running nirodents on ubuntu

[eriktaylor]

hello,

i am trying to run the artsbrainextraction on the Ubuntu terminal.

when i run the script, i get the error:

Could not determine the BIDS root of <{path}>. "\n', 'ValueError: Could not determine the BIDS root of . Only files under a subject directory are currently supported.

Also, how can the script be run from python? I followed the example, tutorial.ipynb notebook, but i get the following error with code from the tutorial notebook:

from ratants_clean import init_brain_extraction_wf
ModuleNotFoundError: No module named 'ratants_clean'

[eilidhmacnicol]

Hi @eriktaylor - thanks for your message.

Can you please provide an example of the command line you are using which gives you the BIDS root error? Have you tried assessing your directory structure with the BIDS Validator? Otherwise, we know of an issue (#46) that has yet to be addressed which means that the file passed needs to have an absolute path. While this would be a trivial change, we are still a small team and we have had some bigger issues taking precedence.

> from ratants_clean import init_brain_extraction_wf
ModuleNotFoundError: No module named 'ratants_clean'

Thanks for spotting this - it is an outdated version that needs updating ASAP. The brain extraction workflow can now be found in nirodents.workflows.brainextraction:

nirodents/nirodents/workflows/brainextraction.py

Line 44 in e8600b7

def init_rodent_brain_extraction_wf(

Thus, it would be called using:
from nirodents.workflows.brainextraction import init_brain_extraction_wf

[eilidhmacnicol]

Okay, the tutorial has been updated.

Let me know re: BIDs directory