[ Music ]
>> The software I'm gonna show,
it takes an input CT images
which is DICOM standard format
and takes STLs or IVs files
which is standard
formats as well.
So let's get started.
On the desktop you should find
the-- an icon called imf.exe.
And if you just double
click on that, okay.
So the first thing you
see when you double click
on this is like two options.
At the database or predict,
okay, and the difference--
did everyone get this?
>> No.
>> No. Yeah, the computer
is a little slow like--
so be patient is
what we're gonna do
because these computers
are slow.
Everyone have this message now?
>> Yeah.
>> Okay. So these are the
two modes that we can run in.
So the first mode which is at
the database which is basically
in this mode, you will need
the CT data 'cause then we will
acquire soft tissue
thicknesses along
with bone thicknesses
and some measurement.
And in the prediction mode,
you don't need the CT,
all what you need just
the IV file or STL file
for the surface model
that you segmented before.
So, we prepared a
tutorial to you.
The tutorial talks
about prediction
and to give you just a general
overview on what we're gonna do,
there are so many about--
might be some specific details
that is different but
I'm gonna start first
with at the database mode show
you some of the visualization
and the CT and then
we're gonna go do a forum
for the predict mode, okay?
So, what you see here
is print standard screen
that like what you saw in
a mirror but there is--
so you have the three screens
and each screen correspond
to a different plain,
so you have the axial,
sagittal and corona.
And the bottom one
is a 3D volume view.
So the first step we're gonna
do is if you click load volume,
okay, and then it will ask
you to browse for your folder.
So on your desktop, if you go
to workshop material
M64 DICOMs just click
on the DICOMS folder
and hit okay.
Okay? I guess you
can't see it from here
because of the resolution
but you should be able
to see it on your screen.
If you go on the viewing tool,
you'll find like few sliders.
So the two bottom
sliders, these are--
correspond to the window
level and the window width
that Dr. Mahfouz
spoke about yesterday.
You remember in the CT.
So, let's move the slide or
window level to the right
and you can see like how
it changes your rendering
for damage.
You see that?
So, this 3D viewer,
it give you an option
to see either this
license registered together
and this allow you to see like
some of the anatomical features
and the volume and you
can manipulate each view
by changing the slide
up corresponding side.
So you can move these
axial slides up and down
and you can look at the features
by moving the axial slider,
okay, and you can move the
sagittal the same way as well
and you can see how
its registered with it.
So-- so this is one
viewing mode, okay?
So if you click on
the other button here,
that switch from this mode
of rendering to another mode
of rendering is what we call
surface-- volume rendering.
Okay, so everyone, if you click
on the button up there, okay?
So what you see here is actually
a volume render of the CT volume
so you can actually, if
you put it all the way,
you can see your, all
about you see is a block.
If you keep moving, you can see
you get rid of the soft tissues
and you can see the bone.
Okay, so that's the effect of
the window level we spoke about.
[ Pause ]
>> Okay? Alright.
So as I said, I'm just gonna,
this part I'm gonna
do to my computer.
You don't have to do
it on your computer
because it might
be a little slow
but I will show you how we
collects points on the crania
and we add these points
to the database, okay,
and then we'll go
through the rest
of the tutorial on
your computer.
So, on the profile tool
here, these are the toolsets
that allow you to load
the segmented model,
the template model was
the fiducial marker on it
and then picking points on
this to get the skin thickness
and the bone thickness.
So, we're gonna start first
with loading the model, okay?
So we load the segmented
surface of IV
and what happens is it overlays
the model on top of the volume,
so you can see here
the segmented model
and the volume as well.
And then we're gonna load
the base mesh which it's
under workshop material.
There is a file called
baseskull.stl, okay?
And once you open this, it
overlays the base skull on top
of the other skull and
register them together, okay?
So the green one is
the template skull
that had the 32 fiducial markers
and the white one is the bone
that you just segmented in
the previous session, okay?
And they are registered
together so that it shows you
where are the location of the
fiducial to help you to pick--
to do your point
selection, okay?
[ Pause ]
>> Alright, so the first step
we're gonna do is taking the
bone and soft tissue thickness
at the 13 landmarks that we use,
there is a file on your desktop,
if you can open it,
called a landmark.
It's a picture file and this
file shows you the 13 locations
that we take the
measurement at, okay?
So, the first one is
supraglabella, glabell, nasion,
end of nasal, the chin-lip
fold, the beneath chin, lateral,
orbit left, suborbital
left, supraorbital,
frontal eminence left,
the supraglabella
and zygomatic arch
midway left, okay?
So, the software allows
you to pick the points
on the surface model at
these landmarks, okay?
So the first thing, if you go
to the profile tools
and hit pick, okay?
So what's gonna do
is just switch back
to the other mode, okay?
So you can go and highlight
points on here, okay,
and they display
for you the X and Y,
Z locations of these
points, okay?
So the reasons we are picking
areas not just a landmark is
if you pick a landmark,
you introduce more
intraobserver error.
But if you have a
selected area, you in--
this will reduce your inter
and intraobserver error.
And then we calculate the
average bone thickness
and skin thickness
of this area, okay?
So once you select these points,
you can see them here, okay,
if you hit the profile button.
So what the software
does now is go
and calculate the bone
thickness, the skull thickness
at these points and using
the volume data, it creates--
it calculate the skin thickness
and it displays for you
down here if you look
here, you see lines, right?
These red lines are
basically the distance
from the skull surface
to the skin, okay?
So if we go back and--
to the viewing tools and
overlaid the volume on top
of that and lets play with our--
so you can see where the end
of the skin hits the line, okay?
>> Can you lighten it?
>> Oh it's too dark.
We try to...
Can you see it now?
[ Inaudible Remark ]
>> Yeah, so the red lines
is basically the lines
from the skull bone
to the skin surface.
[ Inaudible Remark ]
>> Right here.
Everyone see these lines?
Okay. And also if you go here,
there's a profile tools
and you have plot.
What you see here, these arrows
that are moving is basically
what we call line profile.
You remember when Dr.
Mahfouz showed you a picture
of the phantom yesterday and
the line drawings of the phantom
and then you saw this graph.
So basically this is the
same idea but this graph is--
started this bone surface on the
skull and ends at the CT volume,
so you can see here, this
is where the beginning,
where the red dot is and the
end is where the white dot is
and then after this you have
black 'cause your outside the
crania volume.
Okay? And you can switch
between them to see.
Okay. And once you hit
the profile button,
what you would see here
is you'll see two--
each point and you'll
see the bone thickness
and the soft tissue
thickness, okay,
at each of these
locations, alright?
So basically, you--
we calculated the data at this
landmark and if you hit save,
the program will come up and ask
you which landmark it is, okay?
So this was at nasion, so if
you hit nasion and click okay,
so you'll find that this
appear from here and it goes
to another type at the end
called-- called landmark.
And basically the program saves
in the database, the landmark
and the average bone thickness
and the average soft
tissue thickness.
So that's what you
see here, okay?
And then you keep going on
the 13 landmarks and save this
to the database, okay?
So this is-- this is the only
difference between this mode
and the prediction mode is
in this mode, we load that CT
and then we'll gonna go through
in details in the other mode.
So, if you can close
your program actually
and open it again and go to the
other mode, the predict mode,
and let's go through
the full exercise.
So the first step we're gonna
do is loading the segmented bone
model, alright?
So if you go to your desktop,
workshop materials, M64,
you'll find the file
called segmentedsurface.iv,
so let's load this file.
[ Pause ]
>> And then the next step is
loading the template model.
So if you hit load base mesh,
everyone click on load base mesh
and you go to workshop materials
just to find that-- the file--
a file called baseskull.stl,
okay?
So everyone open that so now we
should like see the green model
on top of the white model.
Everyone has this?
Alright. So this viewer has--
you can rotate your model
around and look at it.
You can change the
transparency of the green model
so that you can look
underneath it.
The-- the other slide that
will make the white model,
which is the model you want
to predict transparent, okay?
So everyone can do
this, alright.
Okay, so once these two are
registered, now we are ready
to go and get our measurement
and the bone thickness
and the locations, alright?
So let's start with--
first with bone,
let's start with the
bone measurement first.
So on top here, you
will find two icons.
One called volume
analysis, and the other one
which has a ruler called
anatomical analysis, okay?
Do you see these two buttons?
So if you hit on the
anatomical analysis,
you will go to a
totally different view
with more toolsets, okay?
So on the side here,
you'll find two--
two tool boxes, one
called measurement
and one called landmark, and
one called points, alright?
So these are the three that
we're gonna be using today.
So the first step is in
our model, we use the--
okay, we use five
measurements, okay?
So the first point we're gonna
acquire is the nasion point,
okay?
So in order for you to do that,
click on the points text and
[ Inaudible Remarks ]
>> click on-- if
you-- it's on way--
on the bottom, if you click
on it, it will expand it
and then you should
see set of tools here.
Everyone has this tool?
Okay, so if you click on the
first circle, if you click
on this, okay, so this
will take you to a mode
where you acquire points
on the skull, okay?
So the first is in this--
in this mode, you will require
your escape button 'cause you
might want to rotate, so you
need to switch from the arrow
to the hand on rotate.
And to acquire the points, you
need to be in the arrow mode
so you need to press
escape again, okay?
Alright. So the first thing I'm
gonna do is I'm gonna go acquire
the nasion point, so if
you click on the area
where the nasion is,
this takes a point.
If you think it's
wrong, you can select it
and it will be yellow,
just hit delete.
>> Hit delete?
>> Yes, see this-- select
it, it will be yellow
and then hit the delete button,
and then you can go
and select it again.
So now we want to set this in
the database as nasion, okay?
So, if you click on-- if
you click on the table here,
left click and then do the
right click, and then click save
to the database, okay?
So the program is gonna ask you
for, what is the landmark name?
So this is what we
call the combo box
so I give you selection.
So if you had the arrow here,
okay, and select nasion,
you call see also the three
other landmarks will be acquired
which is basion and prostheon.
[ Laughter ]
So let's hit nasion
and click okay.
So you see the program took
this landmark, the point
and made it a landmark
so it made a big
green circle, alright?
And now, if you hit the landmark
step, if you hit landmarks,
you'll find the landmark
defined called nasion.
Okay?
[ Inaudible Remark ]
>> You can-- you can move,
you can hide and show this
by selecting the arrow
here, see the checkbox here?
You can hide and show
the landmarks, alright?
Okay, so let's now go and
select our basion, okay?
So if you hit the points, type
again, and then in the table,
select your point and hit the
X-- the X here to delete it.
So now let's go find
some basion.
It's under here,
under the [inaudible].
So we need the-- someone
didn't do a very good job
of separating here.
[ Laughter ]
[ Inaudible Remark ]
>> This is gonna--
actually has a fusion
so you can see there is--
so I-- I will select it,
I will select it here.
Sorry now.
[ Pause ]
>> Okay? So we're gonna
do the same step again.
Once you selected your points,
right click on it, and say save
to the database and in this case
we're gonna save it as basion.
Okay? So once you do this,
you'll find another green
dot down there, okay?
You might not be able to
see it so you can go--
if you had the models there
and then you see a slider
here called transparency,
you can actually
make it transparent,
you can make the
skull transparent
and look at it, okay?
[ Pause ]
>> So you can show it and even
you can hide the whole skull
and just look at it.
[ Inaudible Remark ]
>> Okay? Alright.
Okay, so now let's go
select the last one.
[ Pause ]
>> So the prosthion is-- is
usually the most anterior point
on the mid ridge here, right?
So you can see here,
you can see very well.
[ Pause ]
>> Okay, so now we're
gonna do the same thing,
save to the database and
save it as prosthion.
So now we can see
three landmarks.
You should be able to
see three landmarks.
[ Pause ]
>> So everyone see
these three landmarks?
Everyone has them?
Alright. So now you can just
go to the measurement tab again
and you help-- there
is a third button--
there are four buttons here on
the bottom, the last one called
"calculate default measurements"
and if you hit just this button,
so the program is
gonna go and calculate
for you the two measurements we
do using these landmarks, okay,
which is the basion-nasion,
and the basion-prosthion, okay?
And you can see here, it display
for you the two measurements
and the values for
these measurements.
So everyone at the
same point now?
Alright, so now we
need to go get three--
three more measurements that
we use in the projection, okay?
So let's get the transparency
back to the default value, okay?
So, if these two measurements
for the program to show them
to you, it makes them
like transparent,
makes them a little
but transparent.
So if it annoys you, you can
just go to the measurements
and disable them
by unchecking them.
So it's just like remove
them from the display,
they are still there but it
doesn't display it, okay?
Alright? So the three
other measurements
that we use is the
nasal breadth, okay,
and the orbital height, okay,
and then the bi-ocular width--
>> Biaricular breath?
>> Biauricular breadth, alright?
Okay, so first I'm-- for you
to do these two measurements,
if you go to the measurement
tab, hit measurements again,
there is set of tools here
that you can get
measurements with-- with.
So the first one is
getting line measurement,
the second one is getting
an angle measurement, okay,
so in this case, we just want
to do a line measurement, okay?
So right now, on our model, we
have the left orbital height,
that's what we use and
approximate the right
with the same measurement,
so we're just gonna acquire
the left orbital height, okay?
And to do that, go and
click on the ruler, okay?
And then you will need
to click two times.
Click on the first point,
and then while you're still--
your hand is still on the
mouse, drag your mouse down.
So, click and then drag,
and then release once
you hit the other point.
[ Inaudible Remark ]
[ Pause ]
>> Okay, so hit the first
point and then keep your hand
on the left button, then once
you reach the second point,
just release, and it
should pop a dialogue asking
for the measurement, okay?
So when you do that, if you
open the combo box here,
you will see the name of
the-- of the measurements,
so select orbit height
left and click okay.
Okay?
[ Pause ]
>> So do the same thing.
[ Pause ]
>> Okay? Everyone get
the nasal breadth?
Alright. So now the last one
which is biauricular
breadth, alright?
Okay.
[ Pause ]
>> Alright, so for me
to get this measurement,
there is a button here,
if you right click
and show decorations,
right click on your viewer
and say show decoration, okay?
And this will show you
a toolbar here, okay?
Okay, on this toolbar, there is
a little box down here, okay?
So what this box do is it
switches between isometric
and orthogonal viewing, okay?
So let's make it orthogonal.
[ Inaudible Remark ]
>> Oh, right click on the
viewer and say decoration.
So that everyone see
this orthogonal view,
so now you can go and hit one
end and you can keep moving
to see where is your
minimum distance is.
Okay?
>> This is biauricular breath?
What do we...
>> What's that?
>> This the biauricular breath?
>> Yeah.
[ Pause ]
>> Oh I see it now.
[ Pause ]
>> So now let's go get some
bone thickness measurements.
So if you go back to the other
tab, the volume analysis,
if you open your-- the image,
you can see what landmarks we
need to acquire, so let's start
by the supraglabella,
glabella, nasion,
end of nasal, and so on, okay?
[ Pause ]
>> So you can-- as I said, you
can change the transparency
of the model and you can see
where the fiducial marker was
on the base skull
and this can help you
to add the landmark points.
Okay? Alright, so once
you know where you want
to put your landmark, you
go on the Profile Tools,
click on Profile Tools, alright?
And then, you're
gonna click Pick.
Okay? Alright?
And then, basically,
you'll go and select an area
around the glabella point.
Alright, so once you have
this, if you click Profile,
see the Profile button here?
Click Profile, it's gonna
take you back few seconds
and it should come
back with bunch
of measurements here, alright?
Okay? And then the-- it
will come and ask you what--
what's the name of the landmark,
so select supraglabella.
And then this case it
will go to the other table
which you called landmark,
so you can see here,
there is different
tabs down there.
So if you go down to the
one called landmarks,
you will see the average bone
thickness of this landmark.
Okay? Alright.
So I'm gonna go and select
the rest of the landmarks.
Right, so you guys know
how to select landmarks?
>> Can you do it again?
>> Yes, I will do one more time.
So let's get the-- let's
get the glabella, okay?
So click Pick, okay, and then
with the left mouse button,
keep pressing and
select the land--
an area around, or you can just
click one by one if you want.
Okay? And once you select all
of them, you click on Profile,
okay, and then it's gonna
go calculate the distances,
you click Save, select the
glabella, and then I'll go
to the landmark table.
And as we can see here, the
skin thickness is zero 'cause we
don't have a volume so
all-- all of them are zero,
so we're only collecting
bone thickness.
>> So the end of the
nasals is a bunch of points,
a point cloud, not a point?
>> You can just take
a point there.
>> Just take a point?
>> Yeah, you can take a
point there, that's fine.
Okay, if you-- if you don't
know where the landmark is,
basically what you
can do is you can go
to the base model slider and--
and play and change
the transparency
and then it will show you
again where the base model is,
and where the markers is,
and that's gonna help
you pick where it is.
[ Inaudible Remarks ]
>> So you can pick
one and then once it--
it disappear you can go
back and move the slider
and then you can pick again.
[ Pause ]
>> So once you get
your measure--
your 5 measurements and your--
13 landmark, so all what
you need to do is just--
there is a button here
called Predict Soft Tissue,
so just hit this and it
will give you an end.
Okay. So basically, when you
hit your Predict Soft Tissue,
so it will give you the soft
tissue thickness at each
of these landmarks, okay,
in millimeters, alright?
What?
>> so-- so basically
like-- so these--
[ Inaudible Remarks ]
>> So these--
[ Inaudible Remarks ]
>> So this thickness is--
is the same as if you
got this measurement
and went to the table.
So there is-- the model--
there is four parameters here
that the model can
take into consideration
and if it's not available, just
ignore them, which is the age,
the height, the weight and BMI.
So you can go and
enter these parameters
and it can click Predict Again,
and it will enhance
your predictions.
Okay? So [inaudible].
[ Inaudible Remark ]
>> Yeah, you can go on with--
I believe this person was 1--
109-- weight, 109
kilograms, and height,
180 centimeters,
and the BMI was 33.
>> Weight in kilograms?
>> Yes, it's kilograms, yes.
Actually, this tool--
it's actually--
it's a more general tool and
what customizes to this program,
so I'm gonna show you like some
other analysis you can do pretty
quick on the skull and--
and then we can end
our session with this.
So, there are other
tabs here as I said
and the anatomical analysis.
So one-- one more tool on the
measurements that we didn't use
in this application was for
example, the angle, okay?
So the angle is basically
you go and get three points
and it measure for you like the
angle between the three points,
okay, so this is one tool.
There is also a very useful
tool that we use under here
and analysis in general
which is called contour tool
and basically what it
does is it slice anatomy
in a certain direction.
So actually, let's
say, you want to look
at the cross section of--
of the skull in a certain
direction, alright?
So, if you click on
the contour tab, okay,
and hit the first button here,
okay, it will ask you to,
what kind of contours you want?
So there are two
modes of contours,
you can select contours which
is called translational,
so it's basically gonna slice
along an axis, or rotational
which is gonna rotate around
an axis in a certain angle.
So let's for example
select translation, okay?
And you have to select
the first--
the two points that--
of your axis.
If you hit select
on the first point
and then select on
the second point--
[ Pause ]
>> Okay? And it's gonna show you
like what is the direction
it's gonna cut into?
And then it defines
a number of steps
or how may plains
you want to use, so.
Okay, so I'm gonna cut
between these two distance
with 10 steps, and
if you hit Run.
>> Now, if you were doing
this without us here,
how long would it take you?
I mean obviously this
took way longer with..
>> Well, it seems like--
like, takes me like--
'cause I know where--
what is the landmarks are,
takes like 7 minutes with the
measurements and the landmarks.
For a full run.
And actually, a lot right now--
like the way this was developed,
we had two grants going
in parallel actually.
We had the Facial
Reconstruction Grant
and we had the Skull
Sexing Grant.
The Skull Sexing Grant we're
automating the measurements,
so we did the automation
for the measurement.
And this was going on
in the same time and--
and we needed a tool to collect
this data and build the model
but what we're doing right
now is merging the automatic
measurements we're doing from
the other grant with this grant
to eliminate the picking points.
The difference is that in the
other grant 'cause it's dry
bones and we don't take the
mandible into consideration,
so this is where we're merging
the two to get the atlas
for the-- with the mandible also
to get our automatic
measurement.
So, any questions?
Okay, thank you.
>> Thank you.
[ Applause ]
[ Music ]
