Hey guys, in this video I'm going to do another Freesurfer video. This one is about another update
to the hippocampal subfield segmentation. It's basically going over this tutorial page and I'll
put it in the description box below. This is my third video on hippocampal subfield segmentation
because I guess they're really interested in it, because they keep updating the functionality of
it. For this update--well let's go over it--the update is it uses less memory,
they now automatically will segment the nuclei of the amygdala in addition to the hippocampal
subfields, and that's important because in certain parts the hippocampus and the amygdala are right
next to each other. Now you can see what they're calling the amygdala and what they're calling the
hippocampus and you can see if there's any gaps and to make sure that there are no overlaps.
And they're also updating the labeling a little bit. As you can see in this little figure.
The anatomical terms are on the left and these are still in the update and now they
also have these optional hierarchical labels in lavender and they give you--the three are included
automatically. It's common to talk about like the hippocampal head, the hippocampal tail, and so now
you can get these volumes if you want to know like the hippocampal volume of the tail only
versus the head. And this is the old freesurfer 6.0 version in addition to these other two labels.
They have basically new labels, they added the amygdala in addition to the hippocampus, and also
supposedly it uses less RAM as well. I'm going to go over basically a demo in this video of the
update. The first thing to notice that it says in the first sentence is that this is not part
of the stable release yet. As I'm making this video, the stable release is still version 6.0 for
Freesurfer but you can download the developmental versions. So if you go to like the downloads page,
there is a section that lets you download like the developmental version. For Mac as I'm making the
video, the last developmental version was updated on November 7th and so that's the version that
I downloaded. And it's really--I mean it's really easy to go back and forth between the stable and
the developmental versions. I just downloaded them. I moved my Freesurfer stable version to my
desktop and then I just changed the developmental one to where the bash script profile looks for the
folder. So I have it here. And so I will maybe put a link to that in the description box as well for
you guys to find the download but you do need the developmental version for now. This has not been
released as part of a stable update to Freesurfer. Besides that, how you run it is very similar to the
Freesurfer 6.0 version. Like last time in the last video about it, you do need the MATLAB 2012
runtime and it gives you a free link to download it. You don't have to pay for it. And okay so let's
get started with the demo. To run hippocampal subfield segmentation the updated way, you again
need to do recon-all all for all the subjects that you want to do the subfield segmentation
for. So this is assuming that if you go into your subjects folder you have already your subjects
with recon-all done already. If you haven't done that, you have to do that first and then it
just gives you, when you download the Freesurfer developmental build, it will include this
shell script and if you run this shell script providing just the names of the subjects that
you want to run the segmentation on, it will do the whole segmentation. And so I did this on one
subject, which was my own brain and let me see if I still have it. I might have deleted the window.
Oh no, okay. I ran it and basically you just open a terminal window, you type in this shell
command, you add in your subject folder name. This ran for me about 12 minutes and then when it's
done, it gives you like all these citations that wants you to include, but when it's done, if you
go into your subjects--the name of your subjects folder--it changes the MRI folder. Now if you
go into the MRI folder and you look at the newest files that have been changed, it adds a whole bunch
of new files for the left and right hippocampus. There're so many because now you have the three
versions of the labels that you can use depending on which one you want. And you can run in another
terminal window this script to view what the labels look like in the Freeview. I already
have that pulled up here. So it does look different from the Freesurfer 6.0 version again. So going
through that...this is including the left and right hippocampus. Although actually it looks like it's
not showing up on the left but whatever. So yeah that's just a run-through of what the labels look
like and again you can get volumetric data. You can get volumetric data and now for the amygdala
and the hippocampus and with all the new labels as well. Again similar to the Freesurfer 6
version--oh and I should have mentioned, again like the Freesurfer 6.0 version you can use multiple files.
I just used a T1 only but you can use multiple files for the same subject if you have like a
higher resolution or a T2-weighted file that you want to combine or that you want to use both for
you can do that again just like in Freesurfer 6. Basically everything you could do for this
Freesurfer 6 version, you can do for this updated version just with a couple additional functions
and you can do longitudinal again like you could do it in Freesurfer 6 as well. That's all in
here but I'm gonna skip over that and what I was going to say next was about the volume data. Okay
here we go. Okay so it also provides--just when you download the Freesurfer version--it provides these
two scripts so you can get volumetric data for hippocampus and the amygdala. If you want the
hippocampus volumetric data, you use the first line. If you want the amygdala information, the
volumetric information, you use the second line. I did that as well. Let's see...I think yeah, it's
here. You do--you type in the shell script. This is for a hippocampal volumetrics. I just used a T1.
I just put T1. For this flag, you either put T1 or there are a couple different options basically
it'll tell you. It's a different option for T1 or if you use multiple scans or if you want it to be
longitudinal. You do hippocampus, you input T1 or whatever option you're using, and then just the
name of the output file. I was said to output it to a file called results.txt and that can be
opened up in a spreadsheet. This is the results for the hippocampus. It has additional labels in
addition to the Freesurfer 6 version and you can see like hippocampal tail for example, which you
couldn't see before. And hippocampal head etc. and just the additional labels. And then I did the same
thing for the amygdala volumes. Let me pull that up. This will give you--it will tell you in the
tutorial pages as well like what the segmentations are or what the names of the nuclei are and these
all have their own additional labels and you can get the volumetric data for them as well.
Yeah that's pretty much the video. It's just yet another update to the hippocampal subfields
because I know a lot of people have watched my videos on it and they keep updating it, so if
it's something that you're interested in I would look at the more updated versions as a suggestion.
*chiptune music*