Segmentation - Drawing Tablet

I’ve used 3D slicer for generating 3D models. I’ve used the wacom stylus and tablet for drawing the segments. Wacom has a tablet where you can draw directly on the screen, which I think would be really useful in the segmentation process, especially for students with no drawing experience, it would provide more control. Obviously, the threshold tool is extremely useful, but having more control when drawing is always helpful.

Segment editor works well on Windows computers with stylus (and Surface Dial, etc.). You can draw directly on the screen on all Windows touch-enabled PCs and modern stylii are fast, highly sensitive and support tilting. Do you still need Wacom pen? Does Wacom pen work differently?

I use a medium-sized wacom tablet/stylus (Wacom Intuos PTH-651) with a Mac laptop to do segmentations and it works great. I’ve customized pen buttons and tablet buttons for specific functions so I can quickly switch between paint and island removal (for example) to do segmentations. When you switch between functions a few hundred times a day, saving even a couple of seconds per operation adds up.

I’d be curious to hear about what workflow ideas others have for segmentations.

Have you seen the Wacom Cintiq? I was wondering if you could use 3D slicer on it… I

I’m working on a medical imaging elective and I want the students without an “artistic” background as much control as possible. Because i’m in medical library, I need a drawing system that interfaces with PC and MaC, but I like the idea of using a touch screen…

I’m working on models that can be presented in parts.

Also note there are a number of keyboard shortcuts that you can use in Segment Editor:

For example, a very effective shortcut is space key, which switches between last two effects (for example: paint/erase) or activates/deactivates an effect (for example: activate scissors/deactivate scissors so you can rotate the 3D view).

Let me know if you have any other suggestion for additional keyboard shortcuts that would make your workflow more efficient.

Thanks Andras,

Sorry for the very slow reply. I use the space key shortcut constantly.

I was wondering if there’s a way to make the “Editable intensity range” checkbox a shortcut key. I turn it on and off all the time for efficiency - for brush erase and island removal, it runs noticeably faster when Editable intensity range is unchecked (one less compare per voxel adds up).

Any thoughts? I’m sure that adding shortcut keys can rapidly turn into feature creep, with everyone wanting shortcut keys for anything and everything.



Thanks for the feedback. I’ve added a shortcut for toggling masking by master volume intensity by i key. It’ll be available in Thursday’s nightly build.

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Wow, this works GREAT!

I use a left-handed 3 button programmable mouse and a Wacom Intuos tablet. I’ve set up one pen button to select sphere brush and turn on Editable intensity range and a second to select remove islands and turn off Editable intensity range. This allows me to basically do all my editing functions with minimal mouse movement and I never have to reach for the keyboard (“HOTAS, or Hands On Throttle And Stick”, as they say in the aviation world - I have my mouse buttons customized for other functions to speed up workflow.)

This probably just saved me a couple of hours per week in just mouse movement and computation time (island removal with editable intensity range off is a lot faster than with it on).

Thanks again! You guys are awesome!


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Zoom and rotation are possible on 3D view, and I will display sliders or arrow buttons to let the user translate the view.

To inform other users, I am using a XP-Pen Artist 12 drawing tablet with screen and Slicers is running perfectly, including volume rendering.

What do you mean? Display where?
Using shift key, you should be able to translate the view.
Does the tablet has programmable keys? If yes, then you can configure keyboard shortcuts for translating views.

xp-pen artist 12 display tablet has 6 programmable keys and I touch bar . 11.6 inch IPS Screen . 8192 levels of pen pressure . 5080LPI

Could you share a video with Slicer running on the tablet ? This would be very informative.

From what I read here, many people use a drawing tablet in combination with Slicer. That also goes for me, but only when I’m working on a Windows machine.

At home my OS is with Linux Mint 19.1 and there I have an issue during segmentation.
The cursor follows the pen nicely (although it’s appearance changes from a one-pointed arrow to a double-pointed arrow, and back again), but when I’m using to ‘paint’ or ‘erase’ tool, it starts to react veeeeeeery slow!
I’ve tried two different Wacom drawing tablets (Volito and Intuos), but they both show the same problem.
When I check my system settings, it just gives me the information whether I’m using the Volito, or the Intuos and the react normal to every action I take.

Other applications for which a drawing pen is very useful to use, like Gimp or Krita, don’t give any problems.

Is someone familiar with this problem on (other) Linux systems, or is only a Linux Mint issue?

Can you post screenshots and/or videos? They could give some hints what could be the performance bottlenecks.

What graphics card so you have?

How is the performance if you use the same computer and tablets using Windows?

Hello Andras,

First of all I’ve checked if it was up to the computer itself.

At home I’m using a machine with the following hardware configuration:

  • AMD FX 4350 processor
  • AMD Radeon R7 graphical card
  • 8Gb ram
  • Linux Mint 19.1

When I boot up with Linux I’m facing the problem that, when using the ‘paint’ or ‘erase’ option, the cursor lags very much and it takes many seconds to build up the selection/erasion.

At home I also have an external hard drive with Windows 7 professional installed on it and when I boot from this drive, using the same computer, then I don’t face this problem. So you could say that i’ts not a hardware issue, can you?

At work I’m using a computer with this configuration:

  • Intel Xeon E5-2630 v2 processor
  • NVIDIA Quadro K5000 graphical card
  • 48 Gb ram
  • Windows 7 professional

When working in Windows everything works fine, but when I boot this machine up from a Live-USB with Linux Mint 19.1 and then install 3D Slicer I’m having the same problems.

From this I can say that it has certainly nothing to do with hardware.

So my question is: Is this Linux (Mint) related, for I remember that I also had this when I was using a previous version of Linux Mint?

Is slice browsing or Slicer’s performance in general is worse if you use Linux Mint?
What do you show in the scene? Just a volume? Do you show anything in the 3D view?
Are there any warnings or errors in the application log?
Can you attach a profiler to see what methods take the most time?

Is slice browsing or Slicer’s performance in general is worse if you use Linux Mint?
No, I see no difference compared to a Windows 7.

What do you show in the scene? Just a volume? Do you show anything in the 3D view?
I have the ‘Four Up’ display on, showing the CTChest and ‘Show-3D’ is off.

Are there any warnings or errors in the application log?
The error ‘VTK No input data’ shows up when using the drawing pen, although not after every stroke.

Can you attach a profiler to see what methods take the most time?
I don’t know what you mean by this, but all I can say is that when starting a penstroke, during the stroke the selection slows down; the cursor is already in it’s last position, but the trail of cirkels is not completed, if you know what I mean.

I think I will also try Slicer out on another Linux Distro to see if it might be LinuxMint-related.

How do you show CTChest? Using volume rendering? Or just show the slices in the 3D view?

I mean attach a performance profiler to SlicerApp-real process. I don’t use Linux, so I cannot recommend any particular software, but this may help.


I don’t show anything in the 3D view. I just download the CTChest that Slicer provides. Only the axial, sagital and coronal views are filled.

Sorry, but I’m not familiar with programming languages at all. I just push buttons, if you know what I mean. :slight_smile:

Maybe it would be an idea to build a live-usb-stick containing Linux Mint 19.1. Then boot your computer up from the USB-stick, download Slicer and unpack it. Plug in a drawing tablet and try it out.
Hopefully you will experiënce what I mean.

Btw. Despite this Linux issue I’m beginning to appreciate Slicer more and more.

Do you only have this issue if you use the tablet, or it is slow even if it’s disconnected and you use only the mouse?