Threshold fail for Segment Editor

[cyufu (caoyufu)]

Operating system: windows 10 64
Slicer version:4.11.0 2018-11-17

Apply fail

Use for masking→Paint or Scissors（fill inside）fail

Thanks
Cyufu

[cpinter (Csaba Pinter)]

It is hard to know exactly what happens without more information such as the voxel values in the image, but here’s what I think:

• Threshold limits seem to be off, because even before you press apply, we don’t see anything in the preview. There should be a pink “pulsing” in the “in” area of the threshold
• Scissors don’t work for the same reason, because you apply the threshold as mask, and as threshold excludes everything, scissors do not fill anything

What are the scalar values in your image? Is there anything in the log that may help? (About / Report a problem)

[lassoan (Andras Lasso)]

Also, could you go to Volumes module, select the master volume is selected as “Active volume” and take a screenshot of Volume information section and Histogram section?

[cyufu (caoyufu)]

@lassoan

go to Volumes module, select the master volume is selected as “Active volume” and take a screenshot of Volume information section and Histogram section?

Thanks

[lassoan (Andras Lasso)]

There are two unusual properties of this volume:

1. It is very large. Try resample by a spacing factor of 4 in Crop volume module and see if you still have issues.
2. This is a binary volume, i.e., it is already segmented. Instead of segmenting it again, load the volume as a labelmap volume and then import it into segmentation (using Segmentations module Import/Export section).

[cyufu (caoyufu)]

@lassoan

by a spacing factor of 4 in Crop volume module

by a spacing factor of 1 in Crop volume module,success.

thanks

[cpinter (Csaba Pinter)]

@lassoan

This is a binary volume, i.e., it is already segmented. Instead of segmenting it again, load the volume as a labelmap volume and then import it into segmentation (using Segmentations module Import/Export section)

@cyufu Have you tried this? I think it’s unnecessary extra work re-segmenting a segmentation. It’s much easier if you load it according to its data type to begin with.

[cyufu (caoyufu)]

@cpinter

load the volume as a labelmap volume

But it isn’t outline.

thanks

[cpinter (Csaba Pinter)]

@cyufu

But it isn’t outline

Because you loaded it as regular volume. If you open the options after drag&drop in the Add data dialog, you can check a checkbox so that it’s loaded as labelmap. You can also convert it in the Volumes module to labelmap type.

Most data types can be displayed in many ways, so the way something is displayed is not a good indicator of what it is exactly. The Data module for example is a much better way to find these things out.

[cyufu (caoyufu)]

I have opened it correctly.

thanks.