3D Slicer Tutorial #3: Scissors. Grow from seeds.

3D Slicer 4.10.2 on Windows 10
Recorded by Dr. Jan Witowski: janwitowski.com
00:00 Standard View
00:30 Show 3D
02:22 Scissors
05:02 Grow from Seeds
06:50 Processing
08:28 Refining results

[@sajadamiri8797]

thanks too much , god bless you , and also I want to appreciate your great work in my mother language : خیلی از شما ممنونیم افراد بزگی مثل شما کمک میکنن پژوهشگرهای مثل من بتونن راه خودشون رو پیدا کنن❤

[@BackwardSabotage]

amazing. i'm not even studying something health related. i'm just into 3d modelling, got a ct scan recently, have access to all my scans and just wandered what can i do with it. it's fun to see my own skull in my computer. thank you.

[@janwitowski]

That's awesome!! Thanks for sharing :)

[@abodakka]

Great tutorials .. appreciating your amazing explanation

[@christos.21]

GREAT job !!! Thank you very much for this video !!!

[@chencho33333]

Nice the seed trick. tks

[@emt409]

Nice tutorials. Thanks for putting these up. - does 3D slicer utilize a graphics card if I have one installed?

[@janwitowski]

Hi, thanks for the comment. I believe that 3D Slicer only uses GPU for 3D rendering. All other operations are really CPU/RAM-bound. There is a nice thread on Slicer forums that describes why Slicer algorithms usually don't have GPU implementations. discourse.slicer.org/t/questionable-performance-on-gpu-workstation/17140/4?u=janwitowski

[@jackd6134]

My CV system came out good, but unlike your very nice rendition, my liver is very ragged in 3D despite good contrast. Smoothing did not seem to help. I assume you need to initialize only once, thereafter it will auto-update? Also, could you clarify how to remove unwanted areas for seeding?

[@janwitowski]

Good news on segmenting CV system! A few points: (1) After you initialize seeds, it will auto update every time you draw new areas (Paint). You can also remove the seeds (tool Erase), but as far as I remember you will have to cancel Grow from seeds and re-initialize it. Then it will take into consideration removed areas. Also remember that you can always cancel the Grow from seeds preview, look at your seeds, edit them (Paint/Erase) and re-initialize. (2) It might be difficult to achieve perfect liver segmentation without any manual editing. But you should be able to get acceptable results with Grow from seeds... Does it get any better when you apply smoothing to the liver segment? Usually Gaussian filter (as shown in the #4 video on smoothing) gives really good results. If you don't see any change, make sure you have your Liver layer currently activated, not the background layer.

[@user-kw2fd2mv8q]

Hey! Thanks for your videos. Is there a tool to edit an existing segmentation? So let’s say I have segmented a brain into 9 tissue compartments and want to manually correct some mistakes. Can I just draw onto the segmented brain and change the color of misclassified parts?

[@janwitowski]

Yes, of course, this would work pretty much the same as in this video (and in part #2). You just switch between the segmentation layers and fix them by using tools such as Paint or Erase.

[@astronotusx]

Please, what you mean by "add it to the layer" at 10:06? When I try to remove or add the areas I dont want or need, I paint it like you do, but then it does not recalculate, it just keeps the area the same as before and adds only the pixels I painted,

[@onuralozturk]

Hello. Nice tutorial indeed. Do you have any idea about how to segmentate choroid plexus on Brain MRI ?

[@janwitowski]

Thanks. I've never segmented this specific anatomical structure before, but the principles from my tutorial series should apply to any segmentation scenario. My general recommendation will be to fall back to manual segmentation if the structure is complicated to segment. If you have a lot of studies to do segmentation on and need to automatize the process, you should figure out the best semi-automatic approach to this. You can also reach out to the community at discourse.slicer.org.

[@isabeltoledo6565]

Hi jwitos. I can`t use the function, i select the area i want to erase with scissors tool, but then nothing happens? You know why that happens?

[@janwitowski5167]

Most likely it's because you have wrong Segment (layer) selected. You need to set a correct active layer by just clicking on it.

[@izaiasmanoel2815]

isabel, i have the same problem, what did u do tô solve It?

[@jackd6134]

When I select "Show 3D" all I see are the 3 orthogonal slices, not the 3D rendering? If I turn off slice visibility I see nothing.

[@janwitowski]

My bet is that you need to recenter the 3D view. On the top of the 3D view pane, click the tiny crosshair icon that should fix this.

[@jackd6134]

@@janwitowski It did not. From what I read elsewhere, I needed to first turn on the eye in the Volume Rendering module. It then worked. I also found when I turned "Show 3D" off it did not turn off. ah! If you ever need a newbie to show you how things don't work, I am the person. ; )

[@janwitowski]

@@jackd6134 Then you're talking about volume rendering, not surface rendering as shown in this video.

[@marinasalib9413]

Is this considered as a semi automatic segmentation technique?

[@janwitowski]

Yes, I would call it a semi-automatic method, because it requires some user input (e.g., defining initial seeds).