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I am trying to edit a 3D stack in ImageJ. However, after I do, running 3D Viewer yields an flat image without the depth in z. Before editing, running 3D Viewer results in a perfect 3D image. The editing I did was to simply select a brain as an ROI (leaving the skull and skin un-highlighted) and invert it, to create a 2nd ROI of everything but the brain. Then I selected the color of the background, which is black, using the Color Picker, and used the Fill command in the ROI Manager to eliminate the skull and skin and leave nothing but the brain. After I save it as a new image (.dcm) I have the problems with the 3D viewer. I believe I am losing some of the 3D information when I edit the image, but I'm not sure how to edit it while retaining the information in the z dimension. I checked Image Properties, and made the voxel depth the same as the original, but it made no difference. Any ideas would be much appreciated! Thanks in advance!
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