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Can't run GUI due to docker related error #11
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Just for debugging, commented the Traceback (most recent call last):
File "/home/ajw/.local/anaconda/bin/rsHRF", line 8, in <module>
sys.exit(main())
File "/home/ajw/.local/anaconda/lib/python3.9/site-packages/rsHRF/CLI.py", line 442, in main
run_rsHRF()
File "/home/ajw/.local/anaconda/lib/python3.9/site-packages/rsHRF/CLI.py", line 152, in run_rsHRF
from .rsHRF_GUI import run
File "/home/ajw/.local/anaconda/lib/python3.9/site-packages/rsHRF/rsHRF_GUI/__init__.py", line 1, in <module>
from . import core
File "/home/ajw/.local/anaconda/lib/python3.9/site-packages/rsHRF/rsHRF_GUI/core/__init__.py", line 1, in <module>
from .core import Core
File "/home/ajw/.local/anaconda/lib/python3.9/site-packages/rsHRF/rsHRF_GUI/core/core.py", line 5, in <module>
from bids.grabbids import BIDSLayout
ModuleNotFoundError: No module named 'bids.grabbids'
So it is not related to docker, but to the lack of this module. I'll investigate further.
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It seems the problem is that "The grabbids module has been renamed to layout and BIDSLayout.py and BIDSvalidator.py are now layout.py and validation.py, respectively." Changing by
in |
Hey @aweinstein, thank you very much for letting us know about this issue. It indeed was a problem with the BIDSlayout, as we're using a newer version of Pybids in the latest update of the toolbox. However, we forgot to implement this change into the GUI scripts. The GUI should now start up. Take note that for the BIDS version of the GUI, you will need to select the folder where your subjects folders are stored. For example : path/derivatives/fmriprep. Furthermore, the BIDS-data requires at minimum the following entities
P.S : As an alternative you could use the GUI of matlab (as it offers more options than the python version at the moment), or the commandline version in python using the docker/GUI, as the current rsHRF build of those has passed unit tests through the CircleCi. |
Thank you @NigelCol for looking into this. Actually, I am not planning to use the GUI. I just wanted to check that the library was working, and I thought that running the GUI would be the easiest way to do that. So it seems that my cumbersome approach was useful to find this bug :) . Thank you for sharing this project with the community. |
I just installed rsHRF in a Linux machine with an Anaconda installation, using
pip install rsHRF
.rsHRF was installed without a problem. However, if I run
rsHRF --GUI
, I get the errorrsHRF: error: --GUI should not be used inside a Docker container
, although, as far as I know, I'm not running rsHRF inside a Docker container.The text was updated successfully, but these errors were encountered: