# Volume rendering a masked area

**URL:** <https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637>\
**Category:** Support\
**Tags:** volume-rendering, masking\
**Created:** [November 16, 2020, 4:20pm UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637 "2020-11-16T16:20:01Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Jason\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason_c/32/8858_2.png) [@Jason\_C](https://discourse.slicer.org/u/Jason_C)\
**Post date:** [November 16, 2020, 4:20pm UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637/1 "2020-11-16T16:20:01Z")

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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?

Thanks!!

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [November 16, 2020, 4:22pm UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637/2 "2020-11-16T16:22:49Z")

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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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**Author:** ![Jason\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason_c/32/8858_2.png) [@Jason\_C](https://discourse.slicer.org/u/Jason_C)\
**Post date:** [November 17, 2020, 6:29am UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637/3 "2020-11-17T06:29:41Z")

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Thanks.

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.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [November 17, 2020, 6:40am UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637/4 "2020-11-17T06:40:39Z")

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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](https://slicer.readthedocs.io/en/latest/user_guide/settings.html#settings-file-location).

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**Author:** ![Jason\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason_c/32/8858_2.png) [@Jason\_C](https://discourse.slicer.org/u/Jason_C)\
**Post date:** [November 17, 2020, 6:43am UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637/5 "2020-11-17T06:43:53Z")

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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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**Author:** ![Jason\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason_c/32/8858_2.png) [@Jason\_C](https://discourse.slicer.org/u/Jason_C)\
**Post date:** [November 17, 2020, 6:48am UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637/6 "2020-11-17T06:48:50Z")

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

It’s indispensable; thank you, nice work!!! 😃