I have an endocast that I am trying to measure the volume of the olfactory bulbs from. I have the data segmented in Avizo, but unfortunately because of the way the specimen was scanned (it was a fluid specimen) the skull was not in anatomical view when it was CT scanned. As a result, it is very difficult to determine where the borders of the olfactory bulbs are.
I am trying to reorient the segmented data so I can get it in standard anatomical view for further analysis, specifically resegmenting the label field to define the olfactory bulbs separately. I know that it is possible to resegment the CT data in Avizo, but I am trying to avoid this as I know it can cause issues with blurring of boundaries between bone and tissue. I was wondering if there is any way to do this with a segmented label field, isosurface, or other data that has already been segmented and thus the anatomy is better defined.
Hi Russell,
in Amira-Avizo, you can use the Transform Editor of any data-object to change its orientation and position in the global coordinate system.
So, you could use the Transform Editor of your segmented data to rotate it as needed, and afterwards you can use Resample Transformed Image to get get an axes-aligned voxel-grid. (see attached "TransformEditor_snapshot.PNG")
I don't know your workflow, but maybe you could also use the 3D lasso-tool in the Segmentation Editor to select an arbitrarily oriented part of one material and assign that to a new material (see attached screenshot "SegEdit_snapshot.PNG").
For making the selection working only on one specific material, you have to "lock" the other materials appropriately. Remember, you have the "undo" with +Z ...
There might be some issues with the update of the visualisation when using the 3D-lasso, so it might be necessary to toggle off/on the 3D-view of a material.
Kind regards,
Andreas
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