ROI as a separate stack

[Yi-Ling Lin]

I am new to boneJ and CT scan. I have been told to scan multiple bones at the same time to save time, and later use the software that comes with the machine to morph/ROI interpolate to separate the bones. We would need to purchase the software, so I wonder if I can use boneJ instead. I can use boneJ to interpolate ROI, however, I cannot save these ROIs as a separate stack for analysis. Can anyone help?
Thanks

Yi-Ling

[Michael Doube]

Dear Yi-Ling,

There are a couple of approaches here.

The easiest is to scan your bones so that they do not overlap in (x, y, z), in other words, imagine an invisible, cuboid, box surrounding and separating each bone when you lay them out on the CT scanner gantry. Also make sure to raise them from the gantry on a bit of foam - the cheap kind sold for matresses works well (and you can cut it into bits with a bread knife). Once you have your image, open the whole CT scan stack (usually this is by importing a DICOM series), set a rectangular ROI around each bone and Image > Duplicate and tick 'Duplicate Stack', and enter the slice range your bone is present in. The result is a copy of the data from your rectangular ROI (in xy) with slices in the z range you specified. Also the DICOM metadata is copied into the new stack's metadata. Save the new substack image as a single tif: File > Save As > Tiff with a name that makes sense to you.

If your bones are overlapping a bit, then do the box procedure as above then manually paint out the bits of bone you don't want from each duplicated image. We like to do that by drawing a line segment ROI and filling it with a background value ('black', or -1000 HU), and quickly flicking through the stack with 'f' to fill and '>' to go to the next slice. If you have thousands of slices, then you can try making an interpolated ROI to select the unwanted pixels from the image and filling in a single operation.

Best regards,

Michael

[Yi-Ling Lin]

Thank you! I will try it.

Yi-Ling