

[stebo85]

Dear @grojasy

The 26M subject now ran ok with Freesurfer 8.1.0 - I suspect it's a bug in freesurfer 7.2.3 in combination with your data that has a lot of neck regions, which I think causes N4 to randomly consume a lot of memory.

I am now testing this in the 74F subject.

[grojasy]

Can I start using Neurodesk to process other MRI-T1 with freesurfer?

[stebo85]

Dear @grojasy,

Yes, both datasets worked now. Please try other datasets and let us know if something fails again.

Also, if neurodesk is helpful for you, please consider donating to keep the project alive: https://eecs.uq.edu.au/neurodesk