Hello FreeSurfer mailing list,

First off, I am not a scientist and I have no experience running FreeSurfer. I have installed it, and seen it run, but that’s it.

I work for the IT department in the Beckman Institute, part of the University of Illinois. We support a computer lab here called the “Visualization Laboratory” – aka Vislab. (http://itg.beckman.illinois.edu/visualization_laboratory/) The Vislab lab has dozens of very nice workstations in it. (16 x 3GHz Xeon cores, 128GB of mem, NVIDIA Quadro K6000 video, etc.) In short, the Vislab supports research which needs high end computing. (less power than supercomputers, but much better than normal desktops and much easier to access/use than supercomputers) The Vislab has hundreds of active users, students, faculty, postdocs, etc., all of whom do some kind of scientific research.

One of the packages we have recently installed upon request is FreeSurfer. We have installed freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz on our Red Hat Enterprise Linux 6 workstations, as well as on our Windows 7 Enterprise 64bit workstations. We have also installed Oracle’s VirtualBox on a Windows 7 Enterprise 64bit machine, and run the VM freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz inside that virtual environment.

The researchers who requested FreeSurfer are all part of the same group, and they are trying to complete a very large research project which requires FreeSurfer to process large amounts of data. They have normally been running FreeSurfer on the VM in the XUbuntu VirtualBox environment on their own average desktop PC’s. However, they are concerned about their processing time with FreeSurfer, so they are hoping to take advantage of the Vislab computing resources to decrease the processing time in FreeSurfer.

We are running into the following problems/concerns:

1) The FreeSurfer VM (Xubuntu) that runs in VirtualBox is a 32bit host. Is there a 64bit VM available? That 32bit host can only access 4GB of memory, whereas they would like to be able to access more of the workstations 128GB of memory.

2) The users have expressed concern about switching platforms to Red Hat Enterprise Linux6 with the FreeSurfer freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz installed.  They have told us that FreeSurfer on XUbuntu might give different results than if it were run on Red Hat Enterprise Linux 6, given the same dataset. They are concerned about switching platforms in the middle of the research study, and that it might contaminate results. Is this possible? Or should the same version of FreeSurfer provide the same results, even with a different platform?

3) Does anyone else on this list run very large FreeSurfer processes on high end 64bit computers? If a high-end processing method works well for you, I would love to hear about it so I can share it with the researchers here.

Thanks for your time!

____________

Alex Lazarevich

5321 Beckman Institute - 217-244-1565

Information Technology Services - http://its.beckman.illinois.edu

Beckman Institute - http://beckman.illinois.edu

University of Illinois - http://illinois.edu