Retaining 3D data while editing a stack

[Charlotte]

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!

[Charlotte]

After I posted this I read that DICOM images need to be saved as TIFF in ImageJ/Fiji to avoid loss of header information. I was saving them as DICOM images by manually typing in the extension .dcm. I tried a new approach: not changing the image at all and just hitting "save as" and choosing TIFF. When I use 3D viewer after this, I still have lost z data. For some reason when I save the file I am losing information. Does anyone know the trick to saving DICOM images as TIFF without losing data?