`get_dir` gets thrown off by created `seg-` folder about trailmap HOT 7 CLOSED

To make sure I am understanding this right, when you ran segment_brain_batch.py on our example-chunk, the seg-example-chunk folder was inside the example-chunk folder?

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Yes, that is correct. And it only was called seg- (without the -examaple-chunk bit at the end.
This is invoking the example from the top-level folder of the repo using the command given in the readme.
Note however, that I previously also experienced a different behaviour (with the new folder created at the same level as the example-chunk folder). However, I don't recall what I did differently then (maybe invoked the command from a different working directory).
In any case it is working for me now when I restrict reading to tiff files.

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closed by accident (clicked the wrong button).

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This is very weird behavior. I will try to recreate the issue and find out why this could be happening. Thank you for finding this issue.

Please let me know if you have anymore concerns.

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Sorry for the delay, but I found the issue was due to trailing slashes in the input_folder name. I have fixed the issue now.

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Thanks

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just a comment ... I highly recommend using pathlib.Path instead of os.path functionality these days, as it basically eliminates this sort of error.

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