bhklab / med-imagetools

Transparent and reproducible medical image processing pipelines in Python.

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ValueError on head-neck-pet-ct AutoPipeline demo

skim2257 opened this issue · comments

Error when running examples/process_quebec.sh

Processes two patient samples in: https://github.com/bhklab/tcia_samples/Head-Neck-PET-CDT

Traceback (most recent call last):
  File "/cluster/home/sejinkim/pkgs/imgtools/imgtools/autopipeline.py", line 205, in <module>
    pipeline.process_one_subject(subject_id)
  File "/cluster/home/sejinkim/pkgs/imgtools/imgtools/autopipeline.py", line 112, in process_one_subject
    self.graph.loc[subject_id, f"size_{output_stream}"] = image.GetSize()
  File "/cluster/home/sejinkim/miniconda3/envs/imgtools/lib/python3.8/site-packages/pandas/core/indexing.py", line 692, in __setitem__
    iloc._setitem_with_indexer(indexer, value, self.name)
  File "/cluster/home/sejinkim/miniconda3/envs/imgtools/lib/python3.8/site-packages/pandas/core/indexing.py", line 1635, in _setitem_with_indexer
    self._setitem_with_indexer_split_path(indexer, value, name)
  File "/cluster/home/sejinkim/miniconda3/envs/imgtools/lib/python3.8/site-packages/pandas/core/indexing.py", line 1688, in _setitem_with_indexer_split_path
    raise ValueError(
ValueError: Must have equal len keys and value when setting with an iterable

Steps to reproduce:

  1. clone master branch
  2. sh examples/process_quebec.sh