Ali Khan
Ali Khan
Atlas generation is working now, and a newly made hcpUR100myelin template has been generated and pushed to hippunfold-atlases (uses curvature, gyrification, thickness, myelin).. note this atlas must be used with...
Sorry I've been swamped with things haven't been able to bring my attention back to this.. Hoping to get some stuff off my plate this week so I can attend...
Ah the --derivatives flag can just point to the temporary bids folder that you create, so it doesn't need to be a user CLI option. In the dict for modalities...
an example is in the dry run file: ./hippunfold/run.py test_data/bids_dsegtissue test_out participant -np --modality dsegtissue --derivatives test_data/bids_dsegtissue
Closed with #449
No, it looks like like the problem is stemming from the local python environment getting picked up and having conflicts: File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr My recommendation is to...
Recall that the -e flag only clears the environment variables, ie it doesn't control what is on your filesystem. If python sees ~/.local/lib/ it tries to look for packages there..
Ie it is not coming from the environment variables but from the files on the filesystem
ah didn't know about that env var -- yes can be set in the dockerfile -- ~note you would also have to set SINGULARITYENV_PYTHONNOUSERSITE (and for future-proofing maybe: APPTAINERENV_PYTHONNOUSERSITE)~ (nevermind...
just looping back so we can close this if possible -- did this correct the issue @MaeligChauvel ?