RE: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer
Hi all, I am facing the same problem with CentOS 5 and tksurfer.Is there any fix for this problem? Thank you, -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky Sent: Tuesday, February 19, 2008 10:03 AM To: [EMAIL PROTECTED] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer Does glxgears work? That is an app that comes with Linux that exercises the GLX (OpenGL X extension) code. On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote: > Dear FS experts, > > I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, > when I start tkmedit, it looks fine. In tksurfer, it just appear a > sliver of surface without error message. In console, it stock on > reading vertex. > > Is there anyway to correct it ? > > Thanks replay > > Kl chen > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer
Hi Dhruman, I had this problem with a Debian (Etch) system with an ATI card, and the way I got it to work was to install the fglrx driver for the ATI card. I also was missing a bunch of OpenGL stuff, too, but I think the driver was the main issue. I'm unfamiliar with CentOS but these instructions seem to make sense: http://www.linlap.com/wiki/Configuring+the+fglrx+driver+for+ATI+graphics+chips+in+CentOS+and+RHEL+5 mjp On Mar 6, 2008, at 10:15 AM, Goradia, Dhruman D wrote: Hi all, I am facing the same problem with CentOS 5 and tksurfer.Is there any fix for this problem? Thank you, -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky Sent: Tuesday, February 19, 2008 10:03 AM To: [EMAIL PROTECTED] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer Does glxgears work? That is an app that comes with Linux that exercises the GLX (OpenGL X extension) code. On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote: Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer
i just fixed something like this on ubuntu 7.10 with an ati radeon x600. the latest drivers run on aiglx which conflicts with the previous versions which run on xgl. this sometimes even caused X to crash when running tksurfer and even glxgears. on my system this was resolved by simply removing the package xserver-xgl. there should be no reason to uninstall the proprietary fglrx driver. Goradia, Dhruman D wrote: Hi all, I am facing the same problem with CentOS 5 and tksurfer.Is there any fix for this problem? Thank you, -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] On Behalf Of Nick Schmansky Sent: Tuesday, February 19, 2008 10:03 AM To: [EMAIL PROTECTED] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer Does glxgears work? That is an app that comes with Linux that exercises the GLX (OpenGL X extension) code. On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote: Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] rawavg
When FreeSurfer performs the average of 2 or more scans to create rawavg.mgz, is the 001.mgz used as the target to which all other scans are moved /averaged to or is there some between-space alignment amongst the scans? -Joel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] rawavg
001.mgz is used as the target. If you have other scanns in orig (eg, 002.mgz, 003.mg, etc), then those are aligned to 001.mgz, then all are averaged together. doug joel bruss wrote: When FreeSurfer performs the average of 2 or more scans to create rawavg.mgz, is the 001.mgz used as the target to which all other scans are moved /averaged to or is there some between-space alignment amongst the scans? -Joel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 2 Questions about Parcellation
Hello, We are beginning to explore the applicability of FreeSurfer for our research. Having done some initial runs, we have the following questions that I was hoping you might be able to address. 1.) For stats output, it seems there are two atlases for parcellation, resulting in ?h.aparc.stats and ?h.aparc.a2005s.stats. I was wondering if you could tell me which atlases were used during the manual parcellation that ultimately went into creating these two systems? 2.) We were wondering what the entity "unknown" refers to in the ? h.aparc.stats output. What is this capturing? Thanks so much for any assistance you can provide and kudos on this amazing software! Sincerely, Ray ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 2 Questions about Parcellation
thanks Ray: 1. There were two different parcellation schemes, by different neuroanatomists (one by Christophe Destrieux, and one by Rahul Desikan and Ron Killiany). 2. The unknown in the desikan/killiany atlas is medial wall and unfortunately much of the insula, which Ron is working on fixing. cheers, Bruce On Thu, 6 Mar 2008, Raymond Hill wrote: Hello, We are beginning to explore the applicability of FreeSurfer for our research. Having done some initial runs, we have the following questions that I was hoping you might be able to address. 1.) For stats output, it seems there are two atlases for parcellation, resulting in ?h.aparc.stats and ?h.aparc.a2005s.stats. I was wondering if you could tell me which atlases were used during the manual parcellation that ultimately went into creating these two systems? 2.) We were wondering what the entity "unknown" refers to in the ? h.aparc.stats output. What is this capturing? Thanks so much for any assistance you can provide and kudos on this amazing software! Sincerely, Ray ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] optseq2 obscenely long null event
It looks like you have an awful lot of null in there (6+7+8+6+7+8+11)*2 = 106 sec of stimulation The total run length is 130*2 = 260 sec Leaving 260-106 = 154 sec for null. There are only 7*2=14 events total, so the average null will be 154/14 = 11 sec I'm surprised that one null was 75 sec, but not too surprised. doug Jasony Brozinsky wrote: Hi, Optseq2 is returning designs where the last NULL even is upwards of 75 seconds (more than 4 times my psdMax!. Can I keep the rest of the order as is, and just truncate the last NULL event to be equal to my PsdMax value? Below is my command and a sample output file: optseq2 --ntp 130 --tr 2 --cost eff --tprescan 0 --psdwin 0 18 1 --ev EVT3 6 2 --ev EVT4 7 2 --ev EVT5 8 2 --ev EVS3 6 2 --ev EVS4 7 2 --ev EVS5 8 --ev Other 11 2 --tnullmin 2 --tnullmax 2 --nsearch 1 --focb 1000 --nkeep 100 --o utput --log log --polyfit 2 0.27.000 1. EvT4 7.06.000 1. NULL 13.7 11.000 1. Other 24.06.000 1. NULL 30.7 11.000 1. Other 41.04.000 1. NULL 45.38.000 1. EvT5 53.06.000 1. NULL 59.57.000 1. EvS4 66.08.000 1. NULL 74.57.000 1. EvS4 81.04.000 1. NULL 85.16.000 1. EvT3 91.05.000 1. NULL 96.46.000 1. EvS3 102.04.000 1. NULL 106.16.000 1. EvT3 112.06.000 1. NULL 118.68.000 1. EvS5 126.0 12.000 1. NULL 138.38.000 1. EvT5 146.09.000 1. NULL 155.27.000 1. EvT4 162.05.000 1. NULL 167.68.000 1. EvS5 175.02.000 1. NULL 177.46.000 1. EvS3 183.0 77.000 1. NULL Craig Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: problems with retaining wm edits using -autorecon2-cp flag
It should not be happening. Does it happen everytime you make an edit and re-run with autorecon2-cp? Teddy Youn wrote: Hi all, another quick question. I don't know if anyone else has encountered this problem, but after making pial, wm and cp edits our group don't seem to retain all our edits. The OtherUsefulFlags wikipage suggests that FS should retain all the edits from a flag that is more upstream in the autorecon2's workflow. We've noticed that a lot of our manual wm edits for some of our brains are lost when we use -autorecon2-cp flag. Has anyone else encountered this problem? Is there a way to prevent this from happening? -Thanks in advance, Teddy Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 [EMAIL PROTECTED] (401)-714-2847 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
