# Manual Crop how to do it correctly

**URL:** <https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361>\
**Category:** Support\
**Created:** [November 3, 2017, 3:36pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361 "2017-11-03T15:36:59Z")\
**Posts on this page:** 10\
**Page:** 1

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**Author:** ![AndFor](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/andfor/32/822_2.png) [@AndFor](https://discourse.slicer.org/u/AndFor)\
**Post date:** [November 3, 2017, 3:36pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/1 "2017-11-03T15:36:59Z")

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Operating system: win  
Slicer version: 4.9

Hello  
I’ve follow all instruction found here [3D Cropping Volume Rendering](https://discourse.slicer.org/t/3d-cropping-volume-rendering/394/9)  
If i’ve correctly understood, there is not a live crop direct on the main volume.

Then, i’ve make a segmentation - \> exported to labelmap

then Open Mask scalar volume  
Input MrBrainTumor (original volume)  
Mask Volume: Segmentation label 1

Apply, the is ok

Now I go to volume rendering, I can display the main volume or the masked volume , but I see only a solid colored form (the mask selection) but not the tissue volume whit the volume rendering setting

Help please  
Thanks

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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 3, 2017, 3:47pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/2 "2017-11-03T15:47:48Z")

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Note that in recent version of Slicer, the workflow is much simpler than described in the old post, as `Mask Volume` effect allows masking directly from a segment, without leaving the Segment Editor module. `Mask Volume` will show up in the Segment Editor module after installing `SegmentEditorExtraEffects` extension.

See a short demo video here:

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**Author:** ![AndFor](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/andfor/32/822_2.png) [@AndFor](https://discourse.slicer.org/u/AndFor)\
**Post date:** [November 3, 2017, 4:15pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/3 "2017-11-03T16:15:59Z")

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Fantastic thanks  
It work good

And… does is possible to use simoultaneusly 2 separated mask for the same volume?

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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 3, 2017, 4:33pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/4 "2017-11-03T16:33:11Z")

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I don’t really understand what you mean by using separated masks. You can use all the tools in Segment Editor to draw shapes - they don’t have to be connected. You can also combine or separate a segments using `Logical operators` effect; or mask sequentially by using the same volume as `Input volume` and `Output volume` in `Mask volume` effect.

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**Author:** ![AndFor](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/andfor/32/822_2.png) [@AndFor](https://discourse.slicer.org/u/AndFor)\
**Post date:** [November 3, 2017, 6:07pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/5 "2017-11-03T18:07:03Z")

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mmmm I cannot find how to make it  
I’ve tried but dont work

I want try to use threshold AND Scissor, to isolate a little anatomic part and remove all little pixel outside…

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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 3, 2017, 7:00pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/6 "2017-11-03T19:00:43Z")

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Use Threshold effect first, then Scissors effect (erase outside), finally Islands effect (remove small islands).

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<div class="post-metadata">

**Author:** ![AndFor](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/andfor/32/822_2.png) [@AndFor](https://discourse.slicer.org/u/AndFor)\
**Post date:** [November 3, 2017, 9:42pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/7 "2017-11-03T21:42:07Z")

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perfect, tested and work well many thanks

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<div class="post-metadata">

**Author:** ![AndFor](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/andfor/32/822_2.png) [@AndFor](https://discourse.slicer.org/u/AndFor)\
**Post date:** [November 3, 2017, 10:08pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/8 "2017-11-03T22:08:05Z")

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Other little question, how to center the rotation center of 3D view on a specific point of 3D Volume: if I zoom very much, during rotation the volume go out of the window space

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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 3, 2017, 10:27pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/9 "2017-11-03T22:27:16Z")

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Click on the small box button (reset field of view) in the title bar of the 3D view to reset the center of rotation for the current content. I think Shift+LeftMouseDrag also shifts the center of rotation.

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<div class="post-metadata">

**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:** [May 24, 2019, 1:37pm UTC](https://discourse.slicer.org/t/manual-crop-how-to-do-it-correctly/1361/10 "2019-05-24T13:37:02Z")

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A post was split to a new topic: [Edit existing segmentation](https://discourse.slicer.org/t/edit-existing-segmentation/6917)