[ Music ]
>> Okay to start off I am in
Dr. Mahfouz's research lab
at the University of Tennessee
so I have my bachelors
and my masters in
biomedical engineering.
But this is probably
the most exciting for me
because when I was in high
school I was determined I was
gonna go to college
and major in forensics.
Some things kinda changed
that plan a little bit
but this really where
my passion kinda lies.
So some of the work that I
do with Dr. Mahfouz is really
in bridging the gap between our
Biomedical Engineering Program
and our Anthropology
Department at UT.
So what we're gonna do
today in this first hands
on session is go through the
segmentation process taking a CT
data set of a live patient
cranium and then we're going
to segment it and ultimately end
up with a three dimensional
model.
This is really the basis of
most of the work that we do
in our research lab so
and in Dr. Mahfouz's
lectures this morning.
He's given a little
bit of a basis on some
of the orthopedic
implant design and some
of the other projects
that we've done.
And this is where my role in
our lab comes in to manage our
under grads and our
student workers
to really develop these
three dimensional models
on a regular basis.
So we've done studies with
the femur, with the radius,
number of bones in the body
and right now our focus is
obviously on the cranium.
So, has anybody used
segmentation softwares
to create three dimensional
models before?
Okay. So what we're
gonna introduce you
to today is a commercially
available program called Avizo.
This isn't our software that we
wrote so you can use programs
like Amira, Avizo, Mimics, there
are several that are available
for commercial download.
Avizo is just our reference
at the current moment
for the features that it has and
what we're interested in doing.
So it's actually pretty
easy and some of the steps
that we've gone through to
prepare the data set today I
think we're gonna
make this hands
on session a little bit easier.
So I believe on each of you
desktops is an Avizo program
and please stop me or
slow me down if any--
we're not all in the same page.
But the one that we're
gonna open is just the basic
Avizo 6.3.
And so we can close out all of
these screens until you're left
with this basic open
main screen.
So you'll see that this screen
is separated into sections.
You'll have this 3D viewer
which is the very large area.
You have this top area
which is called the pool
and in your hands
on instructions,
I believe everyone has that.
I'm gonna try to follow
those a little bit step
by step 'cause we really did
write out every single detail
of how you're gonna be
going through this process.
And for the very first steps,
we do reference the
pool quite often.
This is the properties area
and then here along the
bottom you have the console
and also the help browser
if ever you kinda caught up
and need some help on this.
So what we wanna start out with
is to go up to the green button
in the pool and press Open Data
and I believe Emam has loaded
this data sets somewhere
on your desktop.
Is that correct?
So if you can change your drop
down menu to find the desktop
on your computers
you should be able
to hopefully get
to this M64 folder.
So if you open this M64 folder,
you'll find a folder called
DYCOMS, you can open up folder
and these are our DYCOMS.
You just wanna click
on the very first one,
scroll to the very
bottom of the page.
You can hold down
your Shift button
and select the very last one.
>> Once you have all
your DYCOMS selected,
you can hit Load and then Okay.
'Cause it likes to keep
reminding us we have a
trial version.
>> Yeah.
>> So did everyone get
their DYCOMS loaded?
>> Yes.
>> So you're gonna go
ahead and hit Okay.
So for these particular
set of DYCOMS, we have--
like I said, we've already
done some image processing
and we've already done a
cropping of our data set.
So I have this I
believe on page 3.
How to Crop Your
Data Set which is
in the segmentation instructions
but we're actually not gonna do
that since we're
already done it for you.
But I am gonna go ahead and go
through it really quickly just
to show you what you would do.
This is not something that
I need you to do right now.
So the reason that you would
do the cropping of data set is
when we-- in a research lab,
we take a lot of the dry bones
for anthropology
department and we lay them
out in a specific
format and then we go
to the hospital and
we CT-Scan those.
So if we're doing a particular
project say where we just want
to look at the right femur, we
have a set of DYCOMS that sent
to us from the hospital
that's 2300 images
and we don't want that.
We need to simplify our
data and for primary reason
of data management file
size we need to reduce that.
So what we will do is we
will crop out everything
out that we're not
looking at and just save
that particular femur.
So we've already done
that but what you could do
in Avizo is you can
right click Bounding Box
and you can right
click this ortho slice
and then it will bring up
an image of our cranium.
Normally like I said, I would be
2300 images long and you'd have
to scroll along through.
So you can kinda play with
your 3D viewer a little bit.
You can-- in this
Properties box down here,
you have a slice number.
You can scroll all the way
through you slice number
and you can kinda get a view
for what you're looking at.
Here in your Properties Menu,
you have this orientation
option as well.
You can change which
view you want to look at.
Again, you can kinda
scroll through.
And so this is where
you would make a note
of which slices correspond
to the boundaries of the bone
that you wanna look at.
And then if you were eventually
decide what those were you could
then go back up to your data
set here and once you click
on these data sets in this
pool area, they kinda go
into shadow mode so that you
know what you've selected.
But you can click
on this crop tool.
Same image that's
in most programs
and then what you could
do is put a number.
You can pick whatever you want
and you'll see how
it corresponds
to the actual data set here.
What surrounded in the green
boxes is actually what you've
cropped down and
everything outside
of those green boxes is
actually what will be cropped
out and no longer saved.
So you can see how if we have
an entire body just cropping it
out to one small little
section would be pretty helpful
and then it would also
use the file size.
>> Lindsey, excuse
me, could you just go
over where the crop
tool is again?
>> Sure. So if you go
back up into the pool.
>> Yeah.
>> And you click on the
green, your main data set--
>> Yeah.
>> To make sure that
it's selected,
this Properties area
will light up.
>> Oh I see and then the
crop tool [inaudible] up.
>> Right. So in the
properties area,
you can just click on that.
So we've already gone through
this and you can kinda see
if I just cancel this out,
we've been a little generous
in our main boundaries
of this or this slice.
We could obviously go through
and we could remove some
of this posterior side
of the scan and we've--
we actually didn't leave much
room at the top so we've--
we're pretty good
on that boundary.
But you could, depending on your
reference, go through and crop
out a little bit more but for
what we're doing today I think
we're in-- we're
pretty good right here.
So, for those of you that did do
this, all you wanna do is click
on these three-- these three
documents that are up there.
That's Glow, Bounding
Box and Ortho Slice.
Once you click on one you
can just Control-Exit--
Control-X rather.
And then it will remove it.
So we wanna go back
to where we were
when we originally
loaded the data set
so that we're just
left with our DYCOMS.
So does everybody
just have the DYCOMS?
So for this particular
data set and this varies
for every single scan
that you're going to have.
These CT-Scans that we
captured were loaded resolution
and we need to convert them to
a high resolution data sample
so that we would have a
very accurate 3D bone model.
So we've gone through some
image processing steps
that aren't always necessary.
So what we're going to do first
before we even open up the data
in order to do the segmentation
is we have to resample the data.
So if you are to right click on
your data set, and you wanna go
down to where it says compute,
so in your instruction,
it says--
>> And the properties area?
>> You go over--
>> You're going to
select cubic width 8--
>> You wanna go down
to resample--
>> From your filter menu.
So in your Filter
Menu, you just scroll
down to cubic width 8
and just select that.
>> And then we want to
click on the Voxel Size
which is in the Mode option.
So click on Voxel Size and
we want to get rid of all
of the numbers that are current
here so we're going to change--
>> So we want to-- want to--
>> -- them on to 0.8.
>> We're trying to make
a high resolution scans,
so that you'll see that the
Voxel Sizes were very large
and we're reducing them and then
we're gonna do an interpolation
to kinda smooth out our data.
[ Inaudible Remarks ]
>> So this is mostly important
because we've used
live patients.
So when we work with the
anthropology department
and we just send the bones
through, we obviously scan those
with as high resolution
as possible
and then we have these-- bone
models that are highly accurate
and we can't do that
with the live patients.
So we have to do
some image processing
to try to fix that exactly.
So you just wanna hit Apply.
So in your instruction, it
says that a new file is going
to appear in the pool and it
had this .resampled file name
so if this is all popped up, you
now want to make sure they click
on that one so that your
properties area changes
once again.
And we know that we're working
on the resampled file
rather than the original.
[ Inaudible Remark ]
>> Yes.
>> Okay, great.
So this particular data set
doesn't have any dental implants
and we did that for
simplicity reasons.
This person really I believe
doesn't have any teeth
so it's beneficial.
But the next step that we
normally would do is we would
right click one of
our data set again,
we wanna go down to
compute and then we want
to select Cast Field
from the Compute option.
And the reason that we're
doing this is the metal
in the CT-Scan sometimes from
the cavity fillings or any
of the dental implant would
cause this severe scattering
in the mouth that would
overcome the mandible and some
of the other portions
of the skull
which was a pretty
severe problem for some
of our data sets and we would
do this to try to reduce
that metal artifact effect.
We would keep with that
unsigned char 8 bit
so you actually don't
even have to click on it.
This was the option
that we were using
for this particular data
set to try to reduce
that metal artifact but we
would just hit Apply just
so this CAS field option was
applied to our data set as well.
So now this third--
modified days that should pop
up with this extension,
the two, hyphen byte.
So does everybody
have that as well?
Okay, so this is where we're
actually gonna begin our
segmentation process.
So if you make sure
that you click
on this third modified data set,
you want to right
click once more.
You wanna go down to
labeling and then you want
to select Label Field and this
is actually gonna open a brand
new segmentation
editor in Avizo.
[ Pause ]
>> So is everyone here?
So if you start at page 4
of your instruction sheet,
it kinda starts there and
gives you a basic overview
of this segmentation editor.
So you can tell the entire--
the entire user interface
of Avizo has now changed.
So you still have this
3D viewer and it's split
into the three views and then it
also gives you where each slices
in the top left hand corner.
This very top section is
called your Materials Section.
We're not gonna edit
this much today
because we're not using
a number of materials.
But if you were segmenting
multiple bones or if you wanted
to separate the crania from the
mandible then you could create a
number of materials and then
you could separate those
for the purpose of what we're
doing today we're just gonna
segment everything
into one main material.
You have your tools
window which is where all
of your segmentation
tool come into play.
So we're gonna go through
these a little bit.
So beginning on page 5
is a brief description
of all of these tools.
So it shows you an image
of just this toolbox area.
Your segmentation tools and
we're gonna do this mostly
for the cervical vertebrae that
we're going to try to remove
from our model because
we cropped it.
I'll start off by the
Zoom buttons here.
You can kinda zoom out.
You have a zoomed
in data window,
you have a magnifying
glass with a plus and minus
and that will zoom in
your data set or zoom out.
But you can see from the
bottom two images that several
of the vertebrae are also
included in that so we want
to try to remove those.
So this is where our
segmentation tools are gonna
come into play to try to
go through and remove this.
So there are several on here
and they're not all described
in your instruction
sheet because some
of them just aren't
relevant to what we're doing.
You will notice that
you have this all slices
and then this current
slice and then a checks--
check box that says "Show in 3D"
and this is one of the really,
I guess the most tricky things
about this Avizo Program is
that the 3D button and the All
Slices Option can save you a lot
of time.
But it can also set
you back greatly.
So when we are spending
hours doing some
of these segmentations for
ones that are very difficult,
you can use the 3D button to
select several materials at once
and I'll kind of show
this in a second.
But you can also accidentally
select them and delete them
and there is current no undo
button that we're aware of.
So we have done these for
hours before and you're tired
and you just kinda
mess up a little bit
and you click a button and your
whole segmentation is gone.
So we kinda put a little feature
in your instruction sheet
to just try to-- it's
really hard especially
when you're first beginning
but try to always be aware
of whether or not you're doing
these segmentation process in 3D
or if you're doing it
just for the single slice
that you're looking at.
It gets a little tedious
and it's a little sometimes
annoying if you do mess up.
So you have the clear
button, looks like an eraser.
So if you ever have anything
that's selected and you'll see
that it'll show up in red
and you don't wanna use that,
you can go ahead and
click that Clear button
and it'll just undo
your selection.
And then you have this plus
button and a minus button.
And what these do is
these take that selection
that you have that's highlighted
in red and it will add it
or subtract it to the material
that you have highlighted
at the top.
So this really comes
into play say,
if you were to separate the
mandible and the cranium.
You can select a
piece of material
or you can select an
area on your image
and then you could select
the crania or mandible
and then add it or
subtract it there.
Your segmentation tools which
are described at the bottom
of page 5 start with your arrow.
You have this arrow which
basically picks any region.
Right now, there is no-- there's
no boundaries on your image.
So if you select anything
it's just gonna select the
entire image.
You also have this brush tool
which is probably the most
convenient of everything.
Your brush tool, if you
select it has the set sizes
that you can select but it
also has this toggle bar
so you can make the brush tool
as big or as little as you want.
And what the brush tool will
do is if you have a boundary,
you could just draw
in your image
and decide what you wanted.
So for example if you
were doing this by hand
which would be very difficult
because it's not that accurate,
then you could add that to
the crania and you can see
that you now have this
purple kinda boundary.
But we'll unselect that
since it's clearly not
where it's supposed to be.
So you also have what
they call the Lasso Tool.
And the Lasso Tool
is pretty convenient
because it will actually
Auto Trace along the edges
of similar pixels.
So if you were to
select the Lasso Tool,
I always use this
Auto Trace option.
It's the best when
you're doing this lasso.
And you can click in
one area and it's--
maybe I should zoom in.
You can click along in edge.
I don't know if you
can see that little--
can you see this yellow line?
>> Yeah.
>> You can see how it just
kinda hugs the boarder
of the white area and
it really won't go
out into the darker space.
So it's fairly accurate in
being able to detect the edges.
And then the last tool
that I think is useful is
what they call this Bloat Tool
which is the very last one.
You can change the
tolerance and the gas width
but we don't modified
that that much.
And what it'll do is you
can start in the center
of a selected range with pixels
and you can just press down
and then reach out and
it will continue to grow.
>> It'll do this region growing
for a set of pixels that's
within that same area.
So these are all the three main
tools that are kinda describe
at the bottom of your
page 5 instruction sheet.
So what I mentioned at the start
of this is we've kind of gone
through already and done
some image processing.
Some steps so that the data
set look the way that it does.
And we did this in order to
create it in a high resolution--
a high resolution scan but
this also made our segmentation
process very uniform
so that normally,
there are some user
interpretation I guess
in their segmentation process
but we kind of eliminated
that by being able
to do this next step
which we're gonna
do as thresholding.
So I guess this would be on your
page 6 in the very beginning
or in the very middle.
I'm sorry that says to
proceed with the segmentation.
So it says in the 3D viewer,
you will click on Selection
at the top here and you're
gonna go down and you are going
to select Threshold and you
should have this new threshold
box that kind of pops up.
[ Pause ]
>> So what I would recommend
is moving it out of the way
of your 3D viewer a little
bit because when we put
in some values, it's actually
gonna modify the images
on your 3D viewer.
So what you want
to do is you want
to select your minimum value to
150-- 150 and your max to 255.
Does everyone have
this window up?
You wanna select all slices
which means that every slice
that we upload into Amira it's
gonna do the same thresholding
process for every
slice and you'll see
that in the top left it
created this model, a rough mesh
of the selection or the--
everything that we have
selected in red so far.
So once you all have
all slices selected,
you just wanna go ahead and
hit Apply and you'll hit Close
and everything should
still be selected.
[ Pause ]
>> Are we all okay here?
So you'll see that inside
and your materials
is already selected.
It's kind of highlighted
and if it's not you just
have to click on it.
We wanna add this to what we're
just gonna call the inside
material and you can go
ahead and hit the plus button
and it will change it to
the color of that material.
You can also-- you can change
the names of these if you want.
So you can-- when you have
multiple materials you can do
that you can also change
the color you wish.
It might be easier, red
is sometimes easier to see
against the gray background
so maybe that'll help
on the screen, they're
kind of the same.
So you'll see that the majority
of all of the bone is selected
and then it also has this
head rest that's in the back
of the patient's head
that's selected as well.
So what we want to do is
we want to go through now
and manually kinda edit
this and make it as good
as we can using those
segmentation tools.
So the first thing that I
would do, normally I wouldn't--
just as a personal preference,
I would not segment
using all three
of these open views
'cause I like to zoom in
and see what I'm doing.
But I think that it's helpful
for this session at least
to kinda see what's
happening in all three views.
So if you select your
pointer tool, just your arrow
from this toolbox and if
you zoom in a little bit,
so I zoomed in twice,
maybe three--
or maybe just one
time would be better,
so that when you're
in this area.
What I wanna do first is I
want to remove that area--
that middle or that-- whatever
that material is that's laying
in the back of the
patient's head.
So if you use your tool, your
Pointer Tool, you can click--
it's probably the easiest to
see in this bottom left view.
You want to try to click as
closely and as accurately
as you can into this
small little red line.
If you click outside the red
line it's just gonna highlight
the rest of the material
in the background.
If that happens you can just
hit your Eraser Button again
and if you have to
zoom in or move around
and you can do that as well.
But you want to try to
select this background
so that it highlights and you
can know that you're accurate
when that whole little kind
of semicircle appears
on the top left.
So did everybody get that?
So we don't really
care about this, right?
It's not part of
our segmentation.
It's not something
that we want in there.
So we can just go ahead and
do is hit the minus button
because we just wanna
go ahead and remove it.
And you'll see that
it's no longer--
no longer has that red
boundary around it.
So we wanna continue
to do this for as much
as the data set as we can.
In scrolling through
you'll see--
I think it's easy in this view.
You'll see this small section
that's just in the center.
Here, obviously that's not
something that we want to have.
So you wanna kinda scroll
through these three views
and try to find any things
that are out of place.
You'll also see in the
bottom left in the very,
very bottom corner, you
have what's probably a piece
of the clavicle or some sort of
piece of shoulder that's there
and what we want to do now is
go through and try to remove
as much of these areas that
are not part of cranium
of what we're gonna be
doing in the analysis on.
So what I would recommend doing,
because now it's really
difficult to kinda stay
in these three views is if
you're zoomed down enough
where you have this background
around your slice you can click
and empty space in one
of them, say if you click
in the top right which is the X,
you can click in
this empty space.
And along this top toolbar here,
this is you four viewers you
can do two, you can two vertical
and then you can do one.
So if you click here
and you know
that you've selected this
one, you can click one
and now you just have the one
viewer there and you can zoom in
and modify your window so
that you can scroll through
and save the data set
as much as you want.
[ Pause ]
>> So what I think we're
gonna do is I'm going
to kinda let you guys go for
a second and try to scroll
through these and
I'm gonna try to walk
around and try to help you.
So what we want you to do and
either of these three views is
to find a slice say
like this one
where you have these little
artifacts that aren't part
of our segmentation, you wanna
go through and remove those,
continue to find things like
that and remove that from
that inside material
until all that we're left
with is the basic crania.
And one of the main problems
that we're gonna face
and what's probably gonna
take us the longest is to try
to remove those vertebral
bodies from the scan.
You can see-- of course, in this
bottom view what is the most
difficult when it comes to these
live patients is the vertebral
bodies really have no separation
between the base of the cranium
and the first C1 and C2.
So you can kinda modify your
data window a little bit.
We're not really gonna do
that so it really kind of is
up to the user's
interpretation of where the base
of the skull ends and the
vertebral bodies start.
So that's gonna be the difficult
part but if you just wanna play
around with Avizo for a
little while, you can play
with these three windows,
you can kinda scroll through,
use your pointer tool
if anything separate it
to select an independent
body and remove it
and then I can come
around and just kind
of show you guys how I would
recommend doing other pieces
that might be more difficult
like the vertebral bodies.
So I'll just walk around
and if you guys know have any
specific questions just call me
on over and I can help you.
So I should kinda
clarify this I guess.
Because I said there is no
separation between the cranium
and the vertebrae, you're not
gonna be able to just click
on it like you do those--
those little areas
that are kinda floating
around in the brain.
So what you're gonna have
to do is pretty much you
use your Paintbrush Tool
and you're gonna have to for a
select certain set of sliced.
You're just gonna have
to go through and use
that Paintbrush Tool,
highlight the area that you want
to remove and then remove it.
So this is just when up to
be a little more tedious.
[ Inaudible Remark ]
>> I have a question?
>> Sure.
>> If you click-- you
click along the left area
but didn't mean to or how
do you unhighlight it?
>> You can just click this
eraser button or clear
like the letter C on your
keyboard clear also means clear
so you can just click
that Clear button as well.
So if you look up here now,
I have it set up to a place
where you can see the main shape
of that vertebral body there
and so I know that this
is separated from my skull
and I know that that's
a vertebral body.
So if I wanted to take my
paintbrush in this view
and I can just start kinda of
going over and I don't have
to be accurate here
'cause I'm just--
I wanna make sure that I
cover that entire area,
you can see even
though it did on slice,
you can see in these bottom two
areas where I've highlighted.
So you can actually
see how it corresponds
to these slices here.
So you can see that
I'm pretty far
down because I'm not
anywhere really near the base
of the cranium.
But when I highlight it in that
one area or in this one slice,
I can then go and I can remove
it and it's no longer there
and there should also be-- if it
was where I had a vertebral body
but you would see blank
line and all three slices.
So it doesn't matter
which view you do this in.
I could do it here
and I can take this
and I can come all the
way down and you'll see,
here I've highlighted
this whole slice
and you see how it corresponds
this one slice over here
and so I can erase it
in that image as well.
And so it doesn't really matter
which view you're working in.
You can choose to view-- that's
why I think it's a little easier
to sometimes click on one
window and zoom it in.
But you can do it on any slice
you want and just go through
and start removing what
you know is not cranium.
Yes?
>> Then how can we select
from this slice to this slice
[ Inaudible ]
>> Great, so there's
many tricks in Avizo
that save you lots of time.
So ideally, what you
can do is this 3D button
that we've mentioned is
going to select materials
that are touching one another
that are continuous
in multiple slices.
So if you come in this, say
top XY plane and you make--
if you cross it out like I
did where there's, you know,
I just removed a slice.
You have this whole volume,
let's say the top portion
of the cranium, then I cut
off a piece of the vertebrae
and I'm still gonna have
the rest of the vertebrae
that still another volume.
But because I separated
this one,
the two are no longer touching.
So what you could do, which
will save you a lot of time
and hopefully if-- I don't know
if these two dots that are right
at the top of that particular
vertebrae will be a problem
but we can see.
So what you could do is
which direction am I going?
I'm going up.
So let's find my slice here.
I've got all of this
that's all touching
and then I have my slice
that I kind of deleted.
So now I can go here so
I'm moving posteriorly
and I should be able
to 3D select the
vertebrae which is great.
'Cause you can see that I
have selected it up there
and it's hard to see-- I think
for me it's hard to see up here
but you can kind of see
that it makes like a mesh
of the vertebrae that I have.
You can see in this view that
it selected the vertebrae
at the bottom.
And so you can scroll
through and you can see how,
you see all of the
red that's selected?
So I've just now selected the
entire volume, same thing here.
I've selected all of these
vertebral bodies that lie
between and this-- this
is probably the best view.
You can see here,
this little blank 1,
really tiny slice is
the one that I removed.
So now you can 3D
select this entire body
and what you just have
to do is go through
and hit your minus button
and all of that's gone.
And it'll be gone
in all three views.
So you just have to
go and scroll through.
So this is where it's
very difficult and this is
where your paintbrush will
probably have to come into play
when you have these
edges that are just,
that are just continuous.
So you would have to come
in knowing your knowledge
of anatomy and go through
and make the decision
on what's vertebral body
and what's the cranium.
So when it comes to
be this very genet--
general area, I guess that's
when you would use
your paint brush
to be a little more specific
and kinda got through.
Does that make sense?
So what's great about
Avizo is it seems
like it can be a little
time consuming and Avizo
with all segmentation programs.
But there's lots of--
there's lots of shortcuts.
Just like thresholding
was a major shortcut.
If we didn't threshold,
you would otherwise have
to use these tools to go through
and select all those pixels
that are the bright white
that are the cranium.
So there's lots of tools
where you can do this
and that three-d button does
come in handy quite often
so that you can do
stuff like that.
So because we are-- we actually
have already segmented this
model and we have it saved into
the folders on your computer.
So we're gonna using that
three dimensional model
for the next session
after lunch.
So we don't actually
have to finalize these.
But you can I guess get a
feel for just the difficulty
in trying to separate
out the cranium,
base of the cranium
versus the vertebrae.
So if you-- I'm assuming
that you guys are not
gonna wanna finish these
when we come back for lunch
'cause we're just gonna move on.
So and to get to an end
point of where you are now,
we're just gonna close out where
your current segmentation stands
and we're gonna make three
dimensional model of it just
to finish up the process
of how you will do this.
So, once you guys are to a
point where you can stop,
you just go ahead and hit
Close and it will take you back
to this main user interface.
If you had your labels,
one thing that I tell our
under grads all the
time is to save, save,
save because the 3D button, with
that 3D button and being able
to erase your entire
segmentation you wanna save it
as often as possible
and we just try
to get the routine
of doing that.
So in case you do mess up,
you can kinda just go back
to your last saved file.
So if you were in
this label's area,
it's just like any program, you
would just go to File and down
to Save Data As and if you
were to do that it just comes
out same name that's currently
in the file which you see
in the pool, it's
just the labels.
You can rename it if you want,
otherwise you can just
go ahead and hit Save.
So now we're back to
closing that out anyway.
So what we're gonna do is create
the three dimensional model.
And so in order to do that,
you want to right click
on your label's file and you
want to go down and select
to surface gen. So this is
gonna generate your surface.
From this smoothing, drop down
menu and the properties area,
you want to select none.
And then you just wanna
go ahead and hit Apply.
Once you see this new
surface file has popped up,
so you can click on this,
you can right click,
and select Surface
View and a surface view
of your file should
actually open.
Now I didn't do much mine
obviously, so I still have all
of these specs that
are scattered around.
But all of yours should probably
look different depending
on how much you've removed.
[ Laughter ]
>> Ah yeah.
>> So on your mouse you all
have that roll button as well,
you can roll while
you're in this area
and it will zoom
in and zoom out.
So you can kind of see what
your model really looks like.
And if you really zoom in,
you can kinda see how
it's really rough.
It's really, really rough.
And so what we need to do
next is go through a series
of smoothing steps in order
to get this skull model
down to what we feel is smooth
so that you can view it.
But not too smooth because we
don't actually wanna remove the
features that we're looking for.
So the first thing
that we're going to do
from the surface file that
we have, you'll see here
that the number of
faces Dr. Mahfouz says
that we were using files
that have 100,000 faces.
But this one has over
1 million right now.
So we're gonna through a series
of steps and try to rem--
reduce this file from over a
million faces down to 100,000.
So you wanna select--
[ Inaudible Remark ]
>> Just click on
the surface file.
>> Oh.
>> So you wanna select
this Simplifier Tool,
looks like a bunch
of crossed lines
with a triangle in the middle.
And once you click on that,
you'll see that this new
option pops up and you'll see
that it has a number
here for faces.
And so in your instructions,
it actually says
that you just wanna
automatically skip
to 100,000 faces.
>> But we did this yesterday
and it doesn't provide you
with a model that's as
smooth as we would like.
So what we would
recommend you do in as going
through this process
several times to reduce down.
So what I would recommend
starting at is 500,000.
So once you've entered
that number into faces,
you wanna select the Preserve
Slice Structure Option directly
under Simply Faces.
And then you wanna go
ahead and hit simplify now.
And the bar, your loading bar
at the bottom should go through.
And what it is doing is
it's simplifying all the way
down to that number.
[ Pause ]
>> So now that's update it and
you'll see that it's reduced it
to close to 500,000 faces.
So the next step that we
wanna do is right click
on your surface file, and you
want to go down to compute
and you want to select
smooth surface.
So you wanna right click
this surface file once it's
down to 500,000 faces, go to
computer and smooth surface.
So just let me know if your
computers are not running
as fast as this one.
So once you're there you
wanna input 20 iterations
and just go ahead and
click Apply at the bottom.
[ Pause ]
>> So you'll see-- I don't know
if yours is the same but we have
so many files now that
I need to scroll down.
Because a new file
has been generated
that has this smooth
name at the end.
And so what this one has done,
we went from over a million
faces to 500,000 faces
and we have smoothed
it so if you want to,
you can right click, you can
select Surface View Again,
and then you can come up to
this original surface view
that you had from the
over 1 million faces.
And you can click on
this little orange box.
And what this is gonna do
is hide the original one.
And you can see how
smooth it went.
So what we would do is would
just repeat those last two steps
to reduce the number of
faces to 100,000 and then do
that smooth surface step
one more time until we ended
with the file that's
at 100,000 faces.
But once you have the smooth
model, you can kinda scroll
through and look at all
of the features that are
on this particular cranium.
And here you can
actually see that mine,
if you can kinda tell, still has
in its higher C1 that's still
attached to base of the cranium.
So this is pretty much
just where you would end
up with the actual
segmentation process.
You would end up with this
model that's 100,000 faces
and then you would then
take this model and input it
into the [background music]
software that we have developed
which is what we're
go over after lunch.
[ Music ]
