Creating an endocast in Avizo using a CT scan

This assumes the CT scans are downloaded and saved in individual folders in the DICOM format

- Open Avizo
- select Open Data
- select your data (cmd+A all files) and click Open
- a window should pop up that says DICOM loaded
- click ok

the data will load and a button will appear in the project view window with the name of your data

-right click on data -> Image Segmentation -> Edit New Label Field
- the segmentation editor should open along with images of the data

Segment the bone first:
- delete the Inside material
- click the add material button under Materials
- rename the material bone

- click the magic wand button, check fill interior, check all slices
- click on an area of bone
- move the threshold around until only bone is selected and as much of the bone as possible is selected without choosing air or other materials (check around the nasal cavity and eye socket for thin bone)
- click the plus sign in the selection box to add it to the bone label
- click the lock to lock this material

Expand the bone segmentation:
- add a new material, as above, and rename it expandedbone
- click the select button next to the bone material, it should select the bone label and make it red
- click the expand button in the selection box 9 times (or until most holes are filled) (*remember how much*)
- click the plus sign in the selection box and add it to the expandedbone label
- since the bone label is locked, it should just add the expanded part to the new label
- click the lock to lock this material

Segment the endocast:
- Creating the expandedbone label should have filled most of the holes/foramina, speeding up the process of filling in the endocranial cavity
- add a new material and rename it endocast
- use the magic wand, check same material only and fill interior (do not check all slices)
- pick a slice above the eyes or right before the first visible remaining holes and click in the volume to fill the endocast
- click the plus sign to add it to the endocast label
- move one slice upwards toward the top of the skull and click inside the endocast, you should be able to now check all slices and it will fill in the volume between the first added slice and the top of the skull
- continue to fill in individual slices (without all slices checked) and larger volumes (once boundaries are made etc.) until the endocast is filled except for the remaining areas with holes

Filling the holes, expanding the endocast:
- lock the endocast material
- click on the expandedbone material and unlock
- use the paint brush or other methods to fill in the remaining holes and add the selection to the expandedbone material
- relock the expandedbone label
- unlock the endocast material and fill in the remaining volume
- once the endocast is completely filled we can now expand it to reach the edge of the bone
- delete the expandedbone label
- keep the bone label locked
- click on the endocast label and click select to choose the material
- click the expand button and expand the material 9 times (or whatever number you did)
- you can expand the endocast label one or two extra times, but check that it does not overflow too much
- click the plus sign to add the expanded selection to the endocast material
- it should now share an edge with the bone material
- fill in the remaining spaces with the paint brush or magic wand and erase overflow areas etc.
- Once the endocast is satisfactory, delete the bone label
- save the project and label

Export the endocast:
Go back to the project view:
- right click on the labels button -> compute -> generate surface -> unconstrained smoothing -> apply
- click continue
- right click on the .surf -> surface view
- under materials, select all and all and then remove
- then select endocast and all and add

- click on the surface view button -> extract surface -> apply
- a green extracted surface button should appear -> surface view
- should just be the endocast
- click on the icon with the red lines (simplification editor)
-simplify the faces a bit, check create level of detail
- right click on extracted surface -> save data as -> rename, and choose .ply or .obj (or whatever format wanted)


You should then end up with an exported 3D surface file:

Morton###endocast.ply


Next place fixed and curve landmarks