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.
I am trying to run a test where I take a pre-existing run of bibsnet [the container] (which included prebibsnet, bibsnet, and postbibsnet), and then move it to a new location, specify a new output directory, and delete the "postbibsnet" folder under the working directory. Then what I am interested in is restarting bibsnet at the "postbibsnet" stage, taking as input the original BIDS data and the working directory (again, after the postbibsnet folder has been deleted).
When I do this, the "postbibsnet" section of the code gets very close to finishing. But based on the attached error log, it seems like the code is expecting some file to be there that doesn't exist. I don't know if this is because the original derivatives folder and the work/postbibsnet folder had been deleted, or if there is some complication that has come up because the pipeline started populating the working directory under one path (for prebibsnet and bibsnet) and is finishing populating the working directory at another path (for postbibsnet). Or I suppose it could be something else more generic to the process of running the container stage by stage.
Any idea what might be going on and how this could be fixed?
"uname": executable file not found in $PATH
Traceback (most recent call last):
File "/home/bibsnet/bibsnet", line 48, in <module>
main()
File "/home/bibsnet/bibsnet", line 39, in main
run_all_stages(STAGES, sub_ses_IDs, json_args["stage_names"]["start"],
File "/home/bibsnet/src/utilities.py", line 223, in run_all_stages
sub_ses_j_args = stage(sub_ses_j_args)
File "/home/bibsnet/src/postbibsnet.py", line 73, in run_postBIBSnet
nii_outfpath = reverse_regn_revert_to_native(
File "/home/bibsnet/src/postbibsnet.py", line 557, in reverse_regn_revert_to_native
preBIBSnet_mat = glob(preBIBSnet_mat_glob).pop()
IndexError: pop from empty list
Add any additional information or context about the problem here.
audreymhoughton
commented
1 year ago
What happened?
I am trying to run a test where I take a pre-existing run of bibsnet [the container] (which included prebibsnet, bibsnet, and postbibsnet), and then move it to a new location, specify a new output directory, and delete the "postbibsnet" folder under the working directory. Then what I am interested in is restarting bibsnet at the "postbibsnet" stage, taking as input the original BIDS data and the working directory (again, after the postbibsnet folder has been deleted).
When I do this, the "postbibsnet" section of the code gets very close to finishing. But based on the attached error log, it seems like the code is expecting some file to be there that doesn't exist. I don't know if this is because the original derivatives folder and the work/postbibsnet folder had been deleted, or if there is some complication that has come up because the pipeline started populating the working directory under one path (for prebibsnet and bibsnet) and is finishing populating the working directory at another path (for postbibsnet). Or I suppose it could be something else more generic to the process of running the container stage by stage.
Any idea what might be going on and how this could be fixed?
What command did you use?
What version of BIBSnet are you using?
bibsnet_clusters-fix-2023.10.16.sif
Directory Structure
No response
Relevant log output
Add any additional information or context about the problem here.
No response