Handle/hole identification and navigation in segmentation MRI volume

Dear all,

I am working with brain MRI data in Slicer 4.4.0 on Ubuntu 14.04.
I have automatically generated gray/white matter segmentations that I need to correct for miss classifications, and especially handles (loops of gray/white matter, which are anatomically impossible).
For this, I am using the Model Maker Module to build 3D meshes of the gray and white matter, and I am then correcting the handles and holes manually.
I have a couple questions about this process:

-Is it possible to click on the mesh and automatically navigate to that position in the red, yellow, and green windows?
-Is there a way of automatically identifying (and maybe fixing) the holes/handles?
-Once I adjust the segmentation in the 2D panes, is there a way to make the 3D mesh update automatically?

Please let me know if you need more information.
Thank you very much for your input!

Hi Jelle,

Please use Slicer 4.8.1 or later, as 4.4.0 is more than three years old now.
Also use the newer Segment Editor module, as it is more advanced than the original Editor module. See documentation for more information, and there are various tutorials, such as this.

To your questions (in 4.8.1 or later):

  • If you hold down shift when moving your mouse in the 3D view, the slice views will jump there
  • There is no feature to identify of holes (as far as I know), but you can identify connected components in the Islands effect. To patch holes you can use many of the tools such as Paint or Surface Cut (in SegmentEditorExtraEffects extension)
  • In Segment Editor, it is automaticaly updated

Dear Csaba,

thank you very much for your reply.
I have now updated Slicer to 4.8.1, and am exploring the options you described.