Local threshold, a new semi-automatic segmentation method, has been added to the Segment Editor. It is available in both the 4.11.0 and 4.10.2 releases through the SegmentEditorExtraEffects extension. This effect adds connected voxels to segments that are within a specified threshold, and attempts t…

[image] lassoan: import SimpleITK as sitk I only have .init_cpython files, the response of slicer was the following: import SimpleITK as sitk Traceback (most recent call last): File “”, line 1, in ModuleNotFoundError: No module named ‘SimpleITK’ [image]

I meant deleting all files and folders in your Slicer settings folder. Probably it is in C:\Users\Félix\AppData\Roaming\NA-MIC. I also see that you have some things installed in C:\Users\Public\NA-MIC, which may be the root cause of all issues. Delete the content of that folder, too. If you don’t …

[image] lassoan: C:\Users\Félix\AppData\Roaming\NA-MIC . Still the same problem

We can do a remote debugging session on your computer, write me your availability in a private message. We can probably find and fix the issue in a 10-20 minutes.

Thank you, that’s very kind but there’s no need for it. I already tried insalling it on a different pc and managed to get the missing tools. However, they were unable to successfully segment the brainvessels of my scans. Thus I had to do it manually :confused: Thanks again for all of your effort to…

Thank you for this great new segment editor tool. I think I might have found a small bug - the ctrl + click didn’t seem to work when using a transform-applied image. If this could be addressed in future versions, I think it would be really helpful (or if this actually isn’t supposed to happen, I wo…

SegmentEditorExtraEffects extension serves as an incubator of new effects. They are not fully developed, but they are made available so that users can try it. If they turn out to be useful then they get hardened and polished and moved to the Slicer core. Local Threshold effect has been proven to be…

For Local threshold, once the region has been established with the yellow demarcating line, how do we fill the segmentation? ‘ctrl click’ is not working no matter what combination of segmentation algorithm I choose

The whole area of the segmented should be filled with the color of the segment you want to create. Adjust the sliders. Make sure that you do not have “editable intensity range” checked by accident and that the “minimum diameter” is adequate. Try “Growcut”. Use the latest Slicer version.

New Segment Editor effect: Local threshold

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lassoan (Andras Lasso) January 10, 2021, 7:31pm 42

Slicer offers lots of others tools and techniques for brain vessel segmentation. If you are not happy with manual segmentation then let us know and we can help.

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New Segment Editor effect: Local threshold

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