Preprocessing 3D Volumes for Tumor Segmentation using PyTorch and MONAI | Part 1/2

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In this video, you will learn how to preprocess 3D volumes (Nifti files) for tumor segmentation tasks, as well as how to use them for organ segmentation and classification tasks.

Monai is an opensource framework based on PyTorch that I used during my internship and found very useful, so I wanted to share my experience with you.

🆕 Learn how to effectively manage and process DICOM files in Python with our comprehensive course, designed to equip you with the skills and knowledge you need to succeed.

• This is the second part, enjoy !

• Code and explanation in this link:

• Subscribe to my newsletter here:

• Here is the link to the documentation:

• Create nifti volumes from group of dicom files:

• Convert dicom files into JPG or PNG:

• Convert JPG or PNG images into dicom files:

• Please visit my website for blogs about my work:

• Visit my store for the effects I use in my videos:

• My bio links here:

Time lapes:
• 00:00 : Introduction
• 01:27 : Tools we are using
• 05:50 : Importing the data
• 27:05 : Defining the functions for the transformations
• 41:00 : The dataloader

#pycad #python #computervision #pytorch #monai
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Learn how to effectively manage and process DICOM files in Python with our comprehensive course, designed to equip you with the skills and knowledge you need to succeed.

pycad
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Thank you I have been searching for this for a long time

mardeenosman
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Great Videos, helps me a lot to get in touch with pytorch and monai

JimBob-lqdb
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It was really helpful, thank you very much.

NikooMoradi
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Can you please share the dataset you have used in this video for the viewers to practice along as you code ?

ezhil
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should i keep the data set in nifti format not dcom?

chillradio
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Hi. As far as I know for 3D images (x. y, z) its not height, width, number of slices. Most of the time, the x direction refers to going left/right on an image, y refers to front/back (or anterior/posterior), and the z direction refers to up/down (superior/inferior). but ur tutorials are great.

fffgization
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Hi

Thanks for sharing this tutorial
Can you make tutorial on training a segmentation model using Monai

kumarsai
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Hi, Thanks for your video. Could you please explain more about four folders of Trainimages, Trainlables, Valimages and Vallables? I followed all the videos regarding the liver segmentation, but when got here I completely lost. you were talking about creating nifti files folder and suddenly jumped into four folders. what are difference between them? Is training folder the same files of niftifolder? what about validation data? where do they come from?

mahdiebehjati
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thanks a lot, can you please make more of these for monai

akainu
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can you explain.what labels exactly are

MuhammadMaab-osgu
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Can you talk in detail about the 4 files TrainData, TrainLabels, ValData, ValLabels? For example how different it is

truongtuankhue
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How can we have the dataset? Thank you for your nice video.

nghethuatsong
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Hey, can you tell me which organ you are working on in this video for segmentation of tutor

favoritetroll
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Is there any way to download the .nii files used in this example to try to replicate it locally?

nayrapumar
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Hey. Nice video, thanks a lot for share. Can you guide where we can find a free dataset to try it ?

cinthiakleiner
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Hello sir, while doing the code of pre-processing part, i have encountered an issue "FutureWarning: <class Class `AddChannel` has been deprecated since version 0.8. please use MetaTensor data type and instead.
warn_deprecated(obj, msg, warning_category)"
After this i have replaced the AddChanneld to EnsureChannelFirstd and also imported the library of MetaTensor. while executing above scripts, my kernel was dead and it doesn't reflecting any thing other than this. Even i dont know where i have to use the metatensor library. Kindly help me resolving this issue sir.

abhinavkumarmishra
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Brother l need medical image data set can you please help in this regard

Nature_Traveller-PR
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Hi! Nice tutorial.
Could you please help me with 3D tooth segmentation. I have 3D CT images of teeth and it is in the .STL file format. I don't know how to preprocess it. Couldn't find much help from Google search.

If I can get any help from you, I'll be very grateful.

anima_kujur
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Can anyone tell me how to download the image files

karthis