FastSurfer surf pipeline did not finish: Missing .label files (not enough memory for mris_sample_parc) about fastsurfer

[dkuegler]

Hi,

first off, you dont need to source FreeSurfer if you are using the docker container.

As for the data: Can you share your log files anyways, so we can have a look?

Kind regards,
David

[mwendhaus]

Thank you very much for the fast reply. I am attaching the recon-all.log, if any other file might be necessary please let me know.
recon-all.log

[dkuegler]

Sorry, can you please send the deep-seg.log and the recon-surf.log?

[mwendhaus]

Of course:
deep-seg.log
recon-surf.log

[dkuegler]

mris_sample_parc gets terminated
Command terminated by signal 9

We have had some issues with mris_sample_parc acquiring excessive amounts of memory. This issue has been fixed in #430 , but we have not released a new docker image yet.
You can try giving docker more memory by for example --shm-size 8G see https://docs.docker.com/engine/reference/run/#runtime-constraints-on-resources and see also https://github.com/Deep-MI/FastSurfer/tree/dev/Docker#example-3-experimental-build-for-amd-gpus

[mwendhaus]

Great, thank you very much for the help!

[mwendhaus]

Just to complete this case, I got the same error using --shm-size 8G, and increased to --shm-size 12G to make sure. This worked fine and all necessary files were generated.

[dkuegler]

@mwendhaus I am confused, you got the same error, BUT all necessary files were generated?

[mwendhaus]

I got the same error as before when I used the flag --shm-size 8G. However, when I further increased the memory to 12G, I did not get the error, and the files were created.

[dkuegler]

Thank you! I believe this underlying issue is solved with the current dev version anyways, but good you were able to run FastSurfer.

[mwendhaus]

Thank you for the help!