search

AICONSlab / HyperMapp3r

AICONSlab's white matter hyperintensities (WMH) segmentation algorithm using CNNs
https://hypermapp3r.readthedocs.io/
GNU General Public License v3.0
16 stars 3 forks source link

stats_wmh #4

Open bhowl opened 2 years ago

bhowl commented 2 years ago

I've had successful runs for bias_corr and seg_wmh on the files in data/test_case. However, I am unable to select a directory when running stats.wmh from the GUI.

When I run stats_wmh from the command line... hypermapper stats_wmh -i ../. -o ../wmh_vols_summary.csv I get the following error:

/home/WSL2user/anaconda3/envs/hypermapper/lib/python3.6/site-packages/nilearn/__init__.py:70: FutureWarning: Python 3.6 support is deprecated and will be removed in release 0.10 of Nilearn. Consider switching to Python 3.8 or 3.9.
  _python_deprecation_warnings()
Using TensorFlow backend.
reading  test_case
reading  test_case2
Traceback (most recent call last):
  File "/home/WSL2user/anaconda3/envs/hypermapper/bin/hypermapper", line 33, in <module>
    sys.exit(load_entry_point('HyperMapp3r', 'console_scripts', 'hypermapper')())
  File "/home/WSL2user/software/HyperMapp3r/hypermapper/cli.py", line 164, in main
    args.func(args)
  File "/home/WSL2user/software/HyperMapp3r/hypermapper/cli.py", line 41, in run_wmh_seg_summary
    summary_wmh_vols.main(args)
  File "/home/WSL2user/software/HyperMapp3r/hypermapper/stats/summary_wmh_vols.py", line 68, in main
    **cols = ['%s_Volume' % wmh_abb[0], '%s_Volume' % wmh_abb[1]]
IndexError: list index out of range**

Also, the hypermapper.log and wmh_seg_summary.log are blank even after successful bias_corr and seg_wmh runs?

Any help is appreciated! Thank you