[Freesurfer] tksurfer display
Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don't want postcentral label to appear in my tksurfer view (as I only want to see labels with more than 300 NVtxs). Can I get that label out from my brain pictures? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 13.048 133418 89.23 52.8 -12.9 32.0 0.00020 0.0 0.00040 186 postcentral 22.938 109465989.46 36.0 17.2 31.1 0.00020 0.0 0.00040 1066 caudalmiddlefrontal Thanks, -Siddharth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
You can run mri_annotation2label on the annotation to break it up into labels, then run mris_label2annot using only the label(s) you want doug On 01/07/2014 04:05 PM, Ray, Siddharth wrote: Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don’t want postcentral label to appear in my tksurfer view (as I only want to see labels with more than 300 NVtxs). Can I get that label out from my brain pictures? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.048 133418 89.23 52.8 -12.9 32.0 0.00020 0.0 0.00040 186 postcentral 2 2.938 109465 989.46 36.0 17.2 31.1 0.00020 0.0 0.00040 1066 caudalmiddlefrontal Thanks, -Siddharth ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote: Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote: Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
Do you mean the threshold? min=2.0 max=5.0 Thanks! 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote: Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
can you resend the image? You don't have the invert button clicked, do you? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Do you mean the threshold? min=2.0 max=5.0 Thanks! 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in th at the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote: Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. _ ___ 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button. I think the image is likely just a mirror image, but I failed to find a invert button. Where is the invert button? Best! Xiangzhen 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 21:56 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the invert button clicked, do you? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Do you mean the threshold? min=2.0 max=5.0 Thanks! 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in th at the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote: Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. _ ___ 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer attachment: test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
Hi Xiangzhen, that is something I have never seen before. I don't think it is a problem with freesurfer, and there is no button that will fix it. I think it must be something in your environment. What are the details of your platform? doug On 06/28/2013 10:18 AM, Xiangzhen Kong wrote: The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button. I think the image is likely just a mirror image, but I failed to find a invert button. Where is the invert button? Best! Xiangzhen 【小孔成像】http://www.conxz.net *From:* Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu *Date:* 2013-06-28 21:56 *To:* Xiangzhen Kong mailto:bnu...@gmail.com *CC:* freesurfer mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the invert button clicked, do you? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Do you mean the threshold? min=2.0 max=5.0 Thanks! 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in th at the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote: Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. _ ___ 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problem
it's on the configure overlay window, but it wouldn't cause what you are showing. I didn't notice this before but your entire color scale bar (including the text!) is mirror imaged. This is very strange, and probably explains why it looks like an rh. Can you give us the details of your environment. I don't have a clue what would cause this. Does the tkmedit window look correct? Freeview? Make sure that the text is not mirror-imaged as in this figure you sent On Fri, 28 Jun 2013, Xiangzhen Kong wrote: The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button. I think the image is likely just a mirror image, but I failed to find a invert button. Where is the invert button? Best! Xiangzhen 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 21:56 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the invert button clicked, do you? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Do you mean the threshold? min=2.0 max=5.0 Thanks! _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? ___ __ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in ?? ?th at the lh and rh have the same number of vertices. All I can think of is t o download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote : Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. ___ __ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. ___ __ ___ 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
The system is CentOS release 6.3. And the package of freesufer is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. I wonder whether the version mismatch(centos4 vs.centos6) causes this strange problem. I think I have to check this. (As I remember, tksurfer of this version works well in centos5.7) PS: tkmedit works well with volumetric data. And freeview also works well. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 22:29 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem it's on the configure overlay window, but it wouldn't cause what you are showing. I didn't notice this before but your entire color scale bar (including the text!) is mirror imaged. This is very strange, and probably explains why it looks like an rh. Can you give us the details of your environment. I don't have a clue what would cause this. Does the tkmedit window look correct? Freeview? Make sure that the text is not mirror-imaged as in this figure you sent On Fri, 28 Jun 2013, Xiangzhen Kong wrote: The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button. I think the image is likely just a mirror image, but I failed to find a invert button. Where is the invert button? Best! Xiangzhen 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 21:56 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the invert button clicked, do you? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Do you mean the threshold? min=2.0 max=5.0 Thanks! _ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? ___ __ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in ?? ?th at the lh and rh have the same number of vertices. All I can think of is t o download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote : Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. ___ __ ___ 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. ___ __ ___ 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] tksurfer display problem
Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.netattachment: test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net test.jpg ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, Xiangzhen Kong bnu...@gmail.com wrote: Actually when I just use tksurfer fsaverage lh inflated, there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, Xiangzhen Kong bnu...@gmail.com wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net test.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tksurfer display issue
Hi all, This issue was posted by someone else in October (please see below). I have the EXACT same problem. Does anyone have any ideas how fix this? Thanks, Nasim === Hi, everyone. The tksurfer can't initial a window in iOS 10.7.5. Has anyone met this before? Last login: Mon Oct 15 10:57:04 on ttys001 freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl $ system_profiler SPSoftwareDataTypeSoftware:System Software Overview: System Version: Mac OS X 10.7.5 (11G63) Kernel Version: Darwin 11.4.2 Boot Volume: Macintosh HD Boot Mode: Normal Secure Virtual Memory: Enabled 64-bit Kernel and Extensions: Yes Time since boot: 1:56 $ tksurfer bert lh pial subject is bert hemiis lh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/canlab06 checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=132501, faces=264998 surfer: single buffered window surfer: tkoInitWindow(bert) then it stopped here and does#t have any respond. I tried several times with different subjects, but failed with the same issue. Does anyone have any ideas? Thanks a lot. Best Wishes Meng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tksurfer display issue
Hi, everyone. The tksurfer can't initial a window in iOS 10.7.5. Has anyone met this before? Last login: Mon Oct 15 10:57:04 on ttys001 freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl $ system_profiler SPSoftwareDataTypeSoftware:System Software Overview: System Version: Mac OS X 10.7.5 (11G63) Kernel Version: Darwin 11.4.2 Boot Volume: Macintosh HD Boot Mode: Normal Secure Virtual Memory: Enabled 64-bit Kernel and Extensions: Yes Time since boot: 1:56 $ tksurfer bert lh pial subject is bert hemiis lh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/canlab06 checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=132501, faces=264998 surfer: single buffered window surfer: tkoInitWindow(bert) then it stopped here and does#t have any respond. I tried several times with different subjects, but failed with the same issue. Does anyone have any ideas? Thanks a lot. Best Wishes Meng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tksurfer display
Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
Can you describe the hardware / video card you are using? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Sep 22, 2011 at 12:12, Peter Glynn pgl...@bu.edu wrote: Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
I am using an nVidia Quadro NVS 295 video card with an Intel(R) Xeon(R) CPU E5530 @2.4 GHz On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn *Sent:* Thu 9/22/2011 10:12 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn *Sent:* Thu 9/22/2011 10:12 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. attachment: Screenshot-bert.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
We worked on this months ago and decided to locally install linux on our dual boot PCs rather than remotely accessing data generated on our linux server via Windows (via SHH with Exceed or Xming). Perhaps there is an OpenGL issue? JIm From: Peter Glynn [mailto:pgl...@bu.edu] Sent: Thu 9/22/2011 11:21 AM To: Alexopoulos, Dimitrios Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn Sent: Thu 9/22/2011 10:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
I found this site for the type of problem we are having with tksurfer http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems Jim From: Peter Glynn [mailto:pgl...@bu.edu] Sent: Thu 9/22/2011 11:21 AM To: Alexopoulos, Dimitrios Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn Sent: Thu 9/22/2011 10:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
I have added this answer to the FAQ: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Sep 22, 2011 at 14:33, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: I found this site for the type of problem we are having with tksurfer http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems Jim -- *From:* Peter Glynn [mailto:pgl...@bu.edu] *Sent:* Thu 9/22/2011 11:21 AM *To:* Alexopoulos, Dimitrios *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer display attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn *Sent:* Thu 9/22/2011 10:12 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
Hello again, After a system reboot, I am seeing these messages when trying to open tkmedit or tksurfer: Xlib: extension GLX missing on display :0.0. GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: :0.0 I've searched around, and seen that changing nv to nvidia and adding Load glx in xorg.conf should work; however, the X server doesn't start when I do either or both. Has anyone had trouble with this? Thanks, Chris Nick Schmansky wrote: what is the version of your driver? ie cat /proc/driver/nvidia/version the latest is around 260.19.12 the problem you see is something we've seen with old nvidia drivers, whereby updating the driver has fixed the problem. not sure why this would just happen now for you. to update (must be root or use sudo): /sbin/init 3 /usr/bin/nvidia-installer --update n. On Fri, 2011-01-14 at 13:19 -0500, Chris Watson wrote: Hi, when trying to look at surfaces in tksurfer, all I see is a small part of the data in the posterior of the brain (see attached for example). There are no errors on the command line when I run tksurfer. This only started happening very recently. Here's some system info: (CentOS 5.5, 64-bit; FreeSurfer v5.0) [freesurfer@occipital TGA]$ uname -a Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux [freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv 40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 560] (rev a1) I wouldn't think I need to update my graphics card driver. But, does anyone know how to fix this? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problem
what is the version of your driver? ie cat /proc/driver/nvidia/version the latest is around 260.19.12 the problem you see is something we've seen with old nvidia drivers, whereby updating the driver has fixed the problem. not sure why this would just happen now for you. to update (must be root or use sudo): /sbin/init 3 /usr/bin/nvidia-installer --update n. On Fri, 2011-01-14 at 13:19 -0500, Chris Watson wrote: Hi, when trying to look at surfaces in tksurfer, all I see is a small part of the data in the posterior of the brain (see attached for example). There are no errors on the command line when I run tksurfer. This only started happening very recently. Here's some system info: (CentOS 5.5, 64-bit; FreeSurfer v5.0) [freesurfer@occipital TGA]$ uname -a Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux [freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv 40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 560] (rev a1) I wouldn't think I need to update my graphics card driver. But, does anyone know how to fix this? Thanks, Chris ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
Hello, Mr. Watson, I had the same problem with ATI videocard on 64-bit CentOS 5.5. It was solved after installation of last Catalyst driver (After disabling SELinux: http://www.crypt.gen.nz/selinux/disable_selinux.html.) - ***I am not quite sure which driver you should use with nvidia. I would also advice to check for errors your installation log-file (It must located in your n-vidia directory somewhere inside /usr/share/). For example, my problem was connected with GCC (I noticed errors inside log file and installed all necessary libraries). Hope it helps. -- Best Regards, Alexander Lebedev I.P. Pavlov State Medical University 197022, Lev Tolstoy str. 6/8 Saint Petersburg, Russian Federation tel.:+7-921-441-79-42 e-mail: awl...@rambler.ru Skype ID: alexander.vl.lebedev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display problem
I d/l'ed the new driver, and it now works. Thanks. Chris Nick Schmansky wrote: what is the version of your driver? ie cat /proc/driver/nvidia/version the latest is around 260.19.12 the problem you see is something we've seen with old nvidia drivers, whereby updating the driver has fixed the problem. not sure why this would just happen now for you. to update (must be root or use sudo): /sbin/init 3 /usr/bin/nvidia-installer --update n. On Fri, 2011-01-14 at 13:19 -0500, Chris Watson wrote: Hi, when trying to look at surfaces in tksurfer, all I see is a small part of the data in the posterior of the brain (see attached for example). There are no errors on the command line when I run tksurfer. This only started happening very recently. Here's some system info: (CentOS 5.5, 64-bit; FreeSurfer v5.0) [freesurfer@occipital TGA]$ uname -a Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux [freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv 40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 560] (rev a1) I wouldn't think I need to update my graphics card driver. But, does anyone know how to fix this? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer display problem
Hi, when trying to look at surfaces in tksurfer, all I see is a small part of the data in the posterior of the brain (see attached for example). There are no errors on the command line when I run tksurfer. This only started happening very recently. Here's some system info: (CentOS 5.5, 64-bit; FreeSurfer v5.0) [freesurfer@occipital TGA]$ uname -a Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux [freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv 40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 560] (rev a1) I wouldn't think I need to update my graphics card driver. But, does anyone know how to fix this? Thanks, Chris inline: tksurfer.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tksurfer display
Dear Freesurfer experts I am new Freesurfer user, I used the command: tksurfer fsaverage lh inflated -annot aparc.annot In the graph showed in the window are only the vertices, not surface, see the figure in the attachment. how to displace the surface in the window, which operation do I need ? (I tried the differerent option in the manu ''View, and I didn't get the surface) Thank you very much Shugao attachment: snapshot.jpg___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
Corinna, run this to ensure the driver is up-to-date: sudo /sbin/init 3 CR to get login prompt login sudo /usr/bin/nvidia-installer update Nick On Tue, 2009-08-11 at 10:01 -0400, corinna bauer wrote: The graphics card is: nVidia Corporation NV34 [GeForce FX 5200] (rev a1). As far as I know it is the most current driver available. 2009/8/10 Nick Schmansky ni...@nmr.mgh.harvard.edu what is the graphics card, and is the driver the most current available? On Mon, 2009-08-10 at 17:28 -0400, corinna bauer wrote: The output from dmesg is: Linux version 2.6.18-128.1.14.el5 (mockbu...@builder16.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Jun 17 06:40:54 EDT 2009 BIOS-provided physical RAM map: BIOS-e820: - 0009b800 (usable) BIOS-e820: 0009b800 - 000a (reserved) BIOS-e820: 000e - 0010 (reserved) BIOS-e820: 0010 - 3ff7 (usable) BIOS-e820: 3ff7 - 3ff7b000 (ACPI data) BIOS-e820: 3ff7b000 - 3ff8 (ACPI NVS) BIOS-e820: 3ff8 - 4000 (reserved) BIOS-e820: fec0 - fec1 (reserved) BIOS-e820: fee0 - fee01000 (reserved) BIOS-e820: ff80 - ffc0 (reserved) BIOS-e820: fff0 - 0001 (reserved) 127MB HIGHMEM available. 896MB LOWMEM available. found SMP MP-table at 000f6120 Memory for crash kernel (0x0 to 0x0) notwithin permissible range disabling kdump Using x86 segment limits to approximate NX protection On node 0 totalpages: 262000 DMA zone: 4096 pages, LIFO batch:0 Normal zone: 225280 pages, LIFO batch:31 HighMem zone: 32624 pages, LIFO batch:7 DMI present. Using APIC driver default ACPI: RSDP (v000 PTLTD ) @ 0x000f6160 ACPI: RSDT (v001 PTLTDRSDT 0x0604 LTP 0x) @ 0x3ff76ee4 ACPI: FADT (v001 INTEL E75050x0604 PTL 0x0008) @ 0x3ff7ae78 ACPI: MADT (v001 PTLTD APIC 0x0604 LTP 0x) @ 0x3ff7aeec ACPI: BOOT (v001 PTLTD $SBFTBL$ 0x0604 LTP 0x0001) @ 0x3ff7af88 ACPI: SPCR (v001 PTLTD $UCRTBL$ 0x0604 PTL 0x0001) @ 0x3ff7afb0 ACPI: DSDT (v001 INTELE7505 0x0604 MSFT 0x010e) @ 0x ACPI: PM-Timer IO Port: 0x1008 ACPI: Local APIC address 0xfee0 ACPI: LAPIC (acpi_id[0x00] lapic_id[0x00] enabled) Processor #0 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x01] lapic_id[0x06] enabled) Processor #6 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x02] lapic_id[0x01] enabled) Processor #1 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x03] lapic_id[0x07] enabled) Processor #7 15:2 APIC version 20 ACPI: LAPIC_NMI (acpi_id[0x00] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x01] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x02] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x03] high edge lint[0x1]) ACPI: IOAPIC (id[0x02] address[0xfec0] gsi_base[0]) IOAPIC[0]: apic_id 2, version 32, address 0xfec0, GSI 0-23 ACPI: IOAPIC (id[0x03] address[0xfec8] gsi_base[24]) IOAPIC[1]: apic_id 3, version 32, address 0xfec8, GSI 24-47 ACPI: IOAPIC (id[0x04] address[0xfec80400] gsi_base[48]) IOAPIC[2]: apic_id 4, version 32, address 0xfec80400, GSI 48-71 ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 high edge) ACPI: INT_SRC_OVR (bus 0 bus_irq 9 global_irq 9 high level) ACPI: IRQ0 used by override. ACPI: IRQ2 used by override. ACPI: IRQ9 used by override. Enabling APIC mode: Flat. Using 3 I/O APICs Using ACPI (MADT) for SMP configuration information Allocating PCI resources starting at 5000 (gap: 4000:bec0) Detected 2392.198 MHz processor. Built 1 zonelists. Total pages: 262000 Kernel command line: ro root=/dev/VolGroup00/LogVol00 rhgb mapped APIC to d000 (fee0) mapped IOAPIC to c000 (fec0) mapped IOAPIC to b000 (fec8) mapped IOAPIC to a000 (fec80400) Enabling fast FPU save and restore... done. Enabling unmasked SIMD FPU exception
[Freesurfer] tksurfer display
When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help. surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display
try: setenv doublebufferflag 1 before running tksurfer --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer corinna...@gmail.com When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help. surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... ___ 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] tksurfer display
That didn't work. Corinna 2009/8/10 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br try: setenv doublebufferflag 1 before running tksurfer --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer corinna...@gmail.com When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help. surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... ___ 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] tksurfer display
Can you post the output of dmesg command --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer corinna...@gmail.com That didn't work. Corinna 2009/8/10 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br try: setenv doublebufferflag 1 before running tksurfer --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer corinna...@gmail.com When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help. surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... ___ 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] tksurfer display
The output from dmesg is: Linux version 2.6.18-128.1.14.el5 (mockbu...@builder16.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Jun 17 06:40:54 EDT 2009 BIOS-provided physical RAM map: BIOS-e820: - 0009b800 (usable) BIOS-e820: 0009b800 - 000a (reserved) BIOS-e820: 000e - 0010 (reserved) BIOS-e820: 0010 - 3ff7 (usable) BIOS-e820: 3ff7 - 3ff7b000 (ACPI data) BIOS-e820: 3ff7b000 - 3ff8 (ACPI NVS) BIOS-e820: 3ff8 - 4000 (reserved) BIOS-e820: fec0 - fec1 (reserved) BIOS-e820: fee0 - fee01000 (reserved) BIOS-e820: ff80 - ffc0 (reserved) BIOS-e820: fff0 - 0001 (reserved) 127MB HIGHMEM available. 896MB LOWMEM available. found SMP MP-table at 000f6120 Memory for crash kernel (0x0 to 0x0) notwithin permissible range disabling kdump Using x86 segment limits to approximate NX protection On node 0 totalpages: 262000 DMA zone: 4096 pages, LIFO batch:0 Normal zone: 225280 pages, LIFO batch:31 HighMem zone: 32624 pages, LIFO batch:7 DMI present. Using APIC driver default ACPI: RSDP (v000 PTLTD ) @ 0x000f6160 ACPI: RSDT (v001 PTLTDRSDT 0x0604 LTP 0x) @ 0x3ff76ee4 ACPI: FADT (v001 INTEL E75050x0604 PTL 0x0008) @ 0x3ff7ae78 ACPI: MADT (v001 PTLTD APIC 0x0604 LTP 0x) @ 0x3ff7aeec ACPI: BOOT (v001 PTLTD $SBFTBL$ 0x0604 LTP 0x0001) @ 0x3ff7af88 ACPI: SPCR (v001 PTLTD $UCRTBL$ 0x0604 PTL 0x0001) @ 0x3ff7afb0 ACPI: DSDT (v001 INTELE7505 0x0604 MSFT 0x010e) @ 0x ACPI: PM-Timer IO Port: 0x1008 ACPI: Local APIC address 0xfee0 ACPI: LAPIC (acpi_id[0x00] lapic_id[0x00] enabled) Processor #0 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x01] lapic_id[0x06] enabled) Processor #6 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x02] lapic_id[0x01] enabled) Processor #1 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x03] lapic_id[0x07] enabled) Processor #7 15:2 APIC version 20 ACPI: LAPIC_NMI (acpi_id[0x00] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x01] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x02] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x03] high edge lint[0x1]) ACPI: IOAPIC (id[0x02] address[0xfec0] gsi_base[0]) IOAPIC[0]: apic_id 2, version 32, address 0xfec0, GSI 0-23 ACPI: IOAPIC (id[0x03] address[0xfec8] gsi_base[24]) IOAPIC[1]: apic_id 3, version 32, address 0xfec8, GSI 24-47 ACPI: IOAPIC (id[0x04] address[0xfec80400] gsi_base[48]) IOAPIC[2]: apic_id 4, version 32, address 0xfec80400, GSI 48-71 ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 high edge) ACPI: INT_SRC_OVR (bus 0 bus_irq 9 global_irq 9 high level) ACPI: IRQ0 used by override. ACPI: IRQ2 used by override. ACPI: IRQ9 used by override. Enabling APIC mode: Flat. Using 3 I/O APICs Using ACPI (MADT) for SMP configuration information Allocating PCI resources starting at 5000 (gap: 4000:bec0) Detected 2392.198 MHz processor. Built 1 zonelists. Total pages: 262000 Kernel command line: ro root=/dev/VolGroup00/LogVol00 rhgb mapped APIC to d000 (fee0) mapped IOAPIC to c000 (fec0) mapped IOAPIC to b000 (fec8) mapped IOAPIC to a000 (fec80400) Enabling fast FPU save and restore... done. Enabling unmasked SIMD FPU exception support... done. Initializing CPU#0 CPU 0 irqstacks, hard=c0755000 soft=c0735000 PID hash table entries: 4096 (order: 12, 16384 bytes) Console: colour VGA+ 80x25 Dentry cache hash table entries: 131072 (order: 7, 524288 bytes) Inode-cache hash table entries: 65536 (order: 6, 262144 bytes) Memory: 1030992k/1048000k available (2124k kernel code, 16344k reserved, 885k data, 228k init, 130496k highmem) Checking if this processor honours the WP bit even in supervisor mode... Ok. Calibrating delay using timer specific routine.. 4786.48 BogoMIPS (lpj=2393244) Security Framework v1.0.0 initialized SELinux: Initializing. SELinux: Starting in permissive mode selinux_register_security: Registering secondary module capability Capability LSM initialized as secondary Mount-cache hash table entries: 512 CPU: After generic identify, caps: bfebfbff 4400 CPU: After vendor identify, caps: bfebfbff 4400 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 0080 4400 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#0. CPU0: Intel P4/Xeon Extended MCE MSRs (12) available CPU0: Thermal monitoring enabled Checking 'hlt' instruction... OK. SMP alternatives: switching to UP code ACPI: Core revision 20060707 CPU0: Intel(R) Xeon(TM) CPU 2.40GHz stepping
Re: [Freesurfer] tksurfer display
what is the graphics card, and is the driver the most current available? On Mon, 2009-08-10 at 17:28 -0400, corinna bauer wrote: The output from dmesg is: Linux version 2.6.18-128.1.14.el5 (mockbu...@builder16.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Jun 17 06:40:54 EDT 2009 BIOS-provided physical RAM map: BIOS-e820: - 0009b800 (usable) BIOS-e820: 0009b800 - 000a (reserved) BIOS-e820: 000e - 0010 (reserved) BIOS-e820: 0010 - 3ff7 (usable) BIOS-e820: 3ff7 - 3ff7b000 (ACPI data) BIOS-e820: 3ff7b000 - 3ff8 (ACPI NVS) BIOS-e820: 3ff8 - 4000 (reserved) BIOS-e820: fec0 - fec1 (reserved) BIOS-e820: fee0 - fee01000 (reserved) BIOS-e820: ff80 - ffc0 (reserved) BIOS-e820: fff0 - 0001 (reserved) 127MB HIGHMEM available. 896MB LOWMEM available. found SMP MP-table at 000f6120 Memory for crash kernel (0x0 to 0x0) notwithin permissible range disabling kdump Using x86 segment limits to approximate NX protection On node 0 totalpages: 262000 DMA zone: 4096 pages, LIFO batch:0 Normal zone: 225280 pages, LIFO batch:31 HighMem zone: 32624 pages, LIFO batch:7 DMI present. Using APIC driver default ACPI: RSDP (v000 PTLTD ) @ 0x000f6160 ACPI: RSDT (v001 PTLTDRSDT 0x0604 LTP 0x) @ 0x3ff76ee4 ACPI: FADT (v001 INTEL E75050x0604 PTL 0x0008) @ 0x3ff7ae78 ACPI: MADT (v001 PTLTD APIC 0x0604 LTP 0x) @ 0x3ff7aeec ACPI: BOOT (v001 PTLTD $SBFTBL$ 0x0604 LTP 0x0001) @ 0x3ff7af88 ACPI: SPCR (v001 PTLTD $UCRTBL$ 0x0604 PTL 0x0001) @ 0x3ff7afb0 ACPI: DSDT (v001 INTELE7505 0x0604 MSFT 0x010e) @ 0x ACPI: PM-Timer IO Port: 0x1008 ACPI: Local APIC address 0xfee0 ACPI: LAPIC (acpi_id[0x00] lapic_id[0x00] enabled) Processor #0 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x01] lapic_id[0x06] enabled) Processor #6 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x02] lapic_id[0x01] enabled) Processor #1 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x03] lapic_id[0x07] enabled) Processor #7 15:2 APIC version 20 ACPI: LAPIC_NMI (acpi_id[0x00] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x01] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x02] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x03] high edge lint[0x1]) ACPI: IOAPIC (id[0x02] address[0xfec0] gsi_base[0]) IOAPIC[0]: apic_id 2, version 32, address 0xfec0, GSI 0-23 ACPI: IOAPIC (id[0x03] address[0xfec8] gsi_base[24]) IOAPIC[1]: apic_id 3, version 32, address 0xfec8, GSI 24-47 ACPI: IOAPIC (id[0x04] address[0xfec80400] gsi_base[48]) IOAPIC[2]: apic_id 4, version 32, address 0xfec80400, GSI 48-71 ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 high edge) ACPI: INT_SRC_OVR (bus 0 bus_irq 9 global_irq 9 high level) ACPI: IRQ0 used by override. ACPI: IRQ2 used by override. ACPI: IRQ9 used by override. Enabling APIC mode: Flat. Using 3 I/O APICs Using ACPI (MADT) for SMP configuration information Allocating PCI resources starting at 5000 (gap: 4000:bec0) Detected 2392.198 MHz processor. Built 1 zonelists. Total pages: 262000 Kernel command line: ro root=/dev/VolGroup00/LogVol00 rhgb mapped APIC to d000 (fee0) mapped IOAPIC to c000 (fec0) mapped IOAPIC to b000 (fec8) mapped IOAPIC to a000 (fec80400) Enabling fast FPU save and restore... done. Enabling unmasked SIMD FPU exception support... done. Initializing CPU#0 CPU 0 irqstacks, hard=c0755000 soft=c0735000 PID hash table entries: 4096 (order: 12, 16384 bytes) Console: colour VGA+ 80x25 Dentry cache hash table entries: 131072 (order: 7, 524288 bytes) Inode-cache hash table entries: 65536 (order: 6, 262144 bytes) Memory: 1030992k/1048000k available (2124k kernel code, 16344k reserved, 885k data, 228k init, 130496k highmem) Checking if this processor honours the WP bit even in supervisor mode... Ok. Calibrating delay using timer specific routine.. 4786.48 BogoMIPS (lpj=2393244) Security Framework v1.0.0 initialized SELinux: Initializing. SELinux: Starting in permissive mode selinux_register_security: Registering secondary module capability Capability LSM initialized as secondary Mount-cache hash table entries: 512 CPU: After generic identify, caps: bfebfbff 4400 CPU: After vendor identify, caps: bfebfbff 4400 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 0080 4400 Intel machine check architecture supported. Intel machine check reporting enabled on
Re: [Freesurfer] tksurfer display
Maybe you can try to update your graphic card driver Date: Wed, 5 Aug 2009 18:24:44 +0100 From: jerome.sal...@psy.ox.ac.uk To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer display Help, Sorry to bother you, but I am looking for my tksurfer hero! I just installed freesurfer on my laptop (centos5 virtual machine, 4Go RAM, NIVDIA quadro 110M, intel duo t2...@1.66ghz). Everything goes well until I tried tksurfer. Only the anterior part of bert's brain is displayed.(medit is ok; refreshing the tksurfer view doesn't change the display). Is there a way to fix my problem or is my graphic card not performant enough ? Thanks a lot for your help Cheers, J -- __ Jerome SALLET Decision and Action Laboratory Department of Experimental Psychology, University of Oxford South Parks Road, OX1 3UD,UK Tel (office): (0044) 1865 271 315 Tel (elsewhere) : (0044) 7 530 060 839 http://psyweb.psy.ox.ac.uk/rushworth/default.htm ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Express your personality in color! Preview and select themes for Hotmail®. http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_express:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display
Two procedures may help you: 1) setenv doublebufferflag 1 2) If you virtual machine is VirtualBox, upgrade to 3.0 and enable OpenGL --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- New Netfilter 3.2 www.Netfilter.com.br --- New Netfilter Small Business 2009/8/5 Jerome Sallet jerome.sal...@psy.ox.ac.uk Help, Sorry to bother you, but I am looking for my tksurfer hero! I just installed freesurfer on my laptop (centos5 virtual machine, 4Go RAM, NIVDIA quadro 110M, intel duo t2...@1.66ghz). Everything goes well until I tried tksurfer. Only the anterior part of bert's brain is displayed.(medit is ok; refreshing the tksurfer view doesn't change the display). Is there a way to fix my problem or is my graphic card not performant enough ? Thanks a lot for your help Cheers, J -- __ Jerome SALLET Decision and Action Laboratory Department of Experimental Psychology, University of Oxford South Parks Road, OX1 3UD,UK Tel (office): (0044) 1865 271 315 Tel (elsewhere) : (0044) 7 530 060 839 http://psyweb.psy.ox.ac.uk/rushworth/default.htm ___ 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] tksurfer display problems vary by OS version
Hello, everyone. I just joined this list in order to post a problem our folks are having with tksurfer displaying brain images. What we are seeing is incorrect display of images depending on what OS tksurfer is run on. In one case, the image is never rendered because some kind of error loop is triggered. In all test cases the same data and Freesurfer version are being used (4.0.1) and the same display hardware and software are being used. The only difference is the host OS running tksurfer. Here's what we are seeing: Operating system Result Fedora Core 4 (32 bit) Success Fedora Core 5 (64 bit) Failure (run away X errors) Cent OS 5 (64 bit) Failure (incorrect image) I am wondering whether anyone else has seen this problem with this particular program? I'll happily provide as much information as I can to any request for further details. I have some images of the correct and incorrect displays but I'm not sure whether I can post attachments to this list. I can certainly provide them directly to anyone who would like to see what we are seeing. Thanks for your help. david -- David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problems vary by OS version
Hi david, I dont know if this will help, and i really do not know the reason why it should work, but if you append the tcltktixbli/lib, /usr/lib and /usr/lib64 on 64 bit version *in this order*, the tksurfer problems are solved. There will still be some unresolved issues with spurious events that will cause the window to refresh many times after each change (with autorefresh on), but other then that, everything will work. also, it help to do an ldd on tksurfer.bin, just to check that all libraries can be located (i.e you should not find any not found in the ldd output, in case you do, solve for that dependency before you proceed. ) sid. On Thu, Feb 26, 2009 at 1:48 PM, David Mischel david.misc...@ucsf.eduwrote: Hello, everyone. I just joined this list in order to post a problem our folks are having with tksurfer displaying brain images. What we are seeing is incorrect display of images depending on what OS tksurfer is run on. In one case, the image is never rendered because some kind of error loop is triggered. In all test cases the same data and Freesurfer version are being used (4.0.1) and the same display hardware and software are being used. The only difference is the host OS running tksurfer. Here's what we are seeing: Operating system Result Fedora Core 4 (32 bit) Success Fedora Core 5 (64 bit) Failure (run away X errors) Cent OS 5 (64 bit) Failure (incorrect image) I am wondering whether anyone else has seen this problem with this particular program? I'll happily provide as much information as I can to any request for further details. I have some images of the correct and incorrect displays but I'm not sure whether I can post attachments to this list. I can certainly provide them directly to anyone who would like to see what we are seeing. Thanks for your help. david -- David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864 ___ 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] tksurfer display question
Hi, using version 4.0.5 look at the attached picture. its the result of: tksurfer code lh inflated -aparc aparc -gray i have selected one region (yellow outline). i would like to - fill this region and some other regions, *but not all regions*! - give the filled regions different color-labelings - i would like to display them (outlined and filled regions) at the *same* time. i have tried numerous ways, without result. any suggestions? thanks, -joost attachment: try.jpg___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display question
Hi Joost, you can use the custom fill tool to fill up to other labels. You can also start with all marked vertices and click in a number of regions, then save them as a label (you can change its color with the change label color button on the 2nd row of icons near the right). cheers, Bruce On Wed, 19 Nov 2008, j janssen wrote: Hi, using version 4.0.5 look at the attached picture. its the result of: tksurfer code lh inflated -aparc aparc -gray i have selected one region (yellow outline). i would like to - fill this region and some other regions, *but not all regions*! - give the filled regions different color-labelings - i would like to display them (outlined and filled regions) at the *same* time. i have tried numerous ways, without result. any suggestions? thanks, -joost ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problems
Hi all, This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted server. I found this posting: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.html Which seemed to indicate that it was not the card itself that made the difference, but rather some software component that made things work. There is an extension to X11, called GLX, which allows the remote side (the client, in X11 speak) to bypass the processing of OpenGL commands and to send them to the server. So, following the advice in the posting above, I downloaded the latest NVidia.run package and unpacked it by using the -x flag - then I copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. Then I ran ldconfig -v to update the ld cache. And voila, I can run tksurfer over X11, VNC and NX now on a server that has no NVidia card, without any problems. I still don't understand what exactly is being provided by NVidia's version of the libraries, but I suspect it has to do with TLS (in the context of OpenGL, not in the crypto sense). This appeared in the output of `ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken system after I installed those files: libnvidia-tls.so.1 = /usr/lib/tls/libnvidia-tls.so.1 mjp On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote: Hi Sid, this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC. cheers, Bruce On Tue, 18 Nov 2008, Siddharth Srivastava wrote: Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated). This small patch responds to all commands from the GIU, but that is all that i see. I have trawled through the archives, both old and new, and there have been references to similar problems, without any definitive way to solve it. What exact aspect of the system configuration has to be examined/re-worked to solve it? Does anyone have any experience with this kind of problem? with regards, sid. ___ 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] tksurfer display question II
I guess you could write one of them into an overlay or curv file and display it filled with the outlined labels, but we don't directly support this On Wed, 19 Nov 2008, j janssen wrote: i´ll rephrase my question: can one display filled labels and other outlined labels at the same time in tksurfer? see my current attachment (made with help from Gimp..): surface+curvature+aparc (outlined)+some label (filled)+some label (filled). mri_annotation2label will give me labels, fine, but it won´t solve my rephrased question, i think. appreciate your help! -joost Or do you want the separate units to have separate colors? If that's your goal you can use mri_annotation2label to turn all the parcellation units into labels and only use the 2 (or more) that you want. cheers, Bruce On Wed, 19 Nov 2008, j janssen wrote: Hi Bruce, to be 100% sure that you guys understand what i want, i have attached the same attachment as before but now i quickly manually-painted in some regions using Gimp. Now, obviously i would like to do this not-manually and within FreeSurfer. is this possible? you can use the custom fill tool to fill up to other labels. how can i use custom fill to fill up a specific label, making it visible in tksurfer while keeping the other labels in 'outlined' status? You can also start with all marked vertices and click in a number of regions, then save them as a label (you can change its color with the change label color button on the 2nd row of icons near the right). with its you refer to 1 label representing all marked vertices for which the color can be customized. look at the attachment, this is not what i would want. maybe i´m missing something obvious, apologies. -joost On Wed, 19 Nov 2008, j janssen wrote: Hi, using version 4.0.5 look at the attached picture. its the result of: tksurfer code lh inflated -aparc aparc -gray i have selected one region (yellow outline). i would like to - fill this region and some other regions, *but not all regions*! - give the filled regions different color-labelings - i would like to display them (outlined and filled regions) at the *same* time. i have tried numerous ways, without result. any suggestions? thanks, -joost ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problems
Hi mjp, Thanks for an account of a working solution to the problem. I just wanted to know if this intervention has to done on the client machine (from where i am viewing the results), or on the server side (on which i am processing the data)? Further, in case of a 64 bit machine, would the source and the destination directories change accordingly? best regards, sid. On Wed, Nov 19, 2008 at 8:50 AM, Mark J. Pearrow [EMAIL PROTECTED] wrote: Hi all, This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted server. I found this posting: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.html Which seemed to indicate that it was not the card itself that made the difference, but rather some software component that made things work. There is an extension to X11, called GLX, which allows the remote side (the client, in X11 speak) to bypass the processing of OpenGL commands and to send them to the server. So, following the advice in the posting above, I downloaded the latest NVidia.run package and unpacked it by using the -x flag - then I copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. Then I ran ldconfig -v to update the ld cache. And voila, I can run tksurfer over X11, VNC and NX now on a server that has no NVidia card, without any problems. I still don't understand what exactly is being provided by NVidia's version of the libraries, but I suspect it has to do with TLS (in the context of OpenGL, not in the crypto sense). This appeared in the output of `ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken system after I installed those files: libnvidia-tls.so.1 = /usr/lib/tls/libnvidia-tls.so.1 mjp On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote: Hi Sid, this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC. cheers, Bruce On Tue, 18 Nov 2008, Siddharth Srivastava wrote: Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated). This small patch responds to all commands from the GIU, but that is all that i see. I have trawled through the archives, both old and new, and there have been references to similar problems, without any definitive way to solve it. What exact aspect of the system configuration has to be examined/re-worked to solve it? Does anyone have any experience with this kind of problem? with regards, sid. ___ 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] tksurfer display problems
hi Sid, This should be done on the server side - where you are processing the data. For example, I have a Dell PowerEdge 1950 that is running 64-bit Debian Gnu/Linux and has Freesurfer/fsfast installed. I log into it from my Mac, which is running os x. So I needed to add those libraries to the Dell machine to make things work. My systems are 64 bit, so I think the instructions I gave should work for you, too. mjp On Nov 19, 2008, at 1:21 PM, Siddharth Srivastava wrote: Hi mjp, Thanks for an account of a working solution to the problem. I just wanted to know if this intervention has to done on the client machine (from where i am viewing the results), or on the server side (on which i am processing the data)? Further, in case of a 64 bit machine, would the source and the destination directories change accordingly? best regards, sid. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] tksurfer display problems
We did for one node, and going to up-grade the rest. A simple answer to your question is to up-grade any node you want to run tksurfer. Help it helps. Xin From: Siddharth Srivastava [mailto:[EMAIL PROTECTED] Sent: Wed 11/19/2008 6:37 PM To: Wang, Xin Subject: Re: [Freesurfer] tksurfer display problems Hi Xin, Thanks for the reply. I am contacting you since you mentioned that you are running freesurfer on a cluster. I contacted my sysad regarding this problem, and they want to know if this upgrade has to be dome on every node of the cluster. can you recommend something regarding this? best regards, sid. On Wed, Nov 19, 2008 at 11:46 AM, Wang, Xin [EMAIL PROTECTED] wrote: We just solved the same problem by upgrading the driver of video card on the cluster. An early massage in the freesurfer archive gives more details. Xin From: Siddharth Srivastava [mailto:[EMAIL PROTECTED] Sent: Wed 11/19/2008 1:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display problems Hi mjp, Thanks for an account of a working solution to the problem. I just wanted to know if this intervention has to done on the client machine (from where i am viewing the results), or on the server side (on which i am processing the data)? Further, in case of a 64 bit machine, would the source and the destination directories change accordingly? best regards, sid. On Wed, Nov 19, 2008 at 8:50 AM, Mark J. Pearrow [EMAIL PROTECTED] wrote: Hi all, This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted server. I found this posting: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.html Which seemed to indicate that it was not the card itself that made the difference, but rather some software component that made things work. There is an extension to X11, called GLX, which allows the remote side (the client, in X11 speak) to bypass the processing of OpenGL commands and to send them to the server. So, following the advice in the posting above, I downloaded the latest NVidia.run package and unpacked it by using the -x flag - then I copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. Then I ran ldconfig -v to update the ld cache. And voila, I can run tksurfer over X11, VNC and NX now on a server that has no NVidia card, without any problems. I still don't understand what exactly is being provided by NVidia's version of the libraries, but I suspect it has to do with TLS (in the context of OpenGL, not in the crypto sense). This appeared in the output of `ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken system after I installed those files: libnvidia-tls.so.1 = /usr/lib/tls/libnvidia-tls.so.1 mjp On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote: Hi Sid, this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC. cheers, Bruce On Tue, 18 Nov 2008, Siddharth Srivastava wrote: Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated
[Freesurfer] tksurfer display problems
Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated). This small patch responds to all commands from the GIU, but that is all that i see. I have trawled through the archives, both old and new, and there have been references to similar problems, without any definitive way to solve it. What exact aspect of the system configuration has to be examined/re-worked to solve it? Does anyone have any experience with this kind of problem? with regards, sid. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problems
Hi Sid, this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC. cheers, Bruce On Tue, 18 Nov 2008, Siddharth Srivastava wrote: Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated). This small patch responds to all commands from the GIU, but that is all that i see. I have trawled through the archives, both old and new, and there have been references to similar problems, without any definitive way to solve it. What exact aspect of the system configuration has to be examined/re-worked to solve it? Does anyone have any experience with this kind of problem? with regards, sid. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display tcl error FS training
Hi Derin, with regard to #2, we haven't setup any official procedure although it is a good idea. You could use the tools Xiao developed for that paper to do so. cheers, Bruce On Thu, 9 Oct 2008, Derin Cobia wrote: Nick, Yes, our tcltktixblt directory was intact and set correctly. The reason I thought it was a BLT lib was it came up missing when I ran fs_lib check. At any rate, the DefaultDepth is already at 24 in our xorg.conf file and the problem persists. Any other thoughts what might be occurring? Would you like me to submit my output as well? Also, any thoughts from anyone with regard to question #2 (see below)? Thanks. -Derin On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote: Derin, To answer your first question, the solution to that particular problem that you reference was not to install the BLT libs (as they are included with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the file /etc/X11/xorg.conf file. Nick Two questions: 1. We installed the latest version of 32-bit FS on several workstations running CentOS 5.1 in our lab. However, once we ran the CentOS updates (~280 of them through up2date), tkmedit now fails to open and tksurfer exhibits behavior exactly as described in this message from the mail archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html Having attempted to troubleshoot it I discovered that a blt lib was missing, but even with re-installation of this tksurfer continues to not display correctly. I believe it's a tcl problem, but I don't understand why performing incremental updates to CentOS would break FS. More importantly, I'm not sure which of the updates does the breaking so I can just avoid it. Any ideas? 2. We are in the process of training new research assistants in how to use FS. Typically we have approached this in a more qualitative way by working side-by-side with them to guide their edits and processing. I was wondering if there is a quantitative way of comparing their work that you (or others) have used when training new recruits in FS. Maybe something like was done in the Han et al (2006) paper, such as compare their thickness (or other) maps with someone we know does well with manual interventions? In essence, we're trying to think of a rigorous way to train new people in FS, thanks! -Derin ___ 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] tksurfer display tcl error FS training
Derin, Can you do this: source $FREESURFER_HOME/bin/tcl_setup then send me the output of: ldd `which tkmedit.bin` and ldd `which tksurfer.bin` I will be looking to see if the proper tcl/tk/tix/blt libs are being used (those in freesurfer/lib/tcltktixblt). Nick On Thu, 2008-10-09 at 11:15 -0500, Derin Cobia wrote: Nick, Yes, our tcltktixblt directory was intact and set correctly. The reason I thought it was a BLT lib was it came up missing when I ran fs_lib check. At any rate, the DefaultDepth is already at 24 in our xorg.conf file and the problem persists. Any other thoughts what might be occurring? Would you like me to submit my output as well? Also, any thoughts from anyone with regard to question #2 (see below)? Thanks. -Derin On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote: Derin, To answer your first question, the solution to that particular problem that you reference was not to install the BLT libs (as they are included with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the file /etc/X11/xorg.conf file. Nick Two questions: 1. We installed the latest version of 32-bit FS on several workstations running CentOS 5.1 in our lab. However, once we ran the CentOS updates (~280 of them through up2date), tkmedit now fails to open and tksurfer exhibits behavior exactly as described in this message from the mail archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html Having attempted to troubleshoot it I discovered that a blt lib was missing, but even with re-installation of this tksurfer continues to not display correctly. I believe it's a tcl problem, but I don't understand why performing incremental updates to CentOS would break FS. More importantly, I'm not sure which of the updates does the breaking so I can just avoid it. Any ideas? 2. We are in the process of training new research assistants in how to use FS. Typically we have approached this in a more qualitative way by working side-by-side with them to guide their edits and processing. I was wondering if there is a quantitative way of comparing their work that you (or others) have used when training new recruits in FS. Maybe something like was done in the Han et al (2006) paper, such as compare their thickness (or other) maps with someone we know does well with manual interventions? In essence, we're trying to think of a rigorous way to train new people in FS, thanks! -Derin ___ 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] tksurfer display broken: fixed
Not exactly sure how or what happened...but did manage to fix my tksurfer display problem. Since others on the list had reported similar problems, I thought I'd post what I did to fix the problem. Since I'm not a Linux guru, my fix is probably just a bandaid...but it did work...and hopefully the info provides some assistance to others. Just to note the following particulars of my system: RHEL5 (DELL Precision 690n box went live April 16, 2008) Linux_x86_64 architecture 2 kernels: drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 NVIDIA Quadro Fx 3450/4000 SDI Driver Version 1.0-9746 Friendly software also installed on the same box=fslv404 MATLAB r2008a is also installed (currently running -lgi on bert...I'll update on the outcome of this friendliness test) As of yesterday, had several possible scenarios outlined: 1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm -- should return to a well-behaved (albeit older) nvidia driver...same as out of the box 2) restore original out of the box settings for entire system via /usr/var/dell/reinstall.sh -- should return ALL system settings to original out of the box...good for freesurfer and fsl apps but not so good for matlab... 3) boot into older kernel (I apparently have a total of 2 listed in /usr/src/kernels) [EMAIL PROTECTED] kernels]# ls -l total 16 drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 I attempted (1) first. However, the driver was not well-behaved for bert (tkmedit or tksurfer). I attempted (3) second. However, no change in behavior. While tarballing to prepare for (3)...since everything worked perfectly fine right out of the box -- before Matlab and before any package updates...I found my *original* /etc/X11/xorg.conf file (from April 16) and cp it into /etc/X11/xorg.conf rebooted. RESULTS: Was *very* happy to see tksurfer tkmedit behave properly for bert. Proper behavior for tksurfer tkmedit was observed in both kernels (after the xorg.conf file replacement). Still waiting to see if matlab behaves for bert's -lgi. I diff'd the original xorg.conf with the broken one and the following lines were returned: Hope this helps others find their bandaid solution to get them up and running again. Cheers, Jenifer [EMAIL PROTECTED] X11]# diff xorg.conf.backup.OLD xorg.conf.backup 1,4c1,2 # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:27 PST 2006 # Xorg configuration created by system-config-display --- # nvidia-settings: X configuration file generated by nvidia-settings # nvidia-settings: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:57 PST 2006 7,10c5,8 Identifier Default Layout Screen 0 Screen0 0 0 InputDeviceMouse0 CorePointer InputDeviceKeyboard0 CoreKeyboard --- Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer 13a12,13 RgbPath /usr/lib64/X11/rgb FontPathunix/:7100 17c17,21 Load glx --- Load dbe Load extmod Load type1 Load freetype Load glx 21c25 Option AllowMouseOpenFail yes --- Option Xinerama 0 25d28 27,32c30,35 Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/input/mice Option Emulate3Buttons no Option ZAxisMapping 4 5 --- Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/input/mice Option Emulate3Buttons no Option ZAxisMapping 4 5 36,39c39,43 Identifier Keyboard0 Driver kbd Option XkbModel pc105 Option XkbLayout us --- # generated from data in /etc/sysconfig/keyboard Identifier Keyboard0 Driver kbd Option XkbLayout us Option XkbModel pc105 43,49c47,53 Identifier Monitor0 VendorName Unknown ModelNameUnknown ### Comment all HorizSync and VertSync values to use DDC: HorizSync30.0 - 110.0 VertRefresh 50.0 - 150.0 Option DPMS --- # HorizSync source: edid, VertRefresh source: edid Identifier Monitor0 VendorName Unknown ModelName DELL 2007WFP HorizSync 30.0 - 83.0 VertRefresh 56.0 - 76.0 Option DPMS 53,55c57,60 Identifier Videocard0 Driver nvidia BoardName NVIDIA PCI-Express Quadro FX 3450 --- Identifier Videocard0 Driver nvidia VendorName NVIDIA Corporation BoardName Quadro
Re: [Freesurfer] tksurfer display broken: fixed
Jenifer, Thanks for the detailed info! Just to be clear, does your current /etc/X11/xorg.conf have the line: Load glx glx is OpenGL on X-Windows, allowing X windows apps, like tksurfer, to run using OpenGL, for accelerated graphics. Ideally, you want to load glx. Nick On Fri, 2008-05-30 at 12:42 -0500, Juranek, Jenifer wrote: Not exactly sure how or what happened...but did manage to fix my tksurfer display problem. Since others on the list had reported similar problems, I thought I'd post what I did to fix the problem. Since I'm not a Linux guru, my fix is probably just a bandaid...but it did work...and hopefully the info provides some assistance to others. Just to note the following particulars of my system: RHEL5 (DELL Precision 690n box went live April 16, 2008) Linux_x86_64 architecture 2 kernels: drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 NVIDIA Quadro Fx 3450/4000 SDI Driver Version 1.0-9746 Friendly software also installed on the same box=fslv404 MATLAB r2008a is also installed (currently running -lgi on bert...I'll update on the outcome of this friendliness test) As of yesterday, had several possible scenarios outlined: 1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm -- should return to a well-behaved (albeit older) nvidia driver...same as out of the box 2) restore original out of the box settings for entire system via /usr/var/dell/reinstall.sh -- should return ALL system settings to original out of the box...good for freesurfer and fsl apps but not so good for matlab... 3) boot into older kernel (I apparently have a total of 2 listed in /usr/src/kernels) [EMAIL PROTECTED] kernels]# ls -l total 16 drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 I attempted (1) first. However, the driver was not well-behaved for bert (tkmedit or tksurfer). I attempted (3) second. However, no change in behavior. While tarballing to prepare for (3)...since everything worked perfectly fine right out of the box -- before Matlab and before any package updates...I found my *original* /etc/X11/xorg.conf file (from April 16) and cp it into /etc/X11/xorg.conf rebooted. RESULTS: Was *very* happy to see tksurfer tkmedit behave properly for bert. Proper behavior for tksurfer tkmedit was observed in both kernels (after the xorg.conf file replacement). Still waiting to see if matlab behaves for bert's -lgi. I diff'd the original xorg.conf with the broken one and the following lines were returned: Hope this helps others find their bandaid solution to get them up and running again. Cheers, Jenifer [EMAIL PROTECTED] X11]# diff xorg.conf.backup.OLD xorg.conf.backup 1,4c1,2 # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:27 PST 2006 # Xorg configuration created by system-config-display --- # nvidia-settings: X configuration file generated by nvidia-settings # nvidia-settings: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:57 PST 2006 7,10c5,8 Identifier Default Layout Screen 0 Screen0 0 0 InputDeviceMouse0 CorePointer InputDeviceKeyboard0 CoreKeyboard --- Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer 13a12,13 RgbPath /usr/lib64/X11/rgb FontPathunix/:7100 17c17,21 Load glx --- Load dbe Load extmod Load type1 Load freetype Load glx 21c25 Option AllowMouseOpenFail yes --- Option Xinerama 0 25d28 27,32c30,35 Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/input/mice Option Emulate3Buttons no Option ZAxisMapping 4 5 --- Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/input/mice Option Emulate3Buttons no Option ZAxisMapping 4 5 36,39c39,43 Identifier Keyboard0 Driver kbd Option XkbModel pc105 Option XkbLayout us --- # generated from data in /etc/sysconfig/keyboard Identifier Keyboard0 Driver kbd Option XkbLayout us Option XkbModel pc105 43,49c47,53 Identifier Monitor0 VendorName Unknown ModelNameUnknown ### Comment all HorizSync and VertSync values to use DDC: HorizSync30.0 - 110.0 VertRefresh 50.0 - 150.0 Option DPMS --- #
RE: [Freesurfer] tksurfer display broken: fixed
Jenifer, I see you have this in your /etc/X11/xorg.conf file: Section Module Load glx EndSection Others having the recent tksurfer problem should make sure they have these lines as well, as tksurfer uses glx. Also, fyi, you can get a higher display resolution than the default. Try changing this line: Modes1024x768 800x600 640x480 to something like this: Modes 1600x1200 1280x1024 1024x768 800x600 640x480 It will use the first mode in the list, and if that doesnt work, it will try the next one. You can delete ones that dont work. In other words, put your desired resolution first in the list. Nick On Fri, 2008-05-30 at 13:37 -0500, Juranek, Jenifer wrote: Hi Nick, I've attached the current /etc/X11/xorg.conf as a text file. Let me know if I can provide any additional info Cheers, Jenifer -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Fri 5/30/2008 1:31 PM To: Juranek, Jenifer Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] tksurfer display broken: fixed Jenifer, Thanks for the detailed info! Just to be clear, does your current /etc/X11/xorg.conf have the line: Load glx glx is OpenGL on X-Windows, allowing X windows apps, like tksurfer, to run using OpenGL, for accelerated graphics. Ideally, you want to load glx. Nick On Fri, 2008-05-30 at 12:42 -0500, Juranek, Jenifer wrote: Not exactly sure how or what happened...but did manage to fix my tksurfer display problem. Since others on the list had reported similar problems, I thought I'd post what I did to fix the problem. Since I'm not a Linux guru, my fix is probably just a bandaid...but it did work...and hopefully the info provides some assistance to others. Just to note the following particulars of my system: RHEL5 (DELL Precision 690n box went live April 16, 2008) Linux_x86_64 architecture 2 kernels: drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 NVIDIA Quadro Fx 3450/4000 SDI Driver Version 1.0-9746 Friendly software also installed on the same box=fslv404 MATLAB r2008a is also installed (currently running -lgi on bert...I'll update on the outcome of this friendliness test) As of yesterday, had several possible scenarios outlined: 1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm -- should return to a well-behaved (albeit older) nvidia driver...same as out of the box 2) restore original out of the box settings for entire system via /usr/var/dell/reinstall.sh -- should return ALL system settings to original out of the box...good for freesurfer and fsl apps but not so good for matlab... 3) boot into older kernel (I apparently have a total of 2 listed in /usr/src/kernels) [EMAIL PROTECTED] kernels]# ls -l total 16 drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 I attempted (1) first. However, the driver was not well-behaved for bert (tkmedit or tksurfer). I attempted (3) second. However, no change in behavior. While tarballing to prepare for (3)...since everything worked perfectly fine right out of the box -- before Matlab and before any package updates...I found my *original* /etc/X11/xorg.conf file (from April 16) and cp it into /etc/X11/xorg.conf rebooted. RESULTS: Was *very* happy to see tksurfer tkmedit behave properly for bert. Proper behavior for tksurfer tkmedit was observed in both kernels (after the xorg.conf file replacement). Still waiting to see if matlab behaves for bert's -lgi. I diff'd the original xorg.conf with the broken one and the following lines were returned: Hope this helps others find their bandaid solution to get them up and running again. Cheers, Jenifer [EMAIL PROTECTED] X11]# diff xorg.conf.backup.OLD xorg.conf.backup 1,4c1,2 # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:27 PST 2006 # Xorg configuration created by system-config-display --- # nvidia-settings: X configuration file generated by nvidia-settings # nvidia-settings: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:57 PST 2006 7,10c5,8 Identifier Default Layout Screen 0 Screen0 0 0 InputDeviceMouse0 CorePointer InputDeviceKeyboard0 CoreKeyboard --- Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer 13a12,13 RgbPath /usr/lib64/X11/rgb FontPathunix/:7100 17c17,21 Load glx --- Load dbe Load extmod Load
RE: [Freesurfer] tksurfer display broken: fixed
I also find it curious you are using 16 bit depth instead of 24. On Fri, 30 May 2008, Nick Schmansky wrote: Jenifer, I see you have this in your /etc/X11/xorg.conf file: Section Module Load glx EndSection Others having the recent tksurfer problem should make sure they have these lines as well, as tksurfer uses glx. Also, fyi, you can get a higher display resolution than the default. Try changing this line: Modes1024x768 800x600 640x480 to something like this: Modes 1600x1200 1280x1024 1024x768 800x600 640x480 It will use the first mode in the list, and if that doesnt work, it will try the next one. You can delete ones that dont work. In other words, put your desired resolution first in the list. Nick On Fri, 2008-05-30 at 13:37 -0500, Juranek, Jenifer wrote: Hi Nick, I've attached the current /etc/X11/xorg.conf as a text file. Let me know if I can provide any additional info Cheers, Jenifer -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Fri 5/30/2008 1:31 PM To: Juranek, Jenifer Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] tksurfer display broken: fixed Jenifer, Thanks for the detailed info! Just to be clear, does your current /etc/X11/xorg.conf have the line: Load glx glx is OpenGL on X-Windows, allowing X windows apps, like tksurfer, to run using OpenGL, for accelerated graphics. Ideally, you want to load glx. Nick On Fri, 2008-05-30 at 12:42 -0500, Juranek, Jenifer wrote: Not exactly sure how or what happened...but did manage to fix my tksurfer display problem. Since others on the list had reported similar problems, I thought I'd post what I did to fix the problem. Since I'm not a Linux guru, my fix is probably just a bandaid...but it did work...and hopefully the info provides some assistance to others. Just to note the following particulars of my system: RHEL5 (DELL Precision 690n box went live April 16, 2008) Linux_x86_64 architecture 2 kernels: drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 NVIDIA Quadro Fx 3450/4000 SDI Driver Version 1.0-9746 Friendly software also installed on the same box=fslv404 MATLAB r2008a is also installed (currently running -lgi on bert...I'll update on the outcome of this friendliness test) As of yesterday, had several possible scenarios outlined: 1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm -- should return to a well-behaved (albeit older) nvidia driver...same as out of the box 2) restore original out of the box settings for entire system via /usr/var/dell/reinstall.sh -- should return ALL system settings to original out of the box...good for freesurfer and fsl apps but not so good for matlab... 3) boot into older kernel (I apparently have a total of 2 listed in /usr/src/kernels) [EMAIL PROTECTED] kernels]# ls -l total 16 drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 I attempted (1) first. However, the driver was not well-behaved for bert (tkmedit or tksurfer). I attempted (3) second. However, no change in behavior. While tarballing to prepare for (3)...since everything worked perfectly fine right out of the box -- before Matlab and before any package updates...I found my *original* /etc/X11/xorg.conf file (from April 16) and cp it into /etc/X11/xorg.conf rebooted. RESULTS: Was *very* happy to see tksurfer tkmedit behave properly for bert. Proper behavior for tksurfer tkmedit was observed in both kernels (after the xorg.conf file replacement). Still waiting to see if matlab behaves for bert's -lgi. I diff'd the original xorg.conf with the broken one and the following lines were returned: Hope this helps others find their bandaid solution to get them up and running again. Cheers, Jenifer [EMAIL PROTECTED] X11]# diff xorg.conf.backup.OLD xorg.conf.backup 1,4c1,2 # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:27 PST 2006 # Xorg configuration created by system-config-display --- # nvidia-settings: X configuration file generated by nvidia-settings # nvidia-settings: version 1.0 ([EMAIL PROTECTED]) Fri Dec 15 10:40:57 PST 2006 7,10c5,8 Identifier Default Layout Screen 0 Screen0 0 0 InputDeviceMouse0 CorePointer InputDeviceKeyboard0 CoreKeyboard --- Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer 13a12,13 RgbPath /usr/lib64/X11/rgb FontPathunix/:7100 17c17,21 Load glx --- Load dbe Load extmod Load type1 Load freetype Load glx 21c25 Option AllowMouseOpenFail yes
[Freesurfer] tksurfer display broken: post re-install nvidia 9746
I re-installed the dell-nvidia driver (original with system).
Some new behavior observed with bert:
tksurfer bert lh pial yields a complete bert window (entire pial surface is
displayed). However, the lower window TkSurfer Tools is not visible.
Also, tkmedit bert norm.mgz fails to launch a display, simply returns a command
prompt.
I've pasted the screen output for tksurfer below:
Any ideas are greatly appreciated.
[EMAIL PROTECTED] subjects]$ tksurfer bert lh pial
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in scripts dir == using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /usr/local/freesurfer/subjects
surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz
surfer: vertices=131168, faces=262332
Loading /usr/local/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(bert)
Tk_Init failed: this isn't a Tk applicationunknown color name Black
Tix_Init failed: this isn't a Tk applicationunknown color name Black
surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Error sourcing /usr/local/freesurfer/lib/tcl/tksurfer.tcl:
this isn't a Tk applicationunknown color name Black
surfer: Error sending tcl command tkm_SetEnableGroupStatus
mg_InflatedVSetLoaded 0:
can't read glEnableGroups(mg_InflatedVSetLoaded): no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_PialVSetLoaded 0:
can't read glEnableGroups(mg_PialVSetLoaded): no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_TimeCourseLoaded
0:
can't read glEnableGroups(mg_TimeCourseLoaded): no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OverlayLoaded 0:
can't read glEnableGroups(mg_OverlayLoaded): no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_CurvatureLoaded 0:
can't read glEnableGroups(mg_CurvatureLoaded): no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_LabelLoaded 0:
can't read glEnableGroups(mg_LabelLoaded): no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldSignLoaded 0:
can't read glEnableGroups(mg_FieldSignLoaded): no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldMaskLoaded 0:
can't read glEnableGroups(mg_FieldMaskLoaded): no such variable
surfer: Error sending tcl command UpdateUndoItemLabel Nothing to Undo:
invalid command name UpdateUndoItemLabel
surfer: Error sending tcl command tkm_SetEnableGroupStatus
mg_OriginalVSetLoaded 1:
can't read glEnableGroups(mg_OriginalVSetLoaded): no such variable
surfer: Error sending tcl command LblLst_SetStructures { 0 Unknown 1
G_cingularis 2 G_cuneus 3 G_frontalis_inf-pars_opercularis 4
G_frontalis_inf-pars_orbitalis 5 G_frontalis_inf-pars_triangularis 6
G_frontalis_medius 7 G_frontalis_sup-pars_lateralis 8
G_frontalis_sup-pars_medialis 9 G_frontomarginalis 10 G_hippocampi 11
G_insularis_breves 12 G_occipitalis_inf 13 G_occipitalis_medius-pars_inf 14
G_occipitalis_medius-pars_sup 15 G_occipitalis_sup 16 G_lateralis 17
G_lingualis 18 G_parahippocampi 19 G_orbitalis 20 G_paracentralis 21
G_parietalis_inf-pars_angularis 22 G_parietalis_inf-pars_supramarginalis 23
G_parietalis_sup 24 G_postcentralis 25 G_precentralis 26 G_precuneus 27
G_rectus_and_S_orbitalis_medialis 28 G_rectus_and_S_orbitalis_medialis2 29
G_subcentralis 30 G_supracingularis 31 G_temporalis_transversalis 32
G_temporalis_inf 33 G_temporalis_medius 34 G_temporalis_sup-pars_lateralis 35
G_temporalis_sup-planum_polare 36 G_temporalis_sup-planum_temporale 37
Plica_falci!
formis 38 Polus_occipitalis 39 Polus_temporalis 40 S_temporalis_transversalis
42 S_angularis 43 S_calcarinus 44 S_centralis_insulae__G_insularis_longus 46
S_centralis 47 S_cingularis 48 S_cingularis-pars_marginalis 49
S_circularis_insulae_ant 50 S_circularis_insulae_inf 51
S_circularis_insulae_sup 52 S_corpori_callosi 53 S_diagonalis 54
S_frontalis_inf 55 S_frontalis_medialis 56 S_frontalis_medius 57
S_frontalis_sup 58 S_frontomarginalis 59 S_intermedius_primus 60
S_intermedius_secundus 61 S_intracingularis 62 S_intraoccipitalis_medius 63
S_intraoccipitotemporalis_lateralis 64 S_intraparietalis 65
S_lateralis-pars_ant-ramus_horizontalis 66
S_lateralis-pars_ant-ramus_verticalis 67 S_lateralis-pars_horizontalis 68
S_lateralis-pars_post 69 S_lunatus 70 S_occipitalis_ant 71 S_occipitalis_inf 72
S_occipitalis_medius 73 S_occipitalis_sup 74 S_occipitalis_transversalis 75
S_occipitopolaris 76 S_occipitotemporalis_lateralis 77
S_occipitotemporalis_medialis 78 S_orbitales 79 S_orbi!
talis_lateralis 80 S_paracalcarinus 81
[Freesurfer] tksurfer display broken: smart over-ride?
Krish Paul, Many thanks for the quick advice. I have downloaded the mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, a smart window pops up reporting that a newer version than /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already installed. I select OK anyway, but a new window pops-up reporting that No packages were given for installation. How do I over-ride the smart system to install the legacy driver I need to make sure that everything is installed in the proper place(s) to make tksurfer happy again? Thanks so much, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display broken: smart over-ride?
I don't understand why you got a mesa-libGL rpm and are trying to install it? I think doing so could really mess up your system so it is a good thing it is not letting you. My email was about adding Section Extensions Option Composite Disable EndSection to your /etc/X11/xorg.conf assuming you are using the propreitary NVIDIA driver. Which you should also upgrade to the latest one. On Wed, 28 May 2008, Juranek, Jenifer wrote: Krish Paul, Many thanks for the quick advice. I have downloaded the mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, a smart window pops up reporting that a newer version than /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already installed. I select OK anyway, but a new window pops-up reporting that No packages were given for installation. How do I over-ride the smart system to install the legacy driver I need to make sure that everything is installed in the proper place(s) to make tksurfer happy again? Thanks so much, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] tksurfer display broken: smart over-ride?
Paul, Actually, I did follow your suggestion *first* to add the 3 lines to X11/xorg.conf (see tailed file below). However, after reboot, the same problem persisted. So I followed Krish's advice to look at a previous thread which referenced the mesa-libGL-*.rpm files @ MGH. My mistake for not knowing which postings are system-dependent...I'm *very* glad the smart system prevented me from making things worse! Any follow-up advice to resolve my problem? Many Thanks, Jenifer Section Device Identifier Videocard0 Driver nvidia VendorName NVIDIA Corporation BoardName Quadro FX 3450/4000 SDI EndSection Section Screen Identifier Screen0 Device Videocard0 MonitorMonitor0 DefaultDepth16 Option metamodes 1600x1024 +0+0; 800x600 +0+0; 640x480 +0+0 SubSection Display Depth 16 Modes 1600x1200 1280x1024 1024x768 800x600 640x480 EndSubSection EndSection Section Extensions Option Composite Disable EndSection -Original Message- From: Paul Raines [mailto:[EMAIL PROTECTED] Sent: Wed 5/28/2008 10:10 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display broken: smart over-ride? I don't understand why you got a mesa-libGL rpm and are trying to install it? I think doing so could really mess up your system so it is a good thing it is not letting you. My email was about adding Section Extensions Option Composite Disable EndSection to your /etc/X11/xorg.conf assuming you are using the propreitary NVIDIA driver. Which you should also upgrade to the latest one. On Wed, 28 May 2008, Juranek, Jenifer wrote: Krish Paul, Many thanks for the quick advice. I have downloaded the mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, a smart window pops up reporting that a newer version than /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already installed. I select OK anyway, but a new window pops-up reporting that No packages were given for installation. How do I over-ride the smart system to install the legacy driver I need to make sure that everything is installed in the proper place(s) to make tksurfer happy again? Thanks so much, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] tksurfer display broken: smart over-ride?
Do you see any warnings (WW) or errors (EE) in your /var/log/Xorg.0.log file? What does running 'glxinfo' say? On Wed, 28 May 2008, Juranek, Jenifer wrote: Paul, Actually, I did follow your suggestion *first* to add the 3 lines to X11/xorg.conf (see tailed file below). However, after reboot, the same problem persisted. So I followed Krish's advice to look at a previous thread which referenced the mesa-libGL-*.rpm files @ MGH. My mistake for not knowing which postings are system-dependent...I'm *very* glad the smart system prevented me from making things worse! Any follow-up advice to resolve my problem? Many Thanks, Jenifer Section Device Identifier Videocard0 Driver nvidia VendorName NVIDIA Corporation BoardName Quadro FX 3450/4000 SDI EndSection Section Screen Identifier Screen0 Device Videocard0 MonitorMonitor0 DefaultDepth16 Option metamodes 1600x1024 +0+0; 800x600 +0+0; 640x480 +0+0 SubSection Display Depth 16 Modes 1600x1200 1280x1024 1024x768 800x600 640x480 EndSubSection EndSection Section Extensions Option Composite Disable EndSection -Original Message- From: Paul Raines [mailto:[EMAIL PROTECTED] Sent: Wed 5/28/2008 10:10 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display broken: smart over-ride? I don't understand why you got a mesa-libGL rpm and are trying to install it? I think doing so could really mess up your system so it is a good thing it is not letting you. My email was about adding Section Extensions Option Composite Disable EndSection to your /etc/X11/xorg.conf assuming you are using the propreitary NVIDIA driver. Which you should also upgrade to the latest one. On Wed, 28 May 2008, Juranek, Jenifer wrote: Krish Paul, Many thanks for the quick advice. I have downloaded the mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, a smart window pops up reporting that a newer version than /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already installed. I select OK anyway, but a new window pops-up reporting that No packages were given for installation. How do I over-ride the smart system to install the legacy driver I need to make sure that everything is installed in the proper place(s) to make tksurfer happy again? Thanks so much, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer display broken
Hi, I recently encountered a problem with tksurfer display (worked perfectly fine a couple of weeks ago). The only change I've made to my linux (centOs 5) system is the recent installation of MATLAB r2008a. Just a note: This was *not* a fun process since the MATLAB 2008a install required deprecated libs (e.g. libXp) which are no longer included with RHEL5. Bottom line: the beginning of my tksurfer display problem does coincide with this process of attempting to install MATLAB r2008a. Although I finally succeeded in getting the MATLAB installed, is there a fix to restore tksurfer display to its proper functionality? In descriptive terms, the tksurfer command launches a window containing a small sliver of the posterior region of the brain. Screen output is pasted below for calling up bert. This morning I upgraded from freesurfer v403 to v404, but the problem still persists. I suspect I broke something in my RHEL5 while trying to fix the Matlab r2008a install failure. BTW...bert looks fine in tkmedit (including aseg+aparc file) Any ideas? Jenifer [EMAIL PROTECTED] freesurfer]$ tksurfer bert rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131848, faces=263692 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display broken
Others ( Paul, Nick) might chip in with a much better answer but my guess is your problem might be related to this thread earlier on the list.. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07324.html --Krish On May 27, 2008, at 11:30 AM, Juranek, Jenifer wrote: Hi, I recently encountered a problem with tksurfer display (worked perfectly fine a couple of weeks ago). The only change I've made to my linux (centOs 5) system is the recent installation of MATLAB r2008a. Just a note: This was *not* a fun process since the MATLAB 2008a install required deprecated libs (e.g. libXp) which are no longer included with RHEL5. Bottom line: the beginning of my tksurfer display problem does coincide with this process of attempting to install MATLAB r2008a. Although I finally succeeded in getting the MATLAB installed, is there a fix to restore tksurfer display to its proper functionality? In descriptive terms, the tksurfer command launches a window containing a small sliver of the posterior region of the brain. Screen output is pasted below for calling up bert. This morning I upgraded from freesurfer v403 to v404, but the problem still persists. I suspect I broke something in my RHEL5 while trying to fix the Matlab r2008a install failure. BTW...bert looks fine in tkmedit (including aseg+aparc file) Any ideas? Jenifer [EMAIL PROTECTED] freesurfer]$ tksurfer bert rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer surfer: Reading header info from /usr/local/freesurfer/subjects/bert/ mri/T1.mgz surfer: vertices=131848, faces=263692 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... ___ 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] tksurfer display broken
This maybe the composite issue if the NVIDIA driver is in use. Edit your /etc/X11/xorg.conf file and put in it: Section Extensions Option Composite Disable EndSection and restart On Tue, 27 May 2008, Krish Subramaniam wrote: Others ( Paul, Nick) might chip in with a much better answer but my guess is your problem might be related to this thread earlier on the list.. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07324.html --Krish On May 27, 2008, at 11:30 AM, Juranek, Jenifer wrote: Hi, I recently encountered a problem with tksurfer display (worked perfectly fine a couple of weeks ago). The only change I've made to my linux (centOs 5) system is the recent installation of MATLAB r2008a. Just a note: This was *not* a fun process since the MATLAB 2008a install required deprecated libs (e.g. libXp) which are no longer included with RHEL5. Bottom line: the beginning of my tksurfer display problem does coincide with this process of attempting to install MATLAB r2008a. Although I finally succeeded in getting the MATLAB installed, is there a fix to restore tksurfer display to its proper functionality? In descriptive terms, the tksurfer command launches a window containing a small sliver of the posterior region of the brain. Screen output is pasted below for calling up bert. This morning I upgraded from freesurfer v403 to v404, but the problem still persists. I suspect I broke something in my RHEL5 while trying to fix the Matlab r2008a install failure. BTW...bert looks fine in tkmedit (including aseg+aparc file) Any ideas? Jenifer [EMAIL PROTECTED] freesurfer]$ tksurfer bert rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer surfer: Reading header info from /usr/local/freesurfer/subjects/bert/ mri/T1.mgz surfer: vertices=131848, faces=263692 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... ___ 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 -- --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
