In this video, I'll
be going over how
to import data into [3D] Slicer.
Now I will be touching
a little bit on how
to navigate
throughout [3D] Slicer,
but I'm going to save most
of that for a later video,
once you've been able to
import your own data.
>> When you open up [3D] Slicer,
you'll see this left
window that has
the two options
for loading data.
You can also always see
these up on the
toolbar up here.
The two options
are load data
or load DICOM data.
And which one
you select will
depend on your data format.
>> Now first I'm
going to show
you the easiest
data format to
load, which is the NRRD.
You click on the
load data tool,
then you click
Choose Files to add.
And finally, you select
the NRRD that
you want to load.
Depending on the
size of the file,
it could take a little
bit of time to load.
>> Okay, now you
can see that
my volume file has loaded.
I can scroll around
and a little bit.
And one thing
I wanted to note is
that I can go into
first the data module
and the volume
will show up here.
The data module will
tell you anything you
have loaded into the
your [3D] Slicer scene.
And second, I can go to
the volumes module,
which tells you
about your volume.
And if I select
this volume that
I just loaded,
you can see that
it actually
has spacing
information saved
in it along with
the images.
>> So this file has a
0.02 millimeter resolution
for each pixel.
If you don't have
image spacing
information [3D] Slicer,
we'll just default to
one millimeter for each.
>> Okay, I've cleared
out the scene,
so now I can show you
how to load in an emit,
a stack of images
that's not saved
as just one file.
So again, we'll go
to the load data.
I will click Choose
Files to add.
And then you will be able
to see here that I have
this folder that has
a bunch of bitmap
files in it.
These are all part
of the same volume
and they're all in order,
but they were generated
that way.
And they are the only thing
that is in this folder.
This will not work
correctly unless the
only thing you have in
the folder you're
loading from
is the images that are
part of the volume.
So I can just select
the first image and
[3D] Slicer will think it's a
scalar overlay to start,
but I can switch
this to volume.
>> Next, I want to
show all options,
which is in the
upper corner here.
>> And I want to uncheck
the single file option.
Basically, this is
telling [3D] Slicer that
the file I've selected is
the first of many.
I can then click
OK. And again,
we'll wait a little
bit as that loads.
>> Now that this
volume is loaded,
we can go into the data tab
again and see the volume.
And then we can go
into the volumes tab
and look at the
volume information.
And we can see that
[3D] Slicer has assigned
the default spacing of
one millimeter
to this volume.
That is because the
data we loaded was
only the images. I
would have to go
into the text file
is associated with
the scan to find out what
the actual image
spacing was.
The final type of
data I would like
to demonstrate
loading is DICOM data.
DICOM is unique to
medical CT scanners,
so if you
ever get fossil
scan within one you are
likely to encounter it.
First,
you can click on the
Load DICOM Data tab
either in the Welcome to [3D] Slicer
module like I just did,
or you can click this
DICOM button up here.
>> This window will appear,
which will allow you to
load the DICOM data.
You can see I already have
one scan loaded called
Patriofelis
we're actually
going to import.
And then you
would navigate to
the folder that
contains the scan.
>> In this case, I'm
going to be loading
Scan2. You will select
the folder and
click import.
Like everything
else, this is
going to take a second.
Once the data is loaded,
this message will
appear that will
tell you the number
of new patients,
quote, unquote, which
is just a scan,
and then the number of
essentially images in
the stack. And now here you
could see Patriofelis2 has been added to
my scan log. Because this
was taken in a format
that is intended
for actual patients,
you can
see I have metadata
like the fact
that this quote,
unquote patient's
name is
Patriofelis2.
>> This is just the
second scan we did of
the other fossils that could
fit into the first scan.
This automatically
generated patient ID.
>> We have the birth date
for Patriofelis
which just had to be
randomly set and
all this other information
that was filled
in automatically.
What I'd like to bring
your attention
to is down here,
you'll see two options.
One is this series
description, that's
just research.
It may be called something
else in your scan.
And then this one
called topogram.
You'll want this first one,
the research to actually
load the volume.
the topogram will
just be a single image.
And if you ended up
getting the wrong one,
you can always go
back and reload.
>> So I'll click Load.
>> And now you can see that
my scan has loaded here.
>> And of course,
if we go back
into this Volumes module,
click on Volume
Information,
you will see that
the image spacing
is all loaded in.
One thing to note
is that it's
not the same for each axis.
>> And that just has to do
with how the CT scanner
works where the x and
y will be the same,
but then the z spacing
or the distance
between the slices will
be a little different sometimes.
Now you may
encounter other types of
data that load a
little differently,
but those three that
I've just shown are
going to cover most
of the scenarios
that you'll encounter.
