Volume rendering a masked area

I’d like to use the volume renderer to render a portion of an MRI, but I only want to render the area covered by (a) specific segmentation(s).

I’m just learning slicer so this might be a rtfm case, but how can I do this? Can I either specify a segmentation to use as a volume renderer mask, or perhaps create a new volume with everything outside the segmentation removed and render that?


Install the SegmentEditorExtraEffects extension and use either the MaskVolume (if you have one segment) or SplitVolume (each segment masked individually and volume reduced to the smallest extend) to extract a new volume based on your mask.

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So, I did that (I’ve actually been using SegmentEditorExtraEffects already it’s pretty great; I didn’t know what mask volume did). Creating the masked volume worked fine. Then I went to the volume renderer; I selected the masked volume, and as soon as I clicked one of the volume renderer presets Slicer crashed. No messages or anything (not even the Windows crash dialog), it just closed; losing the work.

On restart I found that I could no longer import DICOM files (clicking the import button does nothing), could no longer see my DICOM database (empty), and I could no longer click the File, View, or Edit menus unless I clicked the Help menu first then moved the mouse to one of them.

I started ignoring modules and eventually found that the built-in DICOM module was the culprit. Ignoring it, and the menus work (although of course, I can’t load DICOM without it). Including it, and the problems happen.

So whatever happened when I picked a volume renderer preset broke the DICOM module permanently. It looks like I lost the DICOM database too.

I uninstalled and reinstalled Slicer and it’s still broken.

Not really sure what to do.

Version 4.11.

Crash when switching between volume rendering modes is fixed in recent Slicer Preview Releases.

When the application crashed, you’ve lost your settings (Slicer.ini file) and probably Slicer reverted to using a default DICOM database location that contains an old, incompatible database. After you start Slicer, change the DICOM database location in menu: Edit / Application settings / DICOM section and it should all work well. If this does not solve all the problems then you can delete/rename your Slicer.ini file.

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That was it, thank you! The db location got reset. Phew.

Probably should have asked that as a new question.

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Oh on reinstalling extensions I noticed you’re the author of SegmentEditorExtraEffects.

It’s indispensable; thank you, nice work!!! :smiley:

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