How to use local threshold

[Dan_Cheng]

Hi
I am trying to using local threshold in 5.6.2. When I press cmd + left click, there is no segment at all. Can anyone help me? Many thanks!

[lassoan (Andras Lasso)]

The histogram is empty. Is the volume you see in the viewer the same as the source volume of the segmentation?

Have you set anything in the masking section that could prevent painting in the segment?

[muratmaga]

@lassoan While useful, I find the local threshold tool difficult to use. Mostly because I get no feedback when things don’t work and I have no idea what I need to do/change. I am not sure if it is possible but when things are not being painted, would it be possible to give some feedback about what to change?

For example, in here I am trying to segment the enamel within the ROI, but I cannot never seem to finalize the selection. It just keeps blinking. CMD+left click doesn’t seem to do anything. Selection continues to fade in and out.

[jamesobutler (James Butler)]

Generally it is the minimum diameter of the GrowCut algorithm that has to be adjusted for local threshold as the effect is more so a combo effect that is “Threshold+Grow From Seeds”.

local threshold: bugs or features?

Creates a seed for segmentation and then uses that seed for region growing. The seed is generated by thresholding with the chosen intensity range, then keeping the island where you Ctrl-clicked. You can certainly do this, by simply using the Paint effect and then using Grow from seeds effect. Local threshold just automates painting of the seed (replaced 5-10 clicks by one click). When the island at the clicked position is determined, the thresholding result is eroded to prevent small, thin…

@Thomas_K, @lassoan, @pieper and myself diiscussed this same topic about the confusion of the effect at the following hangout (linked below) with Thomas proposing a “Fast local threshold” which always picks the selected voxels such as a “Threshold+Islands” type of combo effect rather than being only based on the Grow From Seeds approach. That way what you click is what you get. From that discussion it seemed that @lassoan recognized the confusion in the current effect, but there was no clear consensus about the integration of such a “Threshold+Islands” type approach.

2024.10.19 Weekly Meeting - 11 AM start!

Agenda item topic: Modification / addition to Local Thresholding segment effect (SlicerSegmentEditorExtraEffects/SegmentEditorLocalThreshold at master · lassoan/SlicerSegmentEditorExtraEffects · GitHub)

The regular “Threshold” effect supports local histogram selection (drawn below), but then you have to use another effect to ultimately pick which selected voxels to keep from the full selection.