search

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

RuntimeError: Could not find a task with the ID 514 #108

Closed shreyagudapati9 closed 2 months ago

shreyagudapati9 commented 4 months ago

A short summary of a question you have for the BIBSnet development team.

Problem Description

Hello, I am currently facing an issue while attempting to run BIBSNet using the following command inside a Singularity container:

singularity run --nv --cleanenv --no-home \
-B /path/to/BIDS:/input \
-B /path/to/output:/output \
/path/to/bibsnet.sif \
/input /output participant -v

Error Encountered

The command fails with the following error message :

bibsnet error

Could someone please provide guidance or suggestions on how to resolve this issue?

Thank you for your help!

dnkennedy commented 3 months ago

I also received this error...

LuciMoore commented 3 months ago

@shreyagudapati9 apologies for the delay - I'm not sure about this, have you tried rebuilding the sif image? perhaps try singularity pull bibsnet.sif docker://dcanumn/bibsnet:release-3.2.0

@tjhendrickson thoughts?

LuciMoore commented 2 months ago

@shreyagudapati9 our latest release has some massive improvements including updated models if you would like to try again. Please re-open this issue if you continue to run into this error!

scott-huberty commented 2 months ago

Re-opened at #133

scott-huberty commented 2 months ago

@shreyagudapati9 @dnkennedy see #134 .

For me the issue was that my user account did not have the necessary file permissions for folders/files inside the container that are needed by BIBSnet. Maybe you can try again after #134 lands and an updated image is pushed to DockerHub.

If you still get this error after that happens then please share, I would be interested to know because this error message Could not find a task with ID is really hard to interpret (i.e. I think many different issues could lead to this same error message), and I think we could do abetter job to try to catch these issues and raise more informative errors messages. But to do that I'd need to know what is causing the issue for you.

dnkennedy commented 1 month ago

Hi, I just reran my example with bibsnet:release-3.4.2. I no longer get the "Could not find a task with ID" error, and my process proceeds farther.

I do get a different error, however, but I guess I'll raise that as a separate issue.

scott-huberty commented 1 month ago

@dnkennedy making Progress! 🚀

LuciMoore commented 1 month ago

@dnkennedy yes please post an issue!

dnkennedy commented 1 month ago

I posted issue https://github.com/DCAN-Labs/BIBSnet/issues/137 as my new problem.