# Gray areas in registered images using 3D Slicer

**URL:** <https://discourse.slicer.org/t/gray-areas-in-registered-images-using-3d-slicer/38132>\
**Category:** Support\
**Created:** [August 30, 2024, 6:25pm UTC](https://discourse.slicer.org/t/gray-areas-in-registered-images-using-3d-slicer/38132 "2024-08-30T18:25:24Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Nastaran](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nastaran/32/77781_2.png) [@Nastaran](https://discourse.slicer.org/u/Nastaran)\
**Post date:** [August 30, 2024, 6:25pm UTC](https://discourse.slicer.org/t/gray-areas-in-registered-images-using-3d-slicer/38132/1 "2024-08-30T18:25:24Z")

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Hello @cpinter

I used 3D Slicer’s General Registration (BRAINS) to register brain CT images from two different modalities. An example of the resulting registered image with the **background filled value set to 0.0** shows gray areas that appeared after the registration process. However, after setting the **background filled value to -1000** , the gray parts changed to black, while other parts turned white.  
Could you please advise on how to address this issue?  
Thank you in advance.

![](https://github.com/user-attachments/assets/7f116db8-a306-48be-96c5-20c662cb3e4a)

![](https://github.com/user-attachments/assets/acb35f98-b455-4fef-a8ac-39a90580ee33)

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**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [August 30, 2024, 6:35pm UTC](https://discourse.slicer.org/t/gray-areas-in-registered-images-using-3d-slicer/38132/2 "2024-08-30T18:35:04Z")

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Please check the actual voxel values in the Data Probe, it might be a window/level issue. If you are not sure what these mean please refer to the documentation. Also I recommend actually using -3000 because that is the typical “background” value for CT as far as I know.

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**Author:** ![Nastaran](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nastaran/32/77781_2.png) [@Nastaran](https://discourse.slicer.org/u/Nastaran)\
**Post date:** [September 2, 2024, 9:42am UTC](https://discourse.slicer.org/t/gray-areas-in-registered-images-using-3d-slicer/38132/3 "2024-09-02T09:42:02Z")

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Thanks for getting back to me.  
I tried using -3000 as you suggested, but the results were the same as with -1000. However, after checking the window/level settings as you recommended, I discovered that the issue was indeed related to them. Thank you for pointing that out!