Narly, We have recently bought 64 Dell 1950PE With Dual processor Xeon Quad Core 16 Gb RAM
I think there are two approaches to the problem:
1) Machine to run recon-all analysis: Maximum performance and memory like the one I put above.
2) Visualization Workstation: I would indicate: AMD Phenon X4 8GB Ram Nvidia GTX260
If you need further advice contact me.
Best Regards
Pedro Paulo Jr
2008/9/26 Narly A Golestani ucjtnag@ucl.ac.uk
Dear all,
I see from previous posts to the list that it is possible to use servers to run freesurfer. I'm in the process of selecting a machine, and would appreciate any input anyone might have on which machine is optimal. In particular I'm concerned about eventual problems described on the mailing list earlier this month (see thread pasted below), regarding the ES1000 chipset that apparently comes with Dell PowerEdge servers (I am no expert with hardware issues such as these so this is all new to me!). Does this chipset come with all of these types of servers, or is it possible to order one with an NVIDIA card installed? Are there better alternatives wrt to which machine to purchase?
thanks in advance for any input you might have, best, Narly.
Re: [Freesurfer] tksurfer woes
Mark J. Pearrow Fri, 12 Sep 2008 12:52:02 -0700
Hi all,
FYI, this same problem has been bugging me for several months. Most ATI chipsets have a nice driver installer bundle that, once installed, will let you run tksurfer without a problem. However, this particular chipset, the ES1000, which is the chipset on Dell PowerEdge servers, is unsupported and seems to have been abandoned by ATI/AMD/whoever they are this week.
If you happen to be unlucky enough to have Dell PowerEdge servers with this chipset and the need to run tksurfer, you're out of luck, until you put a slightly "better" graphics card in. I just managed to install an nVidia 8400GS (the x1 PCI-e version - the poweredge PCI-e bus is x8, which means it won't work with any of the most recent cards, but will work with slightly older x1 cards) and tksurfer works fine now. I can provide the gory details if you're in this boat.
mjp
On Sep 8, 2008, at 9:14 AM, Hoptman, Matthew wrote:
Hi all,
Im having trouble using freesurfers tksurfer program (I only get a sliver of the brain). Here is the error info I get:
[ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer/subjects
surfer: Reading header info from /home/freesurfer/subjects/77059/mri/ T1.mgz
surfer: vertices=184362, faces=368720 Loading /home/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(77059) surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl Reading /home/freesurfer/lib/tcl/tkm_common.tcl Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
The driver info (from /etc/X11/xorg.conf) is: Section "Device" BoardName "ES1000 515E" BusID "14:13:0" Driver "radeon" Identifier "Device[0]" Option "GARTSize" "32" Option "usevnc" "yes"
Section "DRI" Group "video" Mode 0660 EndSection
Im have an onboard ATI ES1000 515E graphics chip.
Any ideas?? Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine
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