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Julian-Wyatt / AnoDDPM

CVPR Workshop paper - AnoDDPM: Anomaly Detection with Denoising Diffusion Probabilistic Models using Simplex Noise
https://julianwyatt.co.uk/anoddpm
MIT License
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What is a directory raw_cleaned ? #23

Closed beautifulchair closed 7 months ago

beautifulchair commented 11 months ago

In dataset.py, a directory raw_cleaned is used. I would like to know how to ready the directory. I understand that I can ready a directory raw by readying ./DATASETS/CancerousDataset/EdinburghDataset and running dataset.py, but this make a raw_new directory. What is the difference between raw_new and raw_cleaned?

Julian-Wyatt commented 11 months ago

If memory serves, the raw_cleaned is the cleaned MRI scans outputted by the BrainSuite program. Raw_new should be the actual volumes before the cleaning step. Let me know if this helps

beautifulchair commented 11 months ago

Thank you for your replying. What is the BrainSuite program? Is it contained in this repository?

Julian-Wyatt commented 11 months ago

Listed in the datasets section of the paper: Section 3.6. We use the brainsuite program for preprocessing; this open source software can be found here: https://brainsuite.org

beautifulchair commented 11 months ago

Thank you very much! I will try it.

beautifulchair commented 11 months ago

I installed BrainSuite app, but I don't understand detail of the cleaning preprocessing. I want to reproduce your work. Do you have detail of the processing, or have some metrics of Experiment with raw datasets before the cleaning step?

I tried with app's default setting, but it didn't go well.

setting about preprocessing
beautifulchair commented 10 months ago

@Julian-Wyatt I look forward to hearing from you.

Julian-Wyatt commented 10 months ago

Hi If memory serves our paper highlights that we just perform skull stripped and non uniformity corrections; performing those two and saving should output similar images to what I used.