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[BUG]error message with reverse transformation in 'cellfinder_cell_standard'

See original GitHub issue

Hi Adam, I’m trying to reverse transform simulated electrode track coordinates to atlas space, with ‘cellfinder_cell_standard’ command on windows 10. Amap registration was successful previously. 190917_488_hor_coronal_10um.nii (raw images), downsampled.nii and simulated_track.xml is provided in the link. Could you take a look if I did something noticeably wrong again?

Command: (cellfinder) E:\idisco\PV_0007>cellfinder_cell_standard --cells "E:/idisco/PV_0007/190917_488_hor_11-37-36_amap/simulated_track.xml" --transformation "E:/idisco/PV_0007/190917_488_hor_11-37-36_amap/registration/control_point_file.nii" --ref "E:/idisco/PV_0007/190917_488_hor_11-37-36_amap/registration/donwsampled.nii" -o "E:/idisco/PV_0007/190917_488_hor_11-37-36_amap/registration/" -x 0.01 -y 0.01 -z 0.01

Error message appeared:

2020-05-10 00:51:35.875226: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library cudart64_101.dll
Traceback (most recent call last):
  File "e:\miniconda3\envs\cellfinder\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "e:\miniconda3\envs\cellfinder\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "E:\miniconda3\envs\cellfinder\Scripts\cellfinder_cell_standard.exe\__main__.py", line 7, in <module>
  File "e:\miniconda3\envs\cellfinder\lib\site-packages\cellfinder\standard_space\cells_to_standard_space.py", line 213, in main
    tools.start_logging(
AttributeError: module 'cellfinder.tools.tools' has no attribute 'start_logging'

Issue Analytics

State:
Created 3 years ago
Comments:11 (6 by maintainers)

Top GitHub Comments

1reaction

adamltysoncommented, May 10, 2020

It’s a bit of both. The full transform is linear (affine transform) then non-linear. To invert the full transform, we invert the affine transform and then rerun the non-linear part (in the opposite direction).

0reactions

adamltysoncommented, May 11, 2020

Closing. See https://github.com/SainsburyWellcomeCentre/cellfinder/issues/110 for the windows issue

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