Closed dualon closed 3 years ago
@dualon Thanks for reporting this!
Indeed, right after the release of v3.0.0-RC2
, there was a bug in checking the availability of modalities that I corrected in commit 80fbee226e64d8e7fe72bfa9639eaffd73c0939c , where I use now pybids
instead the DiffusionPipeline.check_inputs()
to check for modalities:
https://github.com/connectomicslab/connectomemapper3/blob/10e78d98d9a4a25c8872c7c5be7a873cc55438ab/cmp/bidsappmanager/gui.py#L913-L961
Looking at the error traceback
File "/home/dualon/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/bidsappmanager/gui.py", line 919, in __init__
gui=False)
File "/home/dualon/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/pipelines/diffusion/diffusion.py", line 516, in check_input
shutil.copy(src=dwi_file, dst=out_dwi_file)
make me think you are the commit tagged with v3.0.0-RC2
where the check_input()
function is still being used.
Moving to the latest commit 10e78d98d9a4a25c8872c7c5be7a873cc55438ab on the master branch (git checkout 10e78d98d9a4a25c8872c7c5be7a873cc55438ab
) and reinstalling the GUI ((py37cmp-gui) $python setup_gui.py install
) should make it working.
Let me know.
Dear Sébastien, Thanks a lot for the prompt support. I was indeed on RC2, checking out the fix and reinstalling the GUI (this part I missed earlier) has fixed the problem. I closed the issue with my comment, hopefully that's okay with you.
@dualon Great! You're welcome !
Hi
CMP3 seems to fail to create the DTI derivative. Steps to reproduce:
RC1 worked before I reinstalled my PC, which makes the whole story more cryptic. RC1 does not function now either. File permissions are OK. The "code" subdirectory with the config files is also created flawlessly.
How to fix it? :)
See the system info below. I am happy to provide further information upon request.
Kubuntu 20.10. Docker and CMP were installed as described in the documentation. The home folder sits on a different drive as the connectomemapper3 directory.