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medec021
เข้าร่วมเมื่อ 22 ส.ค. 2007
Lung tumor segmentation in a chest CT with 3D Slicer and Local Threshold effect
This short video shows a technique to segment a lung tumor in a chest CT with 3D Slicer.
Run the dataset through the Lung CT Segmenter with airway segmentation and AI TotalSegmentator lung basic.
This will give you the lungs, lobes and the unelegant airway.
If you do not need the lungs or lobes skip this part. But at least admire the quality that AI can segment the lobes from these noisy data.
Then open 3D Slicer and go Segment editor and follow these steps very carefully.
- Disable the upper lobe
- Select the “tumor” segent
- Make it visible (check the box)
- Select the local threshold effect
- Allow Overlap
- Set minimum diameter to 3 mm
- Now the most important part: Adjust the threshold in a way that only bones and the tumor are flickering. (-339 to 3071)
- Then CTRL + left click into the tumor and wait.
- This clip is unedited.
- You will have to do some postprocessing to remove the vascular “fingers” from the tumor.
www.slicer.org/
github.com/rbumm/SlicerLungCTAnalyzer
Run the dataset through the Lung CT Segmenter with airway segmentation and AI TotalSegmentator lung basic.
This will give you the lungs, lobes and the unelegant airway.
If you do not need the lungs or lobes skip this part. But at least admire the quality that AI can segment the lobes from these noisy data.
Then open 3D Slicer and go Segment editor and follow these steps very carefully.
- Disable the upper lobe
- Select the “tumor” segent
- Make it visible (check the box)
- Select the local threshold effect
- Allow Overlap
- Set minimum diameter to 3 mm
- Now the most important part: Adjust the threshold in a way that only bones and the tumor are flickering. (-339 to 3071)
- Then CTRL + left click into the tumor and wait.
- This clip is unedited.
- You will have to do some postprocessing to remove the vascular “fingers” from the tumor.
www.slicer.org/
github.com/rbumm/SlicerLungCTAnalyzer
มุมมอง: 525
วีดีโอ
Colorize CT volume rendering with 3D Slicer and TotalSegmentator
มุมมอง 2669 หลายเดือนก่อน
This short clip shows how to colorize a CT volume rendering (3D Slicer demo sample) using a TotalSegmentator segmentation source. www.slicer.org/ github.com/wasserth/TotalSegmentator
Automatic lung, airway and vesselmask segmentation with Lung CT Segmenter and 3D Slicer
มุมมอง 67610 หลายเดือนก่อน
Explore the streamlined process of segmenting lungs (using lungmask), airways (via local threshold), and vessel masks in the latest 3D Slicer 5.4.0, as showcased in this informative video. To effectively follow along, ensure you have a high-performance computer equipped with an NVIDIA GPU boasting a minimum of 12 GB of video RAM. For optimal performance, our demonstration uses: - NVIDIA GeForce...
Lung and lobe segmentation with "lungmask" AI in 3D Slicer
มุมมอง 4.4K2 ปีที่แล้ว
This video shows how to do an AI lung, lobe, and local threshold (GrowCut) airway segmentation in 3D Slicer with a few mouse clicks. One tracheal markup has to be placed in the CT dataset only. We use the Lung CT Segmenter module from Slicers Lung CT Analyzer extension to combine all this user-friendly. For processing an Nvidia GPU and "CUDA enabled" are strongly recommended. Pytorch must be in...
Lung volume rendering in 3D Slicer
มุมมอง 1.2K2 ปีที่แล้ว
This is an unedited short demo of how to use volume rendering to display the lungs and airways in 3D Slicer. Slowly on purpose. I am using a 3D Slicer COV-19 demo dataset, with patient´s permission.
Segmenting a lung nodule with 3D Slicer and "Local Threshold"
มุมมอง 2.6K2 ปีที่แล้ว
Short clip on how to segment a lung nodule with 3D Slicer and it´s "Local Threshold" Segment Editor Effect. #shorts #memo
How to enable and disable the 3D cube and label in 3D Slicer
มุมมอง 7362 ปีที่แล้ว
This video shows how enable and disable the orange 3D cube and the 3D labels in 3D Slicer. #shorts #memo
How to enable GPU volume rendering in 3D Slicer
มุมมอง 9052 ปีที่แล้ว
This video compares CPU and GPU volume rendering in 3D Slicer and an easy way to switch between the two. #shorts #memo
Easy lung mask generation including airway segmentation with LungCTSegmenter and 3D Slicer
มุมมอง 2.5K2 ปีที่แล้ว
This video shows how easy it is to do a CT lung mask segmentation including an airway segmentation in 3D Slicer. The LungCTSegmenter extension, part of the LungCTAnalyzer, now implements a call to the airway segmentation module of the Chest Imaging Platform. Three kernel modes allow for very detailed, detailed, and less detailed but leak-resistant segmentations. LungCTAnalyzer: github.com/rbumm...
"Tilt Lock" in 3D view of 3D Slicer by Ctrl + "b"
มุมมอง 1983 ปีที่แล้ว
Segmentations easily tumble in 3D Slicers´s 3D view. In Slicer version 4.13, you can toggle the rotation to the azimuth axis only by pressing Ctrl "b". Enjoy.
How to serially smooth segmentations in 3D Slicer
มุมมอง 4583 ปีที่แล้ว
This is a short demonstration of how to serially smooth segmented vertebrae within 3D Slicer by using the new "Apply to all segments" checkbox. This feature will be available in the stable release of 3D Slicer 4.13 and can already be tested in the nightly builds.
How to serially grow vertebral body segmentations in 3D Slicer with the "Margin" Effect
มุมมอง 5033 ปีที่แล้ว
This is a short demonstration of how to serially grow segmented vertebra within 3D Slicer by using the new "Apply to all segments" checkbox. This feature will be available in the stable release of 3D Slicer 4.13 and can already be tested in the nightly builds.
Airway segmentation in 3D Slicer with "Grow from Seeds"
มุมมอง 20K3 ปีที่แล้ว
This video shows my current workflow for semiautomatic airway segmentation using 3D Slicer 4.11.20200930, Slicers´s "Segment Editor" and the "Grow from Seeds" function. The technique requires approximately 15 minutes of manual work. www.slicer.org
Volumetric COVID-19 lung CT analysis with 3D Slicer
มุมมอง 2.5K3 ปีที่แล้ว
This video shows how to create a volumetric analysis of a COVID-19 lung CT using the free and open-source medical imaging software 3D Slicer. The process involves the "Lung CT Analyzer" extension which uses Slicer´s "Segment Editor" with predefined thresholds. Before calling the "Lung CT Analyzer" lung masks need to be produced with Slicer´s "Lung CT Segmenter" as shown here: th-cam.com/video/U...
Easy creation of lung masks from lung CT in 3D Slicer
มุมมอง 3.3K3 ปีที่แล้ว
Easy creation of lung masks from lung CT in 3D Slicer
Thank you very much !!!!!
Splendid! 🤩
Thank you!!
could you create a video on segmenting the cervical articular pillar please!
Please see here: th-cam.com/video/wMMi0QIrCvc/w-d-xo.html - should be also working for the cervical pillar ...
@@rudolfbumm8126 I`m an undergrad student! Segmenting exactly that part has become a tough task for me. It's actually for my project. I have seen the link you attached but wasn't really helpful though.
Very nice segmentation method, neatly explained, thank you!
Hey, thanks for a great video, although I keep getting hideous results with the airways. I appear to be adding too much maybe?
Hi, if you need help please post a question, preferably with a link to this youtube video and an image of the segmentation result, here: discourse.slicer.org/c/support/11
@@rudolfbumm8126 Thank you I am just redoing the segmentation again now and will send you an image if I have the same problem. Thank You :)
@@rudolfbumm8126 Hi again I have posted a question at the above link, thanks Sandie
Dear medec021, thank you very much for this tutorial. Do you provide a tutorial, how to serially segment the vertebral bodies? Is there an automatically function, or does each vertebral body has to be segmented "manually"?
Hi Siegmund, please ask this question under "support" in Slicers discourse forum discourse.slicer.org/c/support/11 (maybe with a link to this youtube video) so I can answer in public and the answer is found by the community. Thanks.