Hello,
I'm trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for "bert" using tksurfer as I'm trying to get used to using Freesurfer, but I'm a little confused to what I'm seeing. When I type in: "tksurfer bert lh inflated" for example, I only see a very small section at the very end of the image...is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it's still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don't know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: "tksurfer bert lh sphere", I see nothing at all.
If someone could shed some light on the matter I'd be extremely grateful.
Thank you
We have same problem. Any advise would be great appreciated.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697
Tel: 1-949-824-2972 E-mail: sumikoa@uci.edumailto:sabe@ucsd.edu
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ahmed, F, Me fahmed@sun.ac.za Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer
Hello,
I'm trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for "bert" using tksurfer as I'm trying to get used to using Freesurfer, but I'm a little confused to what I'm seeing. When I type in: "tksurfer bert lh inflated" for example, I only see a very small section at the very end of the image...is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it's still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don't know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: "tksurfer bert lh sphere", I see nothing at all.
If someone could shed some light on the matter I'd be extremely grateful.
Thank you
________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside of that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I’m trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for “bert” using tksurfer as I’m trying to get used to using Freesurfer, but I’m a little confused to what I’m seeing. When I type in: “tksurfer bert lh inflated” for example, I only see a very small section at the very end of the image…is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it’s still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don’t know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: “tksurfer bert lh sphere”, I see nothing at all. If someone could shed some light on the matter I’d be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have another suggestion. When I am logged to my machine locally, tksurfer works but only if I enable auto-redraw AND the color scale bar. However, when I log in remotely (via FreeNX), I get the same sliver problem described here.
I found a workaround, which is to use VirtualGL. If you can install VirtualGL on your system, then you can run tksurfer like so:
/opt/VirtualGL/bin/vglrun tksurfer bert lh inflated
The idea of VirtualGL is to force the hardware on the server to run the rendering commands, and then stream the resulting images to the client, rather than forcing the client to do the rendering. Thus, I would expect that using VirtualGL from a local session would be exactly the same as not using it from a local session (only slower). Strangely, tksurfer actually works better for me when I use VirtualGL, even if I am running a local session! That is, I no longer have to enable auto-redraw and a color scale bar to see the surface.
So if you can install VirtualGL and its dependencies on your system, it's possible it will improve tksurfer reliability even on local sessions. For some reason. Note that this may impose a performance penalty, but it is not noticeable on my setup.
-Tim
On Wed, Sep 30, 2009 at 11:46 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside of that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I’m trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for “bert” using tksurfer as I’m trying to get used to using Freesurfer, but I’m a little confused to what I’m seeing. When I type in: “tksurfer bert lh inflated” for example, I only see a very small section at the very end of the image…is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it’s still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don’t know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: “tksurfer bert lh sphere”, I see nothing at all. If someone could shed some light on the matter I’d be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ 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
Tim,
Thanks for the pointer to VirtualGL, that seems like a great solution to some of the VNC problems we have.
I've put together a wiki page describing the tksurfer 'sliver' display problem, and potential solutions, here:
http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems
Thanks to everybody on the list who has contributed potential solutions.
Nick
On Wed, 2009-09-30 at 12:12 -0400, Timothy Vickery wrote:
I have another suggestion. When I am logged to my machine locally, tksurfer works but only if I enable auto-redraw AND the color scale bar. However, when I log in remotely (via FreeNX), I get the same sliver problem described here.
I found a workaround, which is to use VirtualGL. If you can install VirtualGL on your system, then you can run tksurfer like so:
/opt/VirtualGL/bin/vglrun tksurfer bert lh inflated
The idea of VirtualGL is to force the hardware on the server to run the rendering commands, and then stream the resulting images to the client, rather than forcing the client to do the rendering. Thus, I would expect that using VirtualGL from a local session would be exactly the same as not using it from a local session (only slower). Strangely, tksurfer actually works better for me when I use VirtualGL, even if I am running a local session! That is, I no longer have to enable auto-redraw and a color scale bar to see the surface.
So if you can install VirtualGL and its dependencies on your system, it's possible it will improve tksurfer reliability even on local sessions. For some reason. Note that this may impose a performance penalty, but it is not noticeable on my setup.
-Tim
On Wed, Sep 30, 2009 at 11:46 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside of that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I’m trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for “bert” using tksurfer as I’m trying to get used to using Freesurfer, but I’m a little confused to what I’m seeing. When I type in: “tksurfer bert lh inflated” for example, I only see a very small section at the very end of the image…is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it’s still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don’t know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: “tksurfer bert lh sphere”, I see nothing at all. If someone could shed some light on the matter I’d be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ 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
Are there any plans to migrate from TK to QT or WXWidgets? ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business
2009/9/30 Nick Schmansky nicks@nmr.mgh.harvard.edu
Tim,
Thanks for the pointer to VirtualGL, that seems like a great solution to some of the VNC problems we have.
I've put together a wiki page describing the tksurfer 'sliver' display problem, and potential solutions, here:
http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems
Thanks to everybody on the list who has contributed potential solutions.
Nick
On Wed, 2009-09-30 at 12:12 -0400, Timothy Vickery wrote:
I have another suggestion. When I am logged to my machine locally, tksurfer works but only if I enable auto-redraw AND the color scale bar. However, when I log in remotely (via FreeNX), I get the same sliver problem described here.
I found a workaround, which is to use VirtualGL. If you can install VirtualGL on your system, then you can run tksurfer like so:
/opt/VirtualGL/bin/vglrun tksurfer bert lh inflated
The idea of VirtualGL is to force the hardware on the server to run the rendering commands, and then stream the resulting images to the client, rather than forcing the client to do the rendering. Thus, I would expect that using VirtualGL from a local session would be exactly the same as not using it from a local session (only slower). Strangely, tksurfer actually works better for me when I use VirtualGL, even if I am running a local session! That is, I no longer have to enable auto-redraw and a color scale bar to see the surface.
So if you can install VirtualGL and its dependencies on your system, it's possible it will improve tksurfer reliability even on local sessions. For some reason. Note that this may impose a performance penalty, but it is not noticeable on my setup.
-Tim
On Wed, Sep 30, 2009 at 11:46 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside
of
that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I’m trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for “bert” using tksurfer as I’m trying to get used to using Freesurfer, but I’m a little confused to what I’m seeing. When I type in: “tksurfer bert lh inflated” for example, I only see a very small section at the very end of the image…is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it’s still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don’t know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: “tksurfer bert lh sphere”, I see nothing at all. If someone could shed some light on the matter I’d be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ 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
The 'freeview' app, now distributed with freesurfer, is built on WxWidgets. Once enough functionality found in tkmedit, tksurfer and tkregister is built into freeview, then freeview will replace those apps. Getting the internal momentum to do this will take some time, because tksurfer, tkmedit and tkregister have 15 years of functionality incorporated into them.
Nick
On Wed, 2009-09-30 at 16:34 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote:
Are there any plans to migrate from TK to QT or WXWidgets?
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business
2009/9/30 Nick Schmansky nicks@nmr.mgh.harvard.edu Tim,
Thanks for the pointer to VirtualGL, that seems like a great solution to some of the VNC problems we have. I've put together a wiki page describing the tksurfer 'sliver' display problem, and potential solutions, here: http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems Thanks to everybody on the list who has contributed potential solutions. Nick On Wed, 2009-09-30 at 12:12 -0400, Timothy Vickery wrote: > I have another suggestion. When I am logged to my machine locally, > tksurfer works but only if I enable auto-redraw AND the color scale > bar. However, when I log in remotely (via FreeNX), I get the same > sliver problem described here. > > I found a workaround, which is to use VirtualGL. If you can install > VirtualGL on your system, then you can run tksurfer like so: > > /opt/VirtualGL/bin/vglrun tksurfer bert lh inflated > > The idea of VirtualGL is to force the hardware on the server to run > the rendering commands, and then stream the resulting images to the > client, rather than forcing the client to do the rendering. Thus, I > would expect that using VirtualGL from a local session would be > exactly the same as not using it from a local session (only slower). > Strangely, tksurfer actually works better for me when I use VirtualGL, > even if I am running a local session! That is, I no longer have to > enable auto-redraw and a color scale bar to see the surface. > > So if you can install VirtualGL and its dependencies on your system, > it's possible it will improve tksurfer reliability even on local > sessions. For some reason. Note that this may impose a performance > penalty, but it is not noticeable on my setup. > > -Tim > > > On Wed, Sep 30, 2009 at 11:46 AM, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > > Abe, > > > > This tksurfer display problem has been a difficult one to debug, due to > > the complexity of opengl and graphics drivers, and the lack of error > > codes (at least that I can find). > > > > Sebastian mentions some possible workarounds in his email. The first > > one to try, assuming you have an Nvidia graphics card, is to update the > > driver. To do this: > > > > su root > > /sbin/init 3 > > /usr/bin/nividia-installer --update > > > > (follow the instructions) > > > > often times this update fixes the tksurfer 'sliver' problem. outside of > > that, you can try overriding the mesa drivers. you'll need to talk to > > your sysadmin to do that. > > > > Nick > > > > > > On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote: > >> We have same problem. Any advise would be great appreciated. > >> > >> > >> > >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >> Sumiko Abe, Ph.D > >> Dept. of Psychiatry & Human Behavior > >> University of California, Irvine > >> 5251 California Dr, #204 > >> Irvine, CA 92697 > >> > >> Tel: 1-949-824-2972 > >> E-mail: sumikoa@uci.edu > >> > >> > >> > >> > >> > >> ______________________________________________________________________ > >> From: freesurfer-bounces@nmr.mgh.harvard.edu > >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, > >> Me <fahmed@sun.ac.za> > >> Sent: Wednesday, September 30, 2009 1:31 AM > >> To: Freesurfer Mailing List > >> Subject: [Freesurfer] tksurfer > >> > >> > >> > >> > >> Hello, > >> > >> > >> > >> > >> > >> I’m trying to view and check the smoothing and inflation surfaces, the > >> white and pial surfaces for “bert” using tksurfer as I’m trying to get > >> used to using Freesurfer, but I’m a little confused to what I’m > >> seeing. When I type in: “tksurfer bert lh inflated” for example, I > >> only see a very small section at the very end of the image…is this > >> correct? When I view the curv files, I do see a green pattern overlaid > >> on the inflated surface, however it’s still so small. When I view the > >> pial and white surfaces, again, the section displayed is very small, I > >> don’t know if this is correct or if this is what I am supposed to be > >> seeing? Also, when I type in: “tksurfer bert lh sphere”, I see nothing > >> at all. > >> > >> > >> > >> > >> > >> If someone could shed some light on the matter I’d be extremely > >> grateful. > >> > >> > >> > >> > >> > >> Thank you > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> ______________________________________________________________________ > >> This message contains confidential information and is intended only > >> for the individual named. If you are not the named addressee you > >> should not disseminate, distribute or copy this e-mail. Please notify > >> the sender immediately by e-mail if you have received this e-mail by > >> mistake and delete this e-mail from your system. E-mail transmission > >> cannot be guaranteed to be secure or error-free as information could > >> be intercepted, corrupted, lost, destroyed, arrive late or incomplete, > >> or contain viruses. The sender therefore does not accept liability for > >> any errors or omissions in the contents of this message, which arise > >> as a result of e-mail transmission. > >> _______________________________________________ > >> 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
not really migrate, although we've been moving away from tk in the newer stuff. On Wed, 30 Sep 2009, Pedro Paulo de Magalhães Oliveira Junior wrote:
Are there any plans to migrate from TK to QT or WXWidgets?
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business
2009/9/30 Nick Schmansky nicks@nmr.mgh.harvard.edu
Tim,
Thanks for the pointer to VirtualGL, that seems like a great solution to some of the VNC problems we have.
I've put together a wiki page describing the tksurfer 'sliver' display problem, and potential solutions, here:
http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems
Thanks to everybody on the list who has contributed potential solutions.
Nick
On Wed, 2009-09-30 at 12:12 -0400, Timothy Vickery wrote:
I have another suggestion. When I am logged to my machine locally, tksurfer works but only if I enable auto-redraw AND the color scale bar. However, when I log in remotely (via FreeNX), I get the same sliver problem described here.
I found a workaround, which is to use VirtualGL. If you can install VirtualGL on your system, then you can run tksurfer like so:
/opt/VirtualGL/bin/vglrun tksurfer bert lh inflated
The idea of VirtualGL is to force the hardware on the server to run the rendering commands, and then stream the resulting images to the client, rather than forcing the client to do the rendering. Thus, I would expect that using VirtualGL from a local session would be exactly the same as not using it from a local session (only slower). Strangely, tksurfer actually works better for me when I use VirtualGL, even if I am running a local session! That is, I no longer have to enable auto-redraw and a color scale bar to see the surface.
So if you can install VirtualGL and its dependencies on your system, it's possible it will improve tksurfer reliability even on local sessions. For some reason. Note that this may impose a performance penalty, but it is not noticeable on my setup.
-Tim
On Wed, Sep 30, 2009 at 11:46 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside
of
that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I?m trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for ?bert? using tksurfer as I?m trying to get used to using Freesurfer, but I?m a little confused to what I?m seeing. When I type in: ?tksurfer bert lh inflated? for example, I only see a very small section at the very end of the image?is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it?s still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don?t know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: ?tksurfer bert lh sphere?, I see nothing at all. If someone could shed some light on the matter I?d be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ 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
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Tim,
How does one install VirtualGL and its dependencies on their system?
Thanks
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Timothy Vickery Sent: 30 September 2009 18:12 To: Nick Schmansky Cc: Ahmed, F, Me fahmed@sun.ac.za; Freesurfer Mailing List; Abe, Sumiko Subject: Re: [Freesurfer] tksurfer
I have another suggestion. When I am logged to my machine locally, tksurfer works but only if I enable auto-redraw AND the color scale bar. However, when I log in remotely (via FreeNX), I get the same sliver problem described here.
I found a workaround, which is to use VirtualGL. If you can install VirtualGL on your system, then you can run tksurfer like so:
/opt/VirtualGL/bin/vglrun tksurfer bert lh inflated
The idea of VirtualGL is to force the hardware on the server to run the rendering commands, and then stream the resulting images to the client, rather than forcing the client to do the rendering. Thus, I would expect that using VirtualGL from a local session would be exactly the same as not using it from a local session (only slower). Strangely, tksurfer actually works better for me when I use VirtualGL, even if I am running a local session! That is, I no longer have to enable auto-redraw and a color scale bar to see the surface.
So if you can install VirtualGL and its dependencies on your system, it's possible it will improve tksurfer reliability even on local sessions. For some reason. Note that this may impose a performance penalty, but it is not noticeable on my setup.
-Tim
On Wed, Sep 30, 2009 at 11:46 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside of that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I'm trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for "bert" using tksurfer as I'm trying to get used to using Freesurfer, but I'm a little confused to what I'm seeing. When I type in: "tksurfer bert lh inflated" for example, I only see a very small section at the very end of the image.is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it's still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don't know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: "tksurfer bert lh sphere", I see nothing at all. If someone could shed some light on the matter I'd be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ 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
Hi,
Thank you so much for all of your great advice for the SILVER problem. All of our compute notes are using ATI graphic/video cards. Is that works for us to update the drivers also?
Thank you,
Sumiko
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697
Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wednesday, September 30, 2009 8:46 AM To: Abe, Sumiko Cc: Ahmed, F, Me fahmed@sun.ac.za; Freesurfer Mailing List Subject: Re: [Freesurfer] tksurfer
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside of that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I'm trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for "bert" using tksurfer as I'm trying to get used to using Freesurfer, but I'm a little confused to what I'm seeing. When I type in: "tksurfer bert lh inflated" for example, I only see a very small section at the very end of the image...is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it's still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don't know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: "tksurfer bert lh sphere", I see nothing at all. If someone could shed some light on the matter I'd be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Hello,
I seem to have a slight problem. I tried to update the Nvidia graphics driver, as I do have this, however, when I typed in:
su root /sbin/init 3
It closed my terminal, closed the desktop and seemed to be restarting VMware, it went to the start up page for VMware, and asked me for username and password, so I typed that in, expecting it to take me into my actual VMware desktop, which it didn't and it instead asked me to type commands in this start up page...now I can't get into the actual desktop...how can I get back in?
Thank you
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 30 September 2009 17:46 To: Abe, Sumiko Cc: Ahmed, F, Me fahmed@sun.ac.za; Freesurfer Mailing List Subject: Re: [Freesurfer] tksurfer
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside of that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I’m trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for “bert” using tksurfer as I’m trying to get used to using Freesurfer, but I’m a little confused to what I’m seeing. When I type in: “tksurfer bert lh inflated” for example, I only see a very small section at the very end of the image…is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it’s still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don’t know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: “tksurfer bert lh sphere”, I see nothing at all. If someone could shed some light on the matter I’d be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please disregard my last email, my computer restarted and after this, VMware loaded up normally.
-----Original Message----- From: Ahmed, F, Me fahmed@sun.ac.za Sent: 01 October 2009 09:24 To: 'Nick Schmansky'; Abe, Sumiko Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] tksurfer
Hello,
I seem to have a slight problem. I tried to update the Nvidia graphics driver, as I do have this, however, when I typed in:
su root /sbin/init 3
It closed my terminal, closed the desktop and seemed to be restarting VMware, it went to the start up page for VMware, and asked me for username and password, so I typed that in, expecting it to take me into my actual VMware desktop, which it didn't and it instead asked me to type commands in this start up page...now I can't get into the actual desktop...how can I get back in?
Thank you
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 30 September 2009 17:46 To: Abe, Sumiko Cc: Ahmed, F, Me fahmed@sun.ac.za; Freesurfer Mailing List Subject: Re: [Freesurfer] tksurfer
Abe,
This tksurfer display problem has been a difficult one to debug, due to the complexity of opengl and graphics drivers, and the lack of error codes (at least that I can find).
Sebastian mentions some possible workarounds in his email. The first one to try, assuming you have an Nvidia graphics card, is to update the driver. To do this:
su root /sbin/init 3 /usr/bin/nividia-installer --update
(follow the instructions)
often times this update fixes the tksurfer 'sliver' problem. outside of that, you can try overriding the mesa drivers. you'll need to talk to your sysadmin to do that.
Nick
On Wed, 2009-09-30 at 05:50 -0700, Abe, Sumiko wrote:
We have same problem. Any advise would be great appreciated.
Sumiko Abe, Ph.D Dept. of Psychiatry & Human Behavior University of California, Irvine 5251 California Dr, #204 Irvine, CA 92697 Tel: 1-949-824-2972 E-mail: sumikoa@uci.edu ______________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfAhmed, F, Me <fahmed@sun.ac.za> Sent: Wednesday, September 30, 2009 1:31 AM To: Freesurfer Mailing List Subject: [Freesurfer] tksurfer Hello, I’m trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for “bert” using tksurfer as I’m trying to get used to using Freesurfer, but I’m a little confused to what I’m seeing. When I type in: “tksurfer bert lh inflated” for example, I only see a very small section at the very end of the image…is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it’s still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don’t know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: “tksurfer bert lh sphere”, I see nothing at all. If someone could shed some light on the matter I’d be extremely grateful. Thank you ______________________________________________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Abe, Sumiko -
Ahmed, F, Me <fahmed＠sun.ac.za> -
Bruce Fischl -
Nick Schmansky -
Pedro Paulo de Magalhães Oliveira Junior -
Timothy Vickery