Hey guys, in this video I just wanted to give a quick introduction or explanation about a new tag
that's available in freesurfer 6.0. So in case anyone was too lazy to read the release notes,
there is a new tag called the parallel tag or a parallel flag that you can add to your
recon-all all reconstructions and this allows for parallelization when freesurfer is running. So if
you have a machine or computer that has multiple cores then you can use the multiple cores to call
the different functions during recon all and this should make finishing recon all or running
recon all faster. If you read this, it basically uses what's called OpenMP to parallelize
and you can specify how many cores you want to use for your recon all processing stream.
It says if you just add the parallel tag that the default will be four cores. It says somewhere
over here that the default is four, but you can change that number as well if you add the flag
openmp and then the number of cores that you want. When I was running it on my work computer--my
work computer is a Mac and it has four cores. The way you can check is you can go to the little
apple. Click "About This Mac" and then go to system report and that will tell you the total number of
processors and the total number of cores. On my laptop--my laptop only has two cores but my
iMac and my work computer has four cores. So if it's four cores, that's the default and all you
have to do is run the parallel flag but if you want to run less or more then you should put
parallel then openmp and then the number of cores that you want to use. If you read this blurb, it
says that recon-all all should be able to run as fast as three hours or less now with this parallel tag.
I have been testing it and I haven't gotten it to go down to three hours. I have two examples
here that I ran on my work computer. This one I ran without a parallel tag. So if you go to scripts
and then the recon all log it exited without errors and it tells you at the bottom that the
runtime was six almost--well, more than six and a half hours. So almost seven hours. And this was
including the qcache tag and besides that it was just the normal recon-all all tags.
That took me a little less than seven hours and then I tried this same NIFTI and the same qcache tag
with the parallel tag at it as well. And if you look at that, it wasn't as fast as three hours
but it took me four, almost five hours. It does speed up the recon-all all runtime but for some
reason for me it hasn't been as fast as three hours like it says it should be but it is faster
and especially if you're you know working eight hours a day you will more easily be able to finish
a recon all in the same day that you started. So that is useful, and I did check as well the stats.
I did asegstats, the table, on both of them just to see if it would output the same results
and it did, so it does look like it is a useful tag that I would add to all my reconstructions
from now on if you're using freesurfer 6.0. And also there is a way to do parallelization in
5.3, so I might make a video in case people are still using 5.3 because I know a lot of people
haven't switched to version 6.0 but it's something that you have to kind of go over manually because
I don't think that there's a tag for 5.3 but they did add a tag for 6.0 so it's very easy to
use and I would recommend it. All right that's it for this video and thank you guys for watching!
*chiptune music*