Whole heart segmentation from cardiac CT in 10 minutes

Segment cardiac CT using free software - 3D Slicer (www.slicer.org):
- Download 3D Slicer: download.slicer.org/
- Download sample data set from github.com/Slicer/SlicerDataS... and rename the file to CTA-cardio2.nrrd
- More tutorials: www.slicer.org/wiki/Documenta...
- Post any questions to Slicer forum: discourse.slicer.org
Sound recording is noisy. Enable closed captioning (click CC icon) to see transcript.

[@danieltalavera9847]

Good job, thanks for explaining it. This is really useful

[@ramongonzalez5484]

I think this is a great video.Maybe the first time we can see how to use "Grow from seeds" tool,for cardiac segmentations .Thanks for sharing¡¡ Any teaching will be very welcome

[@DamienDesign]

Thank you very mush you saved my project in 3d modeling !!!!

[@user-ye9lf4bh7s]

Thanks for the sharing, it's really helpful

[@kemuscollins3010]

thanks for your sharing!

[@ts6603]

respect for seeing the actual parts of the heart out of the ct. needs some experience

[@PerkLabResearch]

Yes, you need to spend a few hours looking at anatomy pictures and CT slices to learn how each structure appears in the CT image. Actually, segmenting the image and looking at 3D reconstructions helps a lot in learning the anatomy.

[@Scar_lord03]

very good work :d

[@nadiadalessandro771]

AMAZING

[@denicho9162]

Mantap, salam dari atma jaya jogjakarta

[@user-ku1wg9co8c]

Nice video! congratulations! I need help, In my segmention editor, the paint function aren´t working, what could be happening?

[@Laureatkabdb]

Thanks for sharing! How can I cite the file that you povided under this video?

[@PerkLabResearch]

If you want to cite a paper then you could use SlicerHeart (github.com/SlicerHeart/SlicerHeart#how-to-cite). If you want to cite the segmentation procedure then probably you should refer to the URL of the youtube video. If you want to cite the data set then you can refer to it as the CTA-cardio2 data set in 3D Slicer Data Store - github.com/Slicer/SlicerDataStore

[@sujaybalebail3556]

Great video! I downloaded the sample data and attempted to segment out the heart on Slicer 4.10.2. My heart appears a lot more grainier than yours. Could you please explain where I could have potentially gone wrong? I tried to follow the video as closely as possible.

[@sujaybalebail3556]

I figured it out! I was watching the segmentation preview!

[@PerkLabResearch]

@@quratulain7936 You can find the download link in the video description ("Download sample data set").

[@minhaanees276]

@@PerkLabResearch can you make a other video how to recognise heat part

[@FeroxWJB]

How did you get the images to load with the cardiac axes displayed?

[@AndrasLasso]

Do you mean the L/R/A/P/I/S axis labels in the 3D view?

[@FeroxWJB]

@@AndrasLasso Disregard. For some reason my default was changed.

[@minhaanees276]

thank you so much which version are support for clinical data 5.01 not support The sample in the description are not work

[@AndrasLasso]

Slicer GUI is continuously evolving. If you get stuck at any specific point then let us know. I've update the download link to the sample image.

[@minhaanees276]

@@AndrasLasso oo thank you so much I have done

[@minhaanees276]

@@AndrasLasso but the data is not working please check it

[@AndrasLasso]

@@minhaanees276 Follow the instructions in the description - rename the file to CTA-cardio2.nrrd after download is completed. We moved hosting of sample data sets to GitHub releases and unfortunately, we cannot have both hash-based and human-readable filenames at the same time. Maybe we'll find some other file hosting solution in the future but for now the manual renaming is necessary.

[@weert7812]

The link on slicer no longer provides the heart file

[@tamilkirikan]

Have you installed any plugins or extensions?

[@AndrasLasso]

SegmentEditorExtraEffects extension was installed to have Surface Cut effect (only used for heart outside surface).

[@hooikajing5742]

What's the different of red, yellow and green view?

[@PerkLabResearch]

They are cross-sectional views in 3 different orientations (axial, sagittal, coronal)

[@francescaflore9318]

The link for download sample data doesn't work. How can I find it?

[@takerrazer120]

I also searching but cant find

[@maxla9691]

I cannot download the data set, can you please tell us how to do?

[@PerkLabResearch]

You can download the dataset from the link and then - important! - rename it, according to the instructions in the video description.

[@maxla9691]

​@@PerkLabResearch Thank for the answer. I missed the renaming part. Sorry about that.

[@user-gl3tp4lu3y]

Could you share a cardiac ct data, thank you!

[@AndrasLasso]

You can find download link in the description.

[@user-gl3tp4lu3y]

Andras Lasso Thanks

[@FocUS_Studies]

I would recommend a microphone for future videos. The audio quality is not the best.

[@JoseLuis-vf1hj]

I can´t see the data... do you can show this information?

[@PerkLabResearch]

You can find the download link in the video description ("Download sample data set").

[@JoseLuis-vf1hj]

@@PerkLabResearch broken link

[@PerkLabResearch]

@@JoseLuis-vf1hj I have tested the link and it works well. You can also download the data set within 3D Slicer: go to Sample Data module and click on CTACardio data set.

[@JoseLuis-vf1hj]

@@PerkLabResearch ok .... thank you

[@lauraj1427]

@@JoseLuis-vf1hj it's broken for me too

[@nicolecristiano3013]

Hello, I have some questions. 1. Which hardware do you use to run this app this fast? 2. Which one and how many graphic card do you use in your software? 3. How do you make work the graphic card on the app? I will appreciate all this answers. Thank you

[@AndrasLasso]

The algorithms are highly optimized, so you don't need a fast computer. The video was captured on a 4-year-old desktop PC (Intel i7 6700K CPU, NVidia GTX 1060 GPU - the GPU does not matter much, as all intensive computations are performed on the CPU).

[@nicolecristiano3013]

@@AndrasLasso thanks for the answer. Could you tell me which algorithms are you talking a about? Properly of the app or about what? Thanks

[@AndrasLasso]

Hardware requirements of the application are quite modest. The only hard requirement is that the graphics card must support OpenGL 3.2 or better. This is fulfilled on all computers bought in the last 5 years.

[@nicolecristiano3013]

@@AndrasLasso how long does it take to process a 3d segmentation image? I mean, perhaps 2 minutes is the normal time and I am thinking it is too much... thanks

[@AndrasLasso]

@@nicolecristiano3013 See timings in the video. Automatic updates based on manually specified seeds takes a few seconds.

[@jasongellis1408]

Can't understand what you're saying for at least half of this video

[@AndrasLasso]

Yes, I know, the recording was noisy and my accent is thick. Enable close captioning (click CC icon) if you are interested in what I'm saying.

[@ezproxylele3652]

3D Slicer is very useful for me. Thanks for ur works of slicer.

[@akhiltadiparthi4612]

I feel u bro

[@drfaridonamdjadi7516]

Not clear at all and it is better deleting

[@AndrasLasso]

Enable closed captioning (CC).

[@denicho9162]

Jahat bro