So it doesn't actually seem like it did what we wanted.
We can say mask(mask = 0) = NA.
So we actually have to take out values that are zero,
otherwise they are going to get mapped to that.
And this is, for example, showing what it would like if you overlaid them.
We can also change col.y="red".
So now we're saying these are the values over 500,000 on the slices of 30,
90, 180, 200.
But again, papayar will allow to do this kind of interactively,
you have play with some of the controls, kind of get a handle on it and
we're not going to go into all those controls here.
But it's good at least for the very basics of putting an image and
an overlay and you use this papaya command.
There is the ITK-SNAP R, if you've ever used that and
you're more comfortable with that.
FSLView also will allow you to do an interactive viewer that
has a little bit more tools, has the ability to do histograms.
If you want to install Mango on your own that is also an option.
But the nice thing about Papaya, or Papayar,
is it allows you to manipulate objects in R like you normally would, and
you just pass in a list of those NIfTI objects.
Just like we've been showing you with some of the other commands and
that's how you can do interactive plotting in your day to day in Papayar, and
if you're using R Studio, will allow you to look at things through the viewer pane,
which I think is very nice.
And it'll actually keep that up for some time as long as you don't cancel this out.
So we can actually close that, and I'll actually close that connection.
But overall, Papaya is great because it's written in pure JavaScript so
that we don't have to depend on a lot of things for R to be able to use it.
Some of the functions, I think some of the functions in oro.nifti
are really good that have been expanded a bit in fslr like ortho2.
They're really good, I think, for customizing figures and
trying to get figures in the way you want them, but they're generally only 2D, but
for interactive viewing.
So if we're scrolling through images, if we're scrolling through slices,
I recommend using papayar, itksnap, or itksnapr, mango, or maybe fslview.
So I think these are some of the options that you have to explore your data
a little bit to find maybe somewhere where some artifacts are,
somewhere some oddities are in your data.
But this is a step towards interactive viewing that is very helpful in analysis.
All right, thank you.