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BrainLesion / tutorials

BrainLes tutotrials
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Two minor changes in AURORA/tutorial.ipynb #29

Closed brunotakara closed 7 months ago

brunotakara commented 8 months ago

Hello, I have successfully ran tutorials in Google Colab by following your instructions. I had to add two minor changes in code so it could run without popping erros, I will write them down here but I am not sure if it was with my Colab's configs or if it will affect other users as well.

1º - Before calling utils.visualize_data() in Data section, I had to run cd tutorials/AURORA because the function wasn't finding the t1.nii.gz file because root was on '../content/'

2º - In NumPy Inputs/ Outputs and Multiple input modalities and other available outputs sections it links to the original BRATS dataset file names instead of the ones provided on tutorial, so I exchanged it to the corresponding names in data folder:

Multiple input modalities and other available outputs section:

_ = inferer.infer(
    t1="data/t1.nii.gz",
    t1c="data/t1c.nii.gz",
    t2="data/t2.nii.gz",
    fla="data/flair.nii.gz",
...

As well as in NumPy Inputs/ Outputs section: t1_np = nib.load("data/t1.nii.gz").get_fdata()

Thanks for sharing your work! Everything is clear and easy to follow!