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DCAN-Labs / BIBSnet

This BIDS App provides the utility of creating a nnU-Net anatomical MRI segmentation and mask with a infant brain trained model. It can easily be included in other processing pipelines and for circumventing JLF within Nibabies.
https://bibsnet.readthedocs.io/en/latest/
Apache License 2.0
4 stars 8 forks source link

Error downloading FSL in Docker build #85

Closed tikal004 closed 3 months ago

tikal004 commented 1 year ago

What happened?

The FSL download times out about half the time and the build fails. I sometimes have to rerun a build 2 or 3 times to get it to go.

Here's an example build log

What command did you use?

This is generated on dockerhub during automated builds.

What version of BIBSnet are you using?

3.0.0

Directory Structure

N/A

Relevant log output

2023-10-13T16:11:07Z #7 19.27 Downloading FSL ...
2023-10-13T16:23:50Z #7 782.9 curl: (56) OpenSSL SSL_read: Connection timed out, errno 110
2023-10-13T16:23:50Z #7 782.9
2023-10-13T16:23:50Z #7 782.9 gzip: stdin: unexpected end of file
2023-10-13T16:23:50Z #7 782.9 tar: Unexpected EOF in archive
2023-10-13T16:23:50Z #7 782.9 tar: Error is not recoverable: exiting now

Add any additional information or context about the problem here.

No response

tjhendrickson commented 1 year ago

Is this still an issue that you are running into?

tikal004 commented 1 year ago

It seems to depend on if MSI is feeling sluggish or not. I have a fix on the fsl-timeout branch that helped get past this, but it instead times out at the curl command for pulling models later on. May be worth merging anyways as it is an improvement

LuciMoore commented 3 months ago

resolved in former versions