[Freesurfer] monkeys' surfaces registration
Hello everybody, I am working with monkeys brain, and I had trouble in both creating an average surface and co-registering the monkeys' surfaces together. I was thus wondering if accessing the canonical spherical template and replacing it by a monkey template with less sulci would solve the problem? If yes, how can I specify to mris_sphere which template to use? If no, has someone a miracle solution to register monkeys' surfaces? Many thanks, Marie Schaer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] monkeys' surfaces registration
Hi Marie, the human template definitely isn't what you want for a monkey brain. Use mris_make_template to build a new target. cheers, Bruce On Wed, 19 Sep 2007, Marie Schaer wrote: Hello everybody, I am working with monkeys brain, and I had trouble in both creating an average surface and co-registering the monkeys' surfaces together. I was thus wondering if accessing the canonical spherical template and replacing it by a monkey template with less sulci would solve the problem? If yes, how can I specify to mris_sphere which template to use? If no, has someone a miracle solution to register monkeys' surfaces? Many thanks, Marie Schaer ___ 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] legacy data and FDR
Hi, Yes, I set the rate to various values to test it, and all resulted in the same threshold. I didn't mask to brain, because that causes an error message (it cites the lack of a brainmap.mgz as the reason, so that at least I know is due to it being processed in an older stream). So I wonder if FDR requires that new processing as well, in stable3. By the way, these are the commands I used for view the data: setenv SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR source /usr/local/freesurfer/nmr-stable3-env cd $SUBJECTS_DIR tkmedit-sess -analysis EMerror -contrast ASevASc -space tal -map sig -s BwGroupError5 -isxavg random -fthresh 1.3 Thanks, Rob Doug Greve wrote: what do you mean by staring p value? Do you mean the FDR itself? Robert Levy wrote: Hi, Is it possible to use FDR in stable3 for data that was processed prior to the introduction of brainmask.mgz? It seems like I can view the data just fine in stable3, or stable2 for that matter (though not stable 4), but FDR gives results that seem wrong. FDR sets the threshold to -log10(p)=4.279537 [p=.5] no matter what the starting pvalue is. Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error: no gl window open
Does it work with other subjects? Was this working before, and did it just suddenly stop working? Have you done anything recently to the software coinciding with it not working, like upgrading to version 4, or is this a new install of version 4? Does tkmedit work? Have you tried updating your graphics drivers? On Sat, 2007-09-15 at 04:29 -0400, Xiangchuan Chen wrote: Hi all, I have got the following error message when running tksurfer to load inflated surface: surfer: ### redraw failed: no gl window open The result is that no surface appears. Any suggestions for solving this issue? My system: HP NC8430 laptop (ATI X1600 video card) Fedora 6 (X86_64) Freesurfer V4.0 Thanks in advance, Xiangchuan Chen -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] legacy data and FDR
Try coping or linking the brain.mgz to brainmask.mgz Robert Levy wrote: Hi, Yes, I set the rate to various values to test it, and all resulted in the same threshold. I didn't mask to brain, because that causes an error message (it cites the lack of a brainmap.mgz as the reason, so that at least I know is due to it being processed in an older stream). So I wonder if FDR requires that new processing as well, in stable3. By the way, these are the commands I used for view the data: setenv SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR source /usr/local/freesurfer/nmr-stable3-env cd $SUBJECTS_DIR tkmedit-sess -analysis EMerror -contrast ASevASc -space tal -map sig -s BwGroupError5 -isxavg random -fthresh 1.3 Thanks, Rob Doug Greve wrote: what do you mean by staring p value? Do you mean the FDR itself? Robert Levy wrote: Hi, Is it possible to use FDR in stable3 for data that was processed prior to the introduction of brainmask.mgz? It seems like I can view the data just fine in stable3, or stable2 for that matter (though not stable 4), but FDR gives results that seem wrong. FDR sets the threshold to -log10(p)=4.279537 [p=.5] no matter what the starting pvalue is. Thanks, Rob -- 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] Alternative Standard Brain
what do you want to use it for? On Wed, 19 Sep 2007, Dick, Rachel wrote: Hi there, Is there a simple way to plug in and use your own standard brain instead of the mni in the recon-all process? I am using the new 4.0 version. Thanks in advance! Rachel Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences Dept. of Psychiatry Behavioral Neuroscience WSU Medical School brain.wayne.edu mailto:[EMAIL PROTECTED] (313)577-6279 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Alternative Standard Brain
Hi there, Is there a simple way to plug in and use your own standard brain instead of the mni in the recon-all process? I am using the new 4.0 version. Thanks in advance! Rachel Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences Dept. of Psychiatry Behavioral Neuroscience WSU Medical School brain.wayne.edu mailto:[EMAIL PROTECTED] (313)577-6279 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you. image001.jpg___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] centos4_x86_64_V4.0.1 vs. centos4_V4.0.1
Hi Nick and Kevin, I installed the centos4_x86_64_v4.0.1 on my laptop. The tkmedit could show volume and surface data, the tksurfer could not display surface brain. Then, I changed it to centos4_v4.0.1. In this version, both tkmedit and tksurfer did their jobs. So, the same issue as v4.0 exists on my laptop. In addition, I am not able to enter number in all the boxes with numbers in both tkmedit and tksurfer. Because I have an ATI x1600 video card in the laptop, is it possible that the insufficient linux support for this card caused this issue? Thanks, Xiangchuan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
