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Update FastSurfer Docker containers #72

Merged
merged 8 commits into from
Aug 17, 2023
Merged

Update FastSurfer Docker containers #72

merged 8 commits into from
Aug 17, 2023

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milanmlft
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  • Use the new Docker containers from HealthBioscienceIDEAS/MedICSS-Project-Repro-Pipelines#24 to run the FastSurfer commands
  • Add separate commands for running FastSurfer with or without GPU support
  • Use t3.large for the Container Service instance to handle FastSurfer

Fixes #70

@milanmlft milanmlft requested a review from p-j-smith August 16, 2023 17:32
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Still need to test whether this runs successfully.

@milanmlft milanmlft mentioned this pull request Aug 17, 2023
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@p-j-smith
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Still need to test whether this runs successfully.

did you have any luck getting the surface reconstruction to run?

@milanmlft milanmlft force-pushed the fix/update-fastsurfer-docker branch from 3ab544c to e486995 Compare August 17, 2023 10:52
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Still need to test whether this runs successfully.

did you have any luck getting the surface reconstruction to run?

Re-running it now an a different image. Seems to be running for longer already than previously, so 🤞

milanmlft
milanmlft commented Aug 17, 2023
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Had to change the limit-cpu value to 2 to get the containers to run on the current setup. We might consider using one of the Compute-optimized EC2 instances for the Container Service though to reduce runtimes. Or completely switch to GPU (#51).

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The FastSurfer analysis runs successfully now but there is still an issue with the output files. For some reason, XNAT fails to upload them (see screenshot), though they are present in the correct path (manually confirmed by sshing into the EC2 instance).
image

I'm going to merge this now but I'll create another issue for this problem: #74.

@milanmlft milanmlft merged commit 2ea983d into main Aug 17, 2023
@milanmlft milanmlft deleted the fix/update-fastsurfer-docker branch August 17, 2023 17:15
@milanmlft milanmlft mentioned this pull request Aug 18, 2023
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@p-j-smith p-j-smith Awaiting requested review from p-j-smith

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pydeface missing when converting NIFTI to 256 conformed MGZ file
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