Freesurfer August 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
75 discussions

Growing spots
by Troy Mcan 02 Aug '07

02 Aug '07

Hi,I have a group of talairach coordinates on a brain that I would like to grow to a specified amount (e.g. 8 mm radius). Is there a function in freesurfer that allows me to do this? Also, some of the points are far away from the main group, but I would like to have them all connected. Is there a blur filter or an equivalent that I can use to accomplish this?Thank you! _________________________________________________________________ Recharge--play some free games. Win cool prizes too! http://club.live.com/home.aspx?icid=CLUB_wlmailtextlink

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writing surface file
by Marie Schaer 02 Aug '07

02 Aug '07

Hello everybody, I would like to write a surface in freesurfer format from a matlab triangular mesh (e.g. list of 67120 vertices associated with 134236 faces). To read the freesurfer surfaces, I usually use the very useful bioelectromagnetism toolbox by Darren Weber, but I am not able to find out why the freesurfer_write_surface function (attached to this mail) do not work with my mesh. It indeed seems to write a surface of adequate size (2.3MB), but when I try to visualize it, tkmedit respond: "(null): vertex 0 x coordinate 282617032931096509022208.000000 ! " Does someone has any hints on that or an available matlab script to write a freesurfer surface? Many thanks for your help, Marie Schaer

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RE: [Freesurfer] Ubuntu, Xeon 64bit multi-core, and freesurfer
by Nicolas Cherbuin 01 Aug '07

01 Aug '07

Thanks for your response Nick! Would you be able to also give us an update on when the next release is going to be available and whether it will include white matter parcellation? I need to reprocess a fairly large number of scans and I would prefer if it includes the latest bells and whistles. Regards, Nic -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, 31 July 2007 12:07 PM To: Nicolas Cherbuin Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Ubuntu, Xeon 64bit multi-core, and freesurfer Nic, Concerning Ubuntu and Freesurfer, we have not used that OS directly ourselves, but I believe people on the list have used Ubuntu and Freesurfer. I think there were some library issues, but nothing that was a show-stopper or overly difficult to fix. We have many Xeon dual core machines in use here, so Freesurfer should run fine on that. Your plan run a recon-all on each processor is fine. Nick On Mon, 2007-07-30 at 11:24 +1000, Nicolas Cherbuin wrote: > Hi, > > > > I am about to order new hardware that will be used to process scans > with freesurfer but also for processing with other packages. Has > anyone had experience with the combination of Xeon quad-core > processors, Ubuntu, and Freesurfer? And if yes are there any issues I > should be aware of? > > > > To my knowledge one Freesurfer process cannot run in parallel on > multiple processors but I intend to process multiple scans > simultaneously, hence the selection of a multi-core architecture. If > somebody has some experience of the difference between 2.33 GHZ, 2.66 > GHZ, and core-duo 3.00 GHZ I would also be interested to hear about > it. > > > > Thanks > > > > Nic > > > > > > ***************************************** > > > > Nicolas Cherbuin > > > Centre for Mental Health Research > Australian National University > Canberra > ACT 0200 > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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measurement of cortical thickness
by T. Song 01 Aug '07

01 Aug '07

Hi All: I am trying to measure the cortical thickness of specific ROI. I got a ROI, and are able to save it to a label file. Should I use mris_thickness to measure the thickness? If so, how do I get the thickness file, using mri_label2vol? Thanks in advance! Tao

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Keyboard Mapping (up arrow)
by Troy Mcan 01 Aug '07

01 Aug '07

Hi,Does anyone know how to access the "up arrow" (history) command in the tksurfer shell. E.g. backspace maps to ctl-h. Thanks! _________________________________________________________________ PC Magazine’s 2007 editors’ choice for best web mail—award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

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Freesurfer August 2007