shnizzedy
commented
1 month ago This may just be a release lag. With the current unstable image I don't hit this issue.
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 latest Docker image (sha256:8b43fb8d198cc31f7cce757fa83ca98f4cf23b5c57800a8c876043b4341d4e7e) and in v 0.4.0 & 0.5.0 installed locally, but not in the unstable docker image or if I install from the main branch.
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.
htwangtw
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
and
this
dataset_description.jsonI 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 https://github.com/bids-apps/giga_connectome/blob/f67c572238cbb1354e8ff776f013a13f4a51f8a7/giga_connectome/postprocess.py#L220 might be outdented too far, but I think I might not be hitting this error or this progress bar
if I have any
imageshere: https://github.com/bids-apps/giga_connectome/blob/f67c572238cbb1354e8ff776f013a13f4a51f8a7/giga_connectome/postprocess.py#L121