Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Connectivity design ill-conditioned
by Zimmerman, Jared Perry 26 May '16

26 May '16

Hi, I'm having a problem running first level connectivity analysis on my resting-state data. When I run selxavg3-sess I keep getting a notice that my design is ill-conditioned but I can't figure out why. I am trying to run analysis on two 124 volume rsfMRI runs in my fsd and the design matrix looks fine to me with dimensions 248x47 (although should ncols be an even number since I'm doing two runs?). Poking around the Xtmp.mat I noticed a few things that are confusing. Notably, flac.funcfspec points only to one of my runs in the fsd, and flac.X is a 124x24 matrix which appears to be the design matrix for just one of my runs (and if there are 24 columns in that, should there be 28 columns in the design matrix for combining both runs?). Any help figuring out why this design is ill-conditioned would be great. I've attached my Xtmp.mat, selxavg3.log and analysis design file to this email, but it's unclear to me if the mailing list will scrub them off. If so I can make them available some other way. Thanks, Jared

2 1

Fwd: Re: XQuartz 2.7.9 Update Inquiry
by Rockers, Elijah D. 26 May '16

26 May '16

Quick update on the GLX errors we experience with remote access of freesurfer, and qdec The below conversations may be of interest. -Eli -------- Forwarded Message -------- Subject: Re: XQuartz 2.7.9 Update Inquiry Date: Wed, 25 May 2016 20:59:55 -0400 From: Magda Tsintou <magda.tsintou(a)gmail.com><mailto:magda.tsintou@gmail.com> To: Ambrose LI <ambrose.li(a)gmail.com><mailto:ambrose.li@gmail.com> CC: MacQueen, Don <macqueen1(a)llnl.gov><mailto:macqueen1@llnl.gov>, Rich Cook <wealthychef(a)gmail.com><mailto:wealthychef@gmail.com>, x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> <x11-users(a)lists.apple.com><mailto:x11-users@lists.apple.com>, Rockers, Elijah D. <edrockers(a)houstonmethodist.org><mailto:edrockers@houstonmethodist.org> Hi Ambrose, Thanks a lot for letting us know. That is very helpful. I would encourage everyone to send to the x.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__x.org&d=DQMFaQ&c=QmPtDi…> mailing list so that we see if they could help us find the support we need to continue our work. I have already emailed them. Let's see how it goes. Thanks again! Best, Magda. On Wed, May 25, 2016 at 8:21 PM, Ambrose LI <ambrose.li(a)gmail.com<mailto:ambrose.li@gmail.com>> wrote: For anyone who need this to continue working: I mentioned this thread on Twitter and it got picked up by the X.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__X.org&d=DQQFaQ&c=QmPtDi…> Foundation. They are requesting that anyone who need IGLX to work to send email to the x.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__x.org&d=DQMFaQ&c=QmPtDi…> mailing lists to let them know what you need. They have no idea that people don't even know IGLX has been deprecated, let alone people are actually still depending on it for work. https://mobile.twitter.com/XOrgFoundation/status/733516667737628674<https://urldefense.proofpoint.com/v2/url?u=https-3A__mobile.twitter.com_XOr…> 2016-05-25 18:59 GMT-04:00 MacQueen, Don <macqueen1(a)llnl.gov<mailto:macqueen1@llnl.gov>>: For what it's worth, see, <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.x.org_wiki_Develop…>https://www.x.org/wiki/Development/Security/Advisory-2014-12-09/ -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062<tel:925-423-1062> From: <<mailto:x11-users-bounces+macq=llnl.gov@lists.apple.com>x11-users-bounces+macq=llnl.gov(a)lists.apple.com<mailto:x11-users-bounces+macq=llnl.gov@lists.apple.com>> on behalf of Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> Date: Wednesday, May 18, 2016 at 4:43 PM To: Magda Tsintou <magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> Cc: "<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>" <x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>>, "Rockers, Elijah D." <<mailto:edrockers@houstonmethodist.org>edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> Subject: Re: XQuartz 2.7.9 Update Inquiry There will be a tsunami of interest in this if IGLX goes away. This is a legitimate user need. -- Rich On May 18, 2016, at 4:31 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: Yes indeed this will be a serious problem in my lab too. We all rely on that to work on our research projects and I think that most neuroimaging labs do the same and I am sure that there are tons of other applications I can not even think of right now. I really hope that a solution for this will come up so that there will be no problems. When I notified my lab they did not even know how to guide me on this. At least there should be some sort of awareness in the labs about that issue so that not everyone needs to figure it out alone. On Wed, May 18, 2016 at 6:39 PM, Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: There's nothing to transition to! I cannot believe that XOrg thinks that nobody needs to do this, it's mind boggling to me. It's going to be a big problem at our lab. > On May 18, 2016, at 8:46 AM, Rockers, Elijah D. <<mailto:edrockers@houstonmethodist.org>edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> wrote: > > Hello again experts, > > Being that XQ is no longer going to support IGLX, this could interfere > with some current application's functionality in our lab. Should I > notify the application developers that they should consider looking to > transition away from GLX? Or is this kind of ssh X forwarding to the mac > not even possible without GLX (are there alternatives to GLX they could > consider?) > > Apologies, even as a computer nerd, the complexity of graphics > software/hardware remains somewhat of a mystery to me, so I'm not 100% > sure I'm even asking the right questions here.. > > Thanks, > > On 05/18/2016 01:00 AM, <mailto:x11-users-request@lists.apple.com> x11-users-request(a)lists.apple.com<mailto:x11-users-request@lists.apple.com> wrote: >> Send X11-users mailing list submissions to >> <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >> or, via email, send a message with subject or body 'help' to >> <mailto:x11-users-request@lists.apple.com> x11-users-request(a)lists.apple.com<mailto:x11-users-request@lists.apple.com> >> >> You can reach the person managing the list at >> <mailto:x11-users-owner@lists.apple.com> x11-users-owner(a)lists.apple.com<mailto:x11-users-owner@lists.apple.com> >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of X11-users digest..." >> >> >> Today's Topics: >> >> 1. Re: XQuartz 2.7.9 Update Inquiry (Jeremy Huddleston Sequoia) >> 2. Re: XQuartz 2.7.9 Update Inquiry (Richard Cook) >> 3. Re: XQuartz 2.7.9 Update Inquiry (Jeremy Huddleston Sequoia) >> 4. Re: XQuartz 2.7.9 Update Inquiry (Rich Cook) >> 5. Re: XQuartz 2.7.9 Update Inquiry (James Gunning) >> 6. Re: XQuartz 2.7.9 Update Inquiry (César) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 17 May 2016 21:59:06 -0700 >> From: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> To: César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com>> >> Cc: "<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>" <<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:31F32838-10D2-424F-A417-7213F78E67A2@apple.com>31F32838-10D2-424F-A417-7213F78E67A2(a)apple.com<mailto:31F32838-10D2-424F-A417-7213F78E67A2@apple.com>> >> Content-Type: text/plain; charset="utf-8" >> >> There was one change, but it didn't completely address the problem. >> >>> On May 17, 2016, at 21:53, César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com>> wrote: >>> >>> Jeremy, was the OpenGL context clipping bug addressed in 2.7.9, or is it still pending? (I sent you a minimal working example showing the bug some time ago) >>> >>> Thanks, >>> >>> César >>> >>> >>> >>> El miércoles, 18 de mayo de 2016, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> escribió: >>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>> >>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>> >>> --Jeremy >>> >>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> >>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>> >>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>> >>>> Many Thanks! >>>> Christopher >>>> >>>> >>>> >>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>> >>>> Hi Christopher, >>>> >>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>> >>>> Best regards, >>>> Magda. >>>> >>>> >>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>> >>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>> >>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>> >>>> Macbook Pro Mid 2012 15" >>>> OSX 10.8.5 >>>> >>>> Thanks! >>>> Christopher >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>> >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: smime.p7s >> Type: application/pkcs7-signature >> Size: 4465 bytes >> Desc: not available >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 17 May 2016 22:18:27 -0700 >> From: Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> >> To: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:4479A8B5-7740-4BFB-B533-B95364D78F23@gmail.com>4479A8B5-7740-4BFB-B533-B95364D78F23(a)gmail.com<mailto:4479A8B5-7740-4BFB-B533-B95364D78F23@gmail.com>> >> Content-Type: text/plain; charset=us-ascii >> >> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >> >>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>> >>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>> >>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>> >>> --Jeremy >>> >>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> >>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>> >>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>> >>>> Many Thanks! >>>> Christopher >>>> >>>> >>>> >>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>> >>>> Hi Christopher, >>>> >>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>> >>>> Best regards, >>>> Magda. >>>> >>>> >>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>> >>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>> >>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>> >>>> Macbook Pro Mid 2012 15" >>>> OSX 10.8.5 >>>> >>>> Thanks! >>>> Christopher >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>> >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>> _______________________________________________ >>> Do not post admin requests to the list. They will be ignored. >>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>> >>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 17 May 2016 22:38:13 -0700 >> From: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> To: Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:6C53050F-0731-4FBB-B83C-E02B54AA3F08@apple.com>6C53050F-0731-4FBB-B83C-E02B54AA3F08(a)apple.com<mailto:6C53050F-0731-4FBB-B83C-E02B54AA3F08@apple.com>> >> Content-Type: text/plain; charset="utf-8" >> >> >>> On May 17, 2016, at 22:18, Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: >>> >>> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. >> That is IGLX. >> >>> But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >>> >>>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>> >>>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>>> >>>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>>> >>>> --Jeremy >>>> >>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>> >>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>>> >>>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>>> >>>>> Many Thanks! >>>>> Christopher >>>>> >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>>> >>>>> Hi Christopher, >>>>> >>>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>> >>>>> Best regards, >>>>> Magda. >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>> >>>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>>> >>>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>>> >>>>> Macbook Pro Mid 2012 15" >>>>> OSX 10.8.5 >>>>> >>>>> Thanks! >>>>> Christopher >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> >>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> >>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: smime.p7s >> Type: application/pkcs7-signature >> Size: 4465 bytes >> Desc: not available >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 17 May 2016 22:42:44 -0700 >> From: Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> >> To: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:B3A6C40B-0280-4068-A564-2D29D14FF451@gmail.com>B3A6C40B-0280-4068-A564-2D29D14FF451(a)gmail.com<mailto:B3A6C40B-0280-4068-A564-2D29D14FF451@gmail.com>> >> Content-Type: text/plain; charset=utf-8 >> >> Hmm, what is going to replace IGLX? How are people going to display OpenGL graphics over remote X11 if not by GLX? Sorry if this is offtopic. >> >>> On May 17, 2016, at 10:38 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>> >>> >>>> On May 17, 2016, at 22:18, Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: >>>> >>>> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. >>> That is IGLX. >>> >>>> But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >>>> >>>>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>>> >>>>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>>>> >>>>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>>>> >>>>> --Jeremy >>>>> >>>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>> >>>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>>>> >>>>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>>>> >>>>>> Many Thanks! >>>>>> Christopher >>>>>> >>>>>> >>>>>> >>>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>>>> >>>>>> Hi Christopher, >>>>>> >>>>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>>> >>>>>> Best regards, >>>>>> Magda. >>>>>> >>>>>> >>>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>>> >>>>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>>>> >>>>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>>>> >>>>>> Macbook Pro Mid 2012 15" >>>>>> OSX 10.8.5 >>>>>> >>>>>> Thanks! >>>>>> Christopher >>>>>> >>>>>> _______________________________________________ >>>>>> Do not post admin requests to the list. They will be ignored. >>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>> >>>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Do not post admin requests to the list. They will be ignored. >>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>> >>>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> >>>>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >> ————— >> Cheers from Rich Cook >> =============================== >> Success is the ability to go from one failure to the next with no loss of enthusiasm. --Winston Churchill >> >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 18 May 2016 15:56:13 +1000 >> From: James Gunning <<mailto:James.Gunning@csiro.au>James.Gunning(a)csiro.au<mailto:James.Gunning@csiro.au>> >> To: Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>>, Jeremy Huddleston Sequoia >> <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:573C03FD.8080509@csiro.au>573C03FD.8080509(a)csiro.au<mailto:573C03FD.8080509@csiro.au>> >> Content-Type: text/plain; charset="utf-8"; Format="flowed" >> >> Hi Rich, Jeremy, all, >> Yes, I think a lot of us care about this a deal. >> Any news welcome. >> James. >> >> >> Rich Cook wrote: >>> Hmm, what is going to replace IGLX? How are people going to display OpenGL graphics over remote X11 if not by GLX? Sorry if this is offtopic. >>> >>>> On May 17, 2016, at 10:38 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>> >>>> >>>>> On May 17, 2016, at 22:18, Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: >>>>> >>>>> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. >>>> That is IGLX. >>>> >>>>> But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >>>>> >>>>>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>>>> >>>>>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>>>>> >>>>>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>>>>> >>>>>> --Jeremy >>>>>> >>>>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>>> >>>>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>>>>> >>>>>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>>>>> >>>>>>> Many Thanks! >>>>>>> Christopher >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>>>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>>>>> >>>>>>> Hi Christopher, >>>>>>> >>>>>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>>>> >>>>>>> Best regards, >>>>>>> Magda. >>>>>>> >>>>>>> >>>>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>>>> >>>>>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>>>>> >>>>>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>>>>> >>>>>>> Macbook Pro Mid 2012 15" >>>>>>> OSX 10.8.5 >>>>>>> >>>>>>> Thanks! >>>>>>> Christopher >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Do not post admin requests to the list. They will be ignored. >>>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>>> >>>>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Do not post admin requests to the list. They will be ignored. >>>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>>> >>>>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>>>>> _______________________________________________ >>>>>> Do not post admin requests to the list. They will be ignored. >>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>> >>>>>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >>> ————— >>> Cheers from Rich Cook >>> =============================== >>> Success is the ability to go from one failure to the next with no loss of enthusiasm. --Winston Churchill >>> >>> >>> _______________________________________________ >>> Do not post admin requests to the list. They will be ignored. >>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>> >>> This email sent to <mailto:james.gunning@csiro.au> james.gunning(a)csiro.au<mailto:james.gunning@csiro.au> >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: James_Gunning.vcf >> Type: text/x-vcard >> Size: 223 bytes >> Desc: not available >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> Message: 6 >> Date: Wed, 18 May 2016 07:59:37 +0200 >> From: César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com>> >> To: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: "<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>" <<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: >> <<mailto:CALGOyxrDB8O1WXGFG-H1AOrDq0XekRb1tE3B4UFqtFo4hxyx6A@mail.gmail.com>CALGOyxrDB8O1WXGFG-H1AOrDq0XekRb1tE3B4UFqtFo4hxyx6A(a)mail.gmail.com<mailto:CALGOyxrDB8O1WXGFG-H1AOrDq0XekRb1tE3B4UFqtFo4hxyx6A@mail.gmail.com>> >> Content-Type: text/plain; charset="utf-8" >> >> Ok, thanks a lot, I look forward to the final fix (it's not a critical bug, >> but it does make my apps look like if they were broken -they run fine, but >> their UI looks broken) >> >> Thanks, >> >> César >> >> >> >> El miércoles, 18 de mayo de 2016, Jeremy Huddleston Sequoia < >> <mailto:jeremyhu@apple.com> jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> escribió: >> >>> There was one change, but it didn't completely address the problem. >>> >>>> On May 17, 2016, at 21:53, César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com> <javascript:;><javascript:;>> >>> wrote: >>>> Jeremy, was the OpenGL context clipping bug addressed in 2.7.9, or is it >>> still pending? (I sent you a minimal working example showing the bug some >>> time ago) >>>> Thanks, >>>> >>>> César >>>> >>>> >>>> >>>> El miércoles, 18 de mayo de 2016, Jeremy Huddleston Sequoia < >>> <mailto:jeremyhu@apple.com> jeremyhu(a)apple.com<mailto:jeremyhu@apple.com> <javascript:;><javascript:;>> escribió: >>>> FWIW, there are security vulnerabilities addressed in the versions of >>> libpng in 2.7.9, so you might want to update at least for the security >>> reasons. >>>> The only issues that I'm aware of as regressions are the issues with >>> IGLX (which isn't really going to be supported much longer) and a >>> regression in the support for tcp connections (which is off by default and >>> discouraged). >>>> --Jeremy >>>> >>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com> >>> <javascript:;><javascript:;>> wrote: >>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 >>> was just released earlier this month, and bugs were one thing I wondered >>> about. I'm pretty out of the loop on this stuff. >>>>> And, no I don't think I have anything to gain from an upgrade. >>> Nothing prompted me to look into an upgrade aside from curiosity and an >>> attempt to stay up to date. I just use XQ to run Inkscape, and so far I >>> haven't had any issues in the little I've used it. It also appears that >>> Inkscape is still standing at the same version (0.91) as when I initially >>> installed it with XQ So, I will take your advice. If it ain't broken... >>>>> Many Thanks! >>>>> Christopher >>>>> >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou < >>> <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> <javascript:;><javascript:;>> wrote: >>>>> Note: Sorry forgot to reply to all so that everyone can keep track of >>> the conversation... >>>>> Hi Christopher, >>>>> >>>>> With your OSX you would certainly not need to update. We recently were >>> discussing some bugs in XQ 2.7.9 that have not been resolved while the >>> version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ >>> 2.7.9 did not allow me to work with certain commands that needed forwarding >>> over ssh and given the limited people who have been working on that fix >>> this may cause problems for some time. I would strongly recommend from my >>> personal experience to stick with XQ 2.7.8 if you have nothing in >>> particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>> Best regards, >>>>> Magda. >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick < >>> <mailto:spacecarrider@gmail.com> spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com> <javascript:;><javascript:;>> wrote: >>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I >>> check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>> So, if I manually download and install 2.7.9 from the website should I >>> just install it over the previous version? >>>>> And on a side note, should I be able to update through 2.7.8, or is >>> it common knowledge that it doesn't work that way since this is more of a >>> framework (for lack of better words) rather than a normal application. >>>>> Macbook Pro Mid 2012 15" >>>>> OSX 10.8.5 >>>>> >>>>> Thanks! >>>>> Christopher >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com> <javascript:;><javascript:;>) >>>>> Help/Unsubscribe/Update your Subscription: >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> <javascript:;><javascript:;> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com> <javascript:;><javascript:;>) >>>>> Help/Unsubscribe/Update your Subscription: >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> <javascript:;><javascript:;> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> _______________________________________________ >> X11-users mailing list >> <mailto:X11-users@lists.apple.com> X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >> >> End of X11-users Digest, Vol 13, Issue 35 >> ***************************************** > > Houston Methodist. 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If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. > > _______________________________________________ > Do not post admin requests to the list. They will be ignored. > X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) > Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://lists.apple.com/mailman/options/x11-users/wealthychef%40gmail.com > > This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> ————— Cheers from Rich Cook =============================== Success is the ability to go from one failure to the next with no loss of enthusiasm. --Winston Churchill _______________________________________________ Do not post admin requests to the list. They will be ignored. 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New to Freesurfer; cortical thickness
by Marja Caverlé 26 May '16

26 May '16

Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer. - Why do I get the unrecognised flag error? I apologise for these questions, they are probably very easy to answer, but I just don't have a clue yet. Thank you guys. Best, Marja

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request for corrected p-values for mni305 space
by Joseph Dien 26 May '16

26 May '16

Hi, just a user request for corrected p-values for the mni305 space analyses (i.e., sig.voxel.nii.gz files). Thanks! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07(a)mac.com Cell Phone: 202-297-8117 http://joedien.com

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Segmentation of deskulled volume
by Aquino Domenico 26 May '16

26 May '16

Dear Freesurfer team, I'm trying to segment a brain from a non standard sequence. It is a 3D IR sequence that I have previously pre-elaborated and deskulled. The software is running from a long time and at the moment is correcting defects (17/128) but I'm not sure it's working properly. I'm sending you the volume in NIFTI_GZ format. Could you please help me in detecting some possible issues? Thanks a lot, Domenico

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recon-all on 0.5mm scan?
by Trisanna Sprung-Much 26 May '16

26 May '16

Hi Freesurfer I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to do with the fact that Freesurfer tried to conform it to 1mm isotropic? When I ran recon-all on the 1mm atlas it created some nice surfaces. Let me know if you would like the .log as I cannot seem to make much sense of it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Rat model in FreeSurfer
by Melanie Ganz 26 May '16

26 May '16

Hi, one of our lab mates who works with small animal models would also like to try FreeSurfer. I know from the mail archive that people have used it like this before. Could any people that have used it on rats please give some info on what they have tried? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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surfaces from 0.5mm scan
by Trisanna Sprung-Much 25 May '16

25 May '16

Hi there My initial email didn't seem to have sent and so I am re-sending it: I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to do with the fact that Freesurfer tried to conform it to 1mm isotropic? When I ran recon-all on the 1mm atlas it created some nice surfaces. Let me know if you would like the .log as I cannot seem to make much sense of it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Need Help
by HARI GURAGAIN 25 May '16

25 May '16

Hello, I am kind of new to the neuroimaging. I was trying to reproduce the following type of figure in freesurfer (3d image with thickness). But I couldn’t do that. Is it possible for anyone to explain how to generate such figure from mri data. Just to clarify, I have the mri data in the form of *.dcm. Is there any specific command to get through it? I tried to work on similar figures using tksurfer *** but couldn’t produce. Your help is greatly appreciated. Thank you, Hari This figure is from one paper. Fig. 4. 3D models of the pial surfaces generated by FreeSurfer with a colored overlay of the local cortical thickness in mm. The top row shows the pial surfaces of the left and right hemisphere based on data with an isotropic resolution of 0.5 mm and the bottom row with an isotropic resolution of 1 mm; both data sets have been acquired at 7 T.

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White matter segmentation
by Mahmoudi, Fariborz 25 May '16

25 May '16

Dear All, I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this? Regards, Fari ________________________________ CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

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Freesurfer