UnboundLocalError: local variable 'connectome_path' referenced before assignment #164
Comments
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This may just be a release lag. With the current I also hit Traceback (most recent call last):
File "/usr/local/bin/giga_connectome", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.9/site-packages/giga_connectome/run.py", line 127, in main
workflow(args)
File "/usr/local/lib/python3.9/site-packages/giga_connectome/workflow.py", line 90, in workflow
run_postprocessing_dataset(
File "/usr/local/lib/python3.9/site-packages/giga_connectome/postprocess.py", line 213, in run_postprocessing_dataset
gc_log.info(f"Saved to:\n{connectome_path}")
UnboundLocalError: local variable 'connectome_path' referenced before assignmentin the current I don't know what your release cycle is like, but I think these bugs have been addressed but the fixes haven't yet been released. |
shnizzedy
changed the title
UnboundLocalError: local variable 'connectome_path' referenced before assignment
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I would like to quickly touch upon the release cycle - the JOSS submission was a long time ago, when we completed some major data processing. At that time, we did have everything updated. However it took a few months before review started. As a collaboration aims to integrate new fMRIPrep versions and better understanding of downstream use cases, I started working on 0.6.x with a new output layout with community feedbacks. The user group is not huge so I don't have a release cycle in mind. |
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Are you thinking 0.5 or 0.6 (or something else) for the JOSS publication? |
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0.5! |
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Okay, I'll rename this issue to reflect a 0.5 fix 👍 |
shnizzedy
changed the title
What version of the bids app were you using?
0.5.1.dev0+gd97c669.d20240412 / docker://bids/giga_connectome@sha256:8b43fb8d198cc31f7cce757fa83ca98f4cf23b5c57800a8c876043b4341d4e7e
Describe your problem in detail.
Running
docker run --rm -it -v $PWD:$PWD bids/giga_connectome:latest $PWD/fmriprep $PWD/docker participant --atlas Schaefer20187Networksona filetree that looks like this
this `dataset_description.json`
{ "Name": "fMRIPrep - fMRI PREProcessing workflow", "BIDSVersion": "1.4.0", "DatasetType": "derivative", "GeneratedBy": [ { "Name": "fMRIPrep", "Version": "20.2.7", "CodeURL": "https://github.com/nipreps/fmriprep/archive/20.2.7.tar.gz" } ], "HowToAcknowledge": "Please cite our paper (https://doi.org/10.1038/s41592-018-0235-4), and include the generated citation boilerplate within the Methods section of the text.", "SourceDatasets": [ { "URL": "https://doi.org/", "DOI": "" } ], "License": "" }I get
this output
What command did you run?
docker run --rm -it -v $PWD:$PWD bids/giga_connectome:latest $PWD/fmriprep $PWD/docker participant --atlas Schaefer20187Networksfrom/Users/jon.clucas/JOSSDescribe what you expected.
Either success or an error relating to the inputs provided.
I think
giga_connectome/giga_connectome/postprocess.py
Line 220 in f67c572
if I have any
imageshere:giga_connectome/giga_connectome/postprocess.py
Line 121 in f67c572
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