Python AI Organ Segmentation Tutorial

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Code:

Relevant Libraries/Software:

[cwtrain]

Wow. This video is almost down to the pennies precisely what I do at my cancer institute. Only I'm attempting to spot tumors with edge-detection nightmares working in 3D space with DICOM slices.

This is absolutely excellent. I'm going to send this video to every single person that asks me: "So what do you do for work?"

[emrek]

I feel like most people in the comments didn't try coding. I tried to replicate the same working environment but encountered countless conflicts. I know these things are a bit of luck but I don't think everyone is so lucky.

[VALedu]

'some other key ' = 42. I am sold. Wonderful video

[ApteraEV]

Since Google is monitoring comments for Keywords... I'll say, thanks for the A.i. content, I'm an aspiring Biomedical Engineer type guy.❤

[ravikrishnakanakamedala]

Wow it's great job for patients for india 🇮🇳

[josephmargaryan]

Wow, great, inspirational. I'm doing a bachelor's thesis on image segmentation on the thyroid. I wish to be as good as you one day.

[fnymrvl]

Bro am doing research in radiology and I love you <3

[lampooner_no_]

There’s a lot of cool segmentation software out there! Recently I’ve been looking at PyRadiomics, maybe there is some interest here to do a video on it.

[daddul]

So helpful, thank you very much for your work!

[inhibited]

got an error from:


found and used :
model.load_state_dict(torch.load(model_path,
that worked

[domillima]

Great video. Hoping you make more in this series. Very instructive. I noted you have 3D slicer on your windows task bar. Say I have a limited number of MRIs in which I want to segment the prostate (using this example since it came up in the video) as a whole gland as well as a specific subsection of the prostate representing a lesion. How can I use slicer to segment these images and then have these segmentations fed into python? Then how would I go about including the features of the segmented area in a model (along with, say, clinical features of the patient and disease) to predict some annotated clinical outcome like cancer recurrence?

I know this is not an easy question but if you're willing to make some more content on this, it would be awesome. Even start with some background information or pointing me towards some sources. Thanks!

[Yalchin]

I think model name change or there are some issues in donwloading the model I mean wholebody_ct_segmentation downloading part

[realchrisward]

This looks incredibly powerful, thank you for sharing. Do you have any advice for how to address the problem that the model/mask is missing parts of organs. Is it just retraining or do the tools also include the ability to manually curate and refine to rois (as an example, it looks like the brain missed a good chunk of one of the hemisphere?)

[leon_noel]

No rap in the beginning? I'm out!

[agustinsaturni]

Do you know how this model works when you "import" a Pelvis CT??? Is it able to recognize the parts of the pelvis or this model only works with Whole body CTs?

[ahmedel-sinousy]

after some search based on what I found, MONAI label is no longer used for segmenting organs. they developed model called 'TotalSegmentor' that is used for this stuff right now. I'm not sure from my info so don't take it as real one if oy trying to segment organs too. I tried code in the notebook but faced problem when trying to download the model. error told that he can't find the http server. so, I tried to use it from 3d slicer itself but found the same problem when trying to use the server itself in MONAI label extension.

[thoughtsbright]

Hey man I do rly wanna to get to this level in python I am a beginner and i am never consistent, so what I do?

[inhibited]

tried using my own ct scan dataset after getting his example to execute for me. "CT = image_loader(CT_folder)" wouldn't work with the following error "InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM'" . Weird. Maybe the ct scan in the hospital has different settings.

[idmtusr]

Thanks for the great tutorial. Can this also be used for CT images of the chest area only?

[tahabukhari]

Is the offer for the UDEMY course going to be available again in the future?