Here is an example of how you can use ImageStack’s ROI functionality to reduce your memory footprint and partially import datasets. This would have more sense if you had the original data, where there are multiple specimens scanned side by side (which I think you are scanning them). But still demonstrates the concept.
- Proceed with ImageStacks as before, but choose to import half-resolution quality.
- Volume render the half-resolution set and create an ROI in volume rendering that only contains Left Mandible.
- Go back to ImageStacks and then change these settings:
- Output Volume: Create a new output volume as and set it as Left Mandible
- Set Region of interest to the new ROI you created in step #2
- change the resolution to full resolution.
These changes reduces the memory footprint to 1/8th of the original dataset. Hit load files to import this new volume.
Go ahead and create a single landmark on the tip of the left incisor.
Repeat these procedures to import the Right mandible, create a single point on the right mandible as well. Then go ahead and import the full dataset (at any resolution) without the ROI and notice that both of these points are indeed in correct spot for incisors on the full dataset. That’s because Slicer preserves the correct offset for the partial volumes you created. Of course, save the data as NRRD file right after the import (so that you don’t repeat the steps).
If you did the cropping of left and right mandible in ImageJ and then bring those datasets to Slicer, you wouldn’t be able to do this, because ImageJ will not preserve the full coordinate system. That’s why I say there is really no reason to do the cropping in ImageJ. In future, we will add the option to put the ROI under transform (so that you can crop in the oblique orientations) as well.