Singularity/Docker

[Adam Raikes]

Hi Frank,

I see Dockerfiles in the UNet Studio repo. Are there official/developmental versions that are compiled and ready somewhere so that I can test with my mouse data?

[Frank Yeh]

Yes, the docker link is
docker pull dsistudio/unetstudio:latest

On Fri, Oct 6, 2023 at 1:13 PM Adam Raikes <raikes....@gmail.com> wrote:
>
> Hi Frank,
>
> I see Dockerfiles in the UNet Studio repo. Are there official/developmental versions that are compiled and ready somewhere so that I can test with my mouse data?
>

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[Adam Raikes]

Thoughts?

[adamraikes@r2u15n1 singularity_images]$ singularity exec unetstudio_latest.sif unet_studio
INFO:    underlay of /etc/localtime required more than 50 (103) bind mounts
/opt/unet-studio/unet_studio: error while loading shared libraries: libQt6Core.so.6: cannot open shared object file: No such file or directory

[Frank Yeh]

It seems that Singularity does not mount the folders storing the
needed libraries.
If you are running on your own computer, you may try install qt6.
Best,
Frank

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[Adam Raikes]

Is it possible to get it with the QT libraries bundled?

Also: 

1. Is there a CLI for the Singularity/Docker containers?

2. Running on Windows with my mouse data, I was running the skull stripping which appears to work rather well. However, the saved, skull-stripped image outputs with different voxel dimensions as my original. The original was collected at 0.075x0.075x0.075mm resolution and the saved file has a 1x1x1mm resolution.

[Frank Yeh]

On Wed, Dec 6, 2023, 5:50 PM Adam Raikes <raikes....@gmail.com> wrote:

Is it possible to get it with the QT libraries bundled?

Also: 

1. Is there a CLI for the Singularity/Docker containers?

Yes, I will update documentation to give some examples.

2. Running on Windows with my mouse data, I was running the skull stripping which appears to work rather well. However, the saved, skull-stripped image outputs with different voxel dimensions as my original. The original was collected at 0.075x0.075x0.075mm resolution and the saved file has a 1x1x1mm resolution.

I will fix it and let you know.

Frank

To view this discussion on the web visit https://groups.google.com/d/msgid/unet-studio/a2dd5bd9-a950-4c84-b911-637cb935d6e1n%40googlegroups.com.