Re: [Freesurfer] Tksurfer Error

2022-07-10 Thread Rachel Wagner 
External Email - Use Caution

Thanks very much Dr. Greve!

Just had another question for you, if you have the time!

I am currently working on displaying my SPM overlay on a 3D brain volume, using 
bbregister, and am getting this: 
https://secure-web.cisco.com/1Y47t3gF3E5zpTqY7OR_RkIvNSeef_CHIYkO-YK-6vd1D17vS9NYSCvba3g_O1eFjmtS6mpdDGb0QX667fxWA9VEo7WyiA4Q1LYPYp5VqCjvhAio-qTT-szuNc4McV8R7RxOw2cP2ozw8-zxrvxOLgpvEDnL23EIzAV1_cOop2q6RqCebdyBWs_5M52SuQ-Y1olfanVQtz3tNleTdujH_C8p_QBWk6_dz7EcaP0M-dGXIJ0O9dWrLiUnUFksz5xC--oEI9xgcsNah-JjbxPzeRFJJpbFWjE_M9nv8yEf4F6dZ8HiHUEjCME0XDSf3iPf9sBMkaLHDil9Q8rRS5pNrK5WMKa0ZQMFzIAknIpLC3rA/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Ddrivesdk

I am hoping to smooth out the surface, so it is more continuous, and change the 
coloring of the brain. Are there options to do so?

Kind Regards,
Rachel




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Sunday, July 10, 2022, 4:09 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tksurfer Error

tksurfer is depracated. Try using tksurferfv instead

On 6/29/2022 4:33 PM, Rachel Wagner wrote:

External Email - Use Caution
Hello,

I am attempting to paint my spm functional data onto freesurfer’s anatomical 
image.

I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg 
register.dat

And got this error:

Tcl_Init failed: Can't find a usable init.tcl in the following directories:
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4



This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1


How can I fix this error?

Thanks,
Rachel



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/18uFsKV3T7bqI7k7n51PEj3Ai3lAoopZ_xXXCkLfme24lyxewgHcgnxoXD0FCQM1PZ-vM4ryzcP41h7fTbiwmAKXp7Kyrkk3-YoE04-h4TcI_2NkupiXtIx5UDa7w5m8FwGfvGl9SwcSl839YOL12UTK4eup8PDiP96ZmO8hKFI3VmY5Twh8cv0JPUk4hfIikzoIxDOuQDpJG6ww9SNG77f3QBUM27qof9HiUeI9BXWHJpGPBQILzkp9RP-rDqKVxDfbqWgK9Ucs6p4eR0tjLWo7VA_utdANSrj-pCDLUk3Qp8m68HWJlx5mfo4ZkR_Q7DIhdKa7FLbL0LOwjVT9xFd2i5lGCt7rQ6DqZYXkGGj4/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Tksurfer Error

2022-07-10 Thread Douglas N. Greve 

tksurfer is depracated. Try using tksurferfv instead

On 6/29/2022 4:33 PM, Rachel Wagner wrote:


External Email - Use Caution

Hello,

I am attempting to paint my spm functional data onto freesurfer’s 
anatomical image.


I ran this code: tksurfer bert lh inflated -overlay updated.img 
-overlay-reg register.dat


And got this error:

Tcl_Init failed: Can't find a usable init.tcl in the following 
directories:


/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4

This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"

Tix_Init failed: Can't find a usable Tix Init.tcl in the following 
directories:


./library

./tix8.1

./library

./tix8.1

/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1

How can I fix this error?

Thanks,

Rachel


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Tksurfer Error

2022-06-29 Thread fsbuild 
External Email - Use Caution

The tksurfer command is deprecated/no longer supported.
You could try using freeview directly or runtksurferfv, which may take 
the same options as tksurfer but run freeview to display things.
- R..

On Jun 29, 2022, at 16:33, Rachel Wagner rwag...@uwo.ca 
wrote:External Email - Use 
CautionHello,I am 
attempting to paint my spm functional data onto freesurfer’s anatomical 
image.I ran this code: tksurfer bert lh inflated -overlay updated.img 
-overlay-reg register.datAnd got this error:Tcl_Init failed: Can't 
find a usable init.tcl in the following 
directories:/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4This
 probably means that Tcl wasn't installed properly.Tk_Init failed: 
invalid command name "tcl_findLibrary"Tix_Init failed: Can't find a usable Tix 
Init.tcl in the following 
directories:./library./tix8.1./library./tix8.1/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1How
 can I fix this 
error?Thanks,Rachel___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Tksurfer Error

2022-06-29 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am attempting to paint my spm functional data onto freesurfer’s anatomical 
image.

I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg 
register.dat

And got this error:

Tcl_Init failed: Can't find a usable init.tcl in the following directories:
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4



This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1


How can I fix this error?

Thanks,
Rachel
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] tksurfer error

2012-02-22 Thread Signe Bray 
Hi,

 I have been experiencing an error with tksurfer. It occurs when I am
trying to generate an occipital patch, following these instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch

I open a surface using: tksurfer SUBJ lh inflated -curv lh.curv

Following the steps, when I click the surface and press the Fill Uncut
Area button, tksurfer crashes with the following error:

tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion
`a[j].inputstride == vptr-stride' failed.

I have also experienced this problem zooming out on a specific surface
patch.

I have seen this problem in different forms on the mailing list, but have
not seen any solutions or workarounds:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19846.html

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14612.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16303.html



My machine info:

-

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.38-8-generic x86_64

-

Thank you,

Signe
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] tksurfer error

2011-03-15 Thread Don Hagler 

Hi,

In response to the message below, I have been getting the exact
same error when running tksurfer on a particular workstation.
tksurfer does display correctly, but the drawing is very slow, as if
running remotely (or not using the video card).  This happens with versions
3.0.5 and 4.5.0.

I tried uninstalling and reinstalling the nvidia driver, but that didn't help.

glxgears and glxinfo work fine, no warnings or error messages.

In Xorg.0.log, there is one warning:
(WW) NVIDIA(0): UBB is incompatible with the Composite extension.  Disabling
(WW) NVIDIA(0): UBB.

After googling, I found that UBB stands for Unified Back Buffer.
http://http.download.nvidia.com/XFree86/Linux-x86/1.0-8178/README/appendix-k.html
This only applies to Quadro GPUs.  This particular workstation has this type:
NVIDIA GPU Quadro FX 580

I haven't yet found a solution.  Evan, do you have a Quadro GPU?
Did you find a solution?


Don

_


Dear freesurfer community,

I am currently trying to view one of the surfaces generated by recon-all
command in tksurfer but when I enter the command:

tksurfer LuceHR_FS_SURF lh inflated.nofix

I receive a series of errors that look like this:

Received X error!
Error code   : 1
Request code : 147
Minor code   : 181

Error text : 'BadRequest (invalid request code or no such operation)'

Subsequently the surface window does not display what I would believe is the
surface I am trying to view and then the only way I can exit the tksurfer
environment is by exiting the terminal that I invoked it in.

Any ideas or solutions?

Thank you very much,

Evan Luther

  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] tksurfer error

2011-02-08 Thread Evan Luther 
Dear freesurfer community,

I am currently trying to view one of the surfaces generated by recon-all
command in tksurfer but when I enter the command:

tksurfer LuceHR_FS_SURF lh inflated.nofix

I receive a series of errors that look like this:

Received X error!
Error code   : 1
Request code : 147
Minor code   : 181

Error text : 'BadRequest (invalid request code or no such operation)'

Subsequently the surface window does not display what I would believe is the
surface I am trying to view and then the only way I can exit the tksurfer
environment is by exiting the terminal that I invoked it in.

Any ideas or solutions?

Thank you very much,

Evan Luther
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tksurfer error

2010-02-10 Thread Bruce Fischl 
have you tried clicking the redraw button?
On Wed, 10 Feb 2010, Daniel 
Ferreira Padilla wrote:

 Dear Freesurfer users,



 I hope you could help me with that problem. I do the recon-all preprocessing
 step and then I try tksurfer. But the following error comes up. Moreover
 tksurfer window open up but it looks like 'empty'. Please find it attached.



 Thank you very much!



 Daniel Ferreira





  freesurfer-Linux-centos4-stable-pub-v4.5.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   /home/Neuropsicologia/freesurfer
 FSFAST_HOME   /home/Neuropsicologia/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii
 SUBJECTS_DIR  /home/Neuropsicologia/DANI/subjects
 MNI_DIR   /home/Neuropsicologia/freesurfer/mni
 FSL_DIR   /home/Neuropsicologia/fsl


 neuropsicolo...@linux-tand:~ cd DANI/subjects


 neuropsicolo...@linux-tand:~/DANI/subjects tksurfer GJ25_3D lh inflated
 -aparc -gray
 surfer: current subjects dir: /home/Neuropsicologia/DANI/subjects
 surfer: not in scripts dir == using cwd for session root
 surfer: session root data dir ($session) set to:
 surfer: /home/Neuropsicologia/DANI/subjects
 surfer: Reading header info from
 /home/Neuropsicologia/DANI/subjects/GJ25_3D/mri/T1.mgz
 surfer: vertices=123902, faces=247800
 surfer: curvature read: min=-1.349975 max=2.259740
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin
 al.txt)
 Found embedded color table in annotation.
 surfer: single buffered window
 surfer: tkoInitWindow(GJ25_3D)
 surfer: using interface
 /home/Neuropsicologia/freesurfer/lib/tcl/tksurfer.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_common.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_wrappers.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/fsgdfPlot.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkUtils.tcl
 Successfully parsed tksurfer.tcl
 reading white matter vertex locations...
 %






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2010-02-10 Thread Daniel Ferreira Padilla 
Yes, I click over the redraw button but it doesn’t work. It is strange but
despite tksurfer window is empty, when I click on it, labels and values
appear in tksurfer tools window.

Any other idea?

Thank you very much in advance

-Mensaje original-
De: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Enviado el: miércoles, 10 de febrero de 2010 15:49
Para: Daniel Ferreira Padilla
CC: freesurfer@nmr.mgh.harvard.edu
Asunto: Re: [Freesurfer] tksurfer error

have you tried clicking the redraw button?
On Wed, 10 Feb 2010, Daniel 
Ferreira Padilla wrote:

 Dear Freesurfer users,



 I hope you could help me with that problem. I do the recon-all
preprocessing
 step and then I try tksurfer. But the following error comes up. Moreover
 tksurfer window open up but it looks like 'empty'. Please find it
attached.



 Thank you very much!



 Daniel Ferreira





  freesurfer-Linux-centos4-stable-pub-v4.5.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   /home/Neuropsicologia/freesurfer
 FSFAST_HOME   /home/Neuropsicologia/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii
 SUBJECTS_DIR  /home/Neuropsicologia/DANI/subjects
 MNI_DIR   /home/Neuropsicologia/freesurfer/mni
 FSL_DIR   /home/Neuropsicologia/fsl


 neuropsicolo...@linux-tand:~ cd DANI/subjects


 neuropsicolo...@linux-tand:~/DANI/subjects tksurfer GJ25_3D lh inflated
 -aparc -gray
 surfer: current subjects dir: /home/Neuropsicologia/DANI/subjects
 surfer: not in scripts dir == using cwd for session root
 surfer: session root data dir ($session) set to:
 surfer: /home/Neuropsicologia/DANI/subjects
 surfer: Reading header info from
 /home/Neuropsicologia/DANI/subjects/GJ25_3D/mri/T1.mgz
 surfer: vertices=123902, faces=247800
 surfer: curvature read: min=-1.349975 max=2.259740
 reading colortable from annotation file...
 colortable with 36 entries read (originally

/autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin
 al.txt)
 Found embedded color table in annotation.
 surfer: single buffered window
 surfer: tkoInitWindow(GJ25_3D)
 surfer: using interface
 /home/Neuropsicologia/freesurfer/lib/tcl/tksurfer.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_common.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_wrappers.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/fsgdfPlot.tcl
 Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkUtils.tcl
 Successfully parsed tksurfer.tcl
 reading white matter vertex locations...
 %








___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2010-02-10 Thread Nick Schmansky 
you can try some of the things suggested here:

https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems

although those suggestions are targetted at the 'sliver' problem, where
you get a display of only a tiny section of the brain.  you dont seem to
be getting any display.

n.

On Wed, 2010-02-10 at 16:18 +, Daniel Ferreira Padilla wrote:
 Yes, I click over the redraw button but it doesn’t work. It is strange but
 despite tksurfer window is empty, when I click on it, labels and values
 appear in tksurfer tools window.
 
 Any other idea?
 
 Thank you very much in advance
 
 -Mensaje original-
 De: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
 Enviado el: miércoles, 10 de febrero de 2010 15:49
 Para: Daniel Ferreira Padilla
 CC: freesurfer@nmr.mgh.harvard.edu
 Asunto: Re: [Freesurfer] tksurfer error
 
 have you tried clicking the redraw button?
 On Wed, 10 Feb 2010, Daniel 
 Ferreira Padilla wrote:
 
  Dear Freesurfer users,
 
 
 
  I hope you could help me with that problem. I do the recon-all
 preprocessing
  step and then I try tksurfer. But the following error comes up. Moreover
  tksurfer window open up but it looks like 'empty'. Please find it
 attached.
 
 
 
  Thank you very much!
 
 
 
  Daniel Ferreira
 
 
 
 
 
   freesurfer-Linux-centos4-stable-pub-v4.5.0 
  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /home/Neuropsicologia/freesurfer
  FSFAST_HOME   /home/Neuropsicologia/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii
  SUBJECTS_DIR  /home/Neuropsicologia/DANI/subjects
  MNI_DIR   /home/Neuropsicologia/freesurfer/mni
  FSL_DIR   /home/Neuropsicologia/fsl
 
 
  neuropsicolo...@linux-tand:~ cd DANI/subjects
 
 
  neuropsicolo...@linux-tand:~/DANI/subjects tksurfer GJ25_3D lh inflated
  -aparc -gray
  surfer: current subjects dir: /home/Neuropsicologia/DANI/subjects
  surfer: not in scripts dir == using cwd for session root
  surfer: session root data dir ($session) set to:
  surfer: /home/Neuropsicologia/DANI/subjects
  surfer: Reading header info from
  /home/Neuropsicologia/DANI/subjects/GJ25_3D/mri/T1.mgz
  surfer: vertices=123902, faces=247800
  surfer: curvature read: min=-1.349975 max=2.259740
  reading colortable from annotation file...
  colortable with 36 entries read (originally
 
 /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin
  al.txt)
  Found embedded color table in annotation.
  surfer: single buffered window
  surfer: tkoInitWindow(GJ25_3D)
  surfer: using interface
  /home/Neuropsicologia/freesurfer/lib/tcl/tksurfer.tcl
  Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_common.tcl
  Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_wrappers.tcl
  Reading /home/Neuropsicologia/freesurfer/lib/tcl/fsgdfPlot.tcl
  Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkUtils.tcl
  Successfully parsed tksurfer.tcl
  reading white matter vertex locations...
  %
 
 
 
 
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] TKSURFER error- open GL in Fedora

2009-11-30 Thread Massieh Moayedi 
Hi,

I can't seem to run tksurfer in Fedora 7.  We are using a Wacom Tablet 
monitor, and since we installed it, we cannot run tksurfer.  We get the 
following error:

surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(fsaverage)
Can't create a context!
surfer: failed, trying double buffered window
Can't create a context!
surfer: failed, no suitable display found

Does anyone know how to go about this?

massih


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer error in ubuntu...

2009-07-30 Thread Gonzalo Rojas 
Hi:

   How can I solve the following error ?


ubuntu:~ tksurfer rezende rh pial
surfer: current subjects dir: /home/image/bin/freesurfer/subjects
surfer: not in scripts dir == using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/image
surfer: Reading header info from 
/home/image/bin/freesurfer/subjects/rezende/mri/T1.mgz
surfer: vertices=119258, faces=238512
Loading /home/image/bin/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(rezende)
Window type not found!
surfer: failed, trying double buffered window
surfer: using interface /home/image/bin/freesurfer/lib/tcl/tksurfer.tcl
Reading /home/image/bin/freesurfer/lib/tcl/tkm_common.tcl
Reading /home/image/bin/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /home/image/bin/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/image/bin/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...


  Sincerely,


-- 
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error in ubuntu...

2009-07-30 Thread Bruce Fischl 
Hi Gonzalo,

are you running over vnc or something similar?

Bruce
On Thu, 30 Jul 2009, Gonzalo 
Rojas wrote:

 Hi:

   How can I solve the following error ?


 ubuntu:~ tksurfer rezende rh pial
 surfer: current subjects dir: /home/image/bin/freesurfer/subjects
 surfer: not in scripts dir == using cwd for session root
 surfer: session root data dir ($session) set to:
 surfer: /home/image
 surfer: Reading header info from
 /home/image/bin/freesurfer/subjects/rezende/mri/T1.mgz
 surfer: vertices=119258, faces=238512
 Loading /home/image/bin/freesurfer/surface_labels.txt
 surfer: ### redraw failed: no gl window open
 surfer: single buffered window
 surfer: tkoInitWindow(rezende)
 Window type not found!
 surfer: failed, trying double buffered window
 surfer: using interface /home/image/bin/freesurfer/lib/tcl/tksurfer.tcl
 Reading /home/image/bin/freesurfer/lib/tcl/tkm_common.tcl
 Reading /home/image/bin/freesurfer/lib/tcl/tkm_wrappers.tcl
 Reading /home/image/bin/freesurfer/lib/tcl/fsgdfPlot.tcl
 Reading /home/image/bin/freesurfer/lib/tcl/tkUtils.tcl
 Successfully parsed tksurfer.tcl
 reading white matter vertex locations...


  Sincerely,



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2009-04-02 Thread Pedro Paulo de Magalhães Oliveira Junior 
It seems that you are using running this Centos inside a VMWare.
TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in
current vmware

---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter  SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br



2009/4/1 Elisa Dell'Oglio dellog...@bwh.harvard.edu

 Attached is the output of dmesg. I am not very familiar with evaluating the
 output of glxgear. Here is a sample of the frames per second that is
 printing:

 7920 frames in 5.0 seconds = 1569.891 FPS
 8280 frames in 5.0 seconds = 1654.312 FPS
 7920 frames in 5.0 seconds = 1576.902 FPS
 8520 frames in 5.0 seconds = 1688.239 FPS
 9000 frames in 5.0 seconds = 1789.300 FPS
 8520 frames in 5.1 seconds = 1683.927 FPS
 8359 frames in 5.1 seconds = 1650.856 FPS
 8280 frames in 5.0 seconds = 1653.440 FPS
 8280 frames in 5.0 seconds = 1643.529 FPS
 8040 frames in 5.0 seconds = 1599.484 FPS
 9227 frames in 5.1 seconds = 1825.203 FPS
 8760 frames in 5.1 seconds = 1732.738 FPS
 8160 frames in 5.0 seconds = 1630.169 FPS
 8400 frames in 5.0 seconds = 1677.716 FPS
 8520 frames in 5.0 seconds = 1701.086 FPS
 8021 frames in 5.1 seconds = 1587.792 FPS

 thanks,

 Elisa


 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 Try running glxgears

 Can you post the output of *dmesg *command



 2009/4/1 Elisa Dell'Oglio dellog...@bwh.harvard.edu

 Thanks you. I actually tried this already (I saw this solution was
 suggested to users that experienced the same problem). Unfortunately this is
 not working, I still get the error message:
 surfer: ### redraw failed: no gl window open

 Is there anything else that you would suggest to try?

 Thank you in advance,
 Elisa

 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 If you are using tcsh

 setenv doublebufferflag 1

 in bash

 export doublebufferflag=1

 ---
 Pedro Paulo de M. Oliveira Junior
 Diretor de Operações
 Netfilter  SpeedComm Telecom
 --- Novo Netfilter 3.0 www.netfilter.com.br



 On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio 
 dellog...@bwh.harvard.edu wrote:

 Hi all,

 I am running freesurfer on CentOS (5.2-x86_64). I get the folowing
 error when I launch tksurfer:
 surfer: ### redraw failed: no gl window open.
 The result is that no surface is shown.

 Any advice on how to solve the problem?

 Thanks,
 Elisa



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





 --
 Elisa Dell'Oglio, MS
 Research Associate to Dr. Bakshi
 Brigham  Women's Hospital, Harvard Medical School
 Laboratory for Neuroimaging Research
 One Brookline Place, Suite 602
 Brookline, MA 02445, USA
 Tel: 617-732-6977
 Fax: 617-732-6540
 Email: dellog...@bwh.harvard.edu





 --
 Elisa Dell'Oglio, MS
 Research Associate to Dr. Bakshi
 Brigham  Women's Hospital, Harvard Medical School
 Laboratory for Neuroimaging Research
 One Brookline Place, Suite 602
 Brookline, MA 02445, USA
 Tel: 617-732-6977
 Fax: 617-732-6540
 Email: dellog...@bwh.harvard.edu

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2009-04-02 Thread Nick Schmansky 
FYI, Freesurfer running with a VirtualBox on Windows is available in
v4.2.0 (not yet v4.3.0) here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.2.0

Get the file FSVboxVDI_PPJ.rar and read the file README-
FSVboxVDI_PPJ.txt.  

This was created and tested by Pedro Paulo de Magalhães Oliveira and
tested by myself.  Thanks Pedro Paulo for providing this distribution.

Nick


On Wed, 2009-04-01 at 14:33 -0300, Pedro Paulo de Magalhães Oliveira
Junior wrote:
 I suggest you to migrate your virtual machine to
 VirtualBox: http://www.virtualbox.org/
 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer error

2009-04-01 Thread Elisa Dell'Oglio 
Hi all,

I am running freesurfer on CentOS (5.2-x86_64). I get the folowing error
when I launch tksurfer:
surfer: ### redraw failed: no gl window open.
The result is that no surface is shown.

Any advice on how to solve the problem?

Thanks,
Elisa
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2009-04-01 Thread Pedro Paulo de Magalhães Oliveira Junior 
If you are using tcsh

setenv doublebufferflag 1

in bash

export doublebufferflag=1

---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter  SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br



On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio dellog...@bwh.harvard.eduwrote:

 Hi all,

 I am running freesurfer on CentOS (5.2-x86_64). I get the folowing error
 when I launch tksurfer:
 surfer: ### redraw failed: no gl window open.
 The result is that no surface is shown.

 Any advice on how to solve the problem?

 Thanks,
 Elisa



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2009-04-01 Thread Elisa Dell'Oglio 
Thanks you. I actually tried this already (I saw this solution was suggested
to users that experienced the same problem). Unfortunately this is not
working, I still get the error message:
surfer: ### redraw failed: no gl window open

Is there anything else that you would suggest to try?

Thank you in advance,
Elisa

2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 If you are using tcsh

 setenv doublebufferflag 1

 in bash

 export doublebufferflag=1

 ---
 Pedro Paulo de M. Oliveira Junior
 Diretor de Operações
 Netfilter  SpeedComm Telecom
 --- Novo Netfilter 3.0 www.netfilter.com.br



 On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio 
 dellog...@bwh.harvard.eduwrote:

 Hi all,

 I am running freesurfer on CentOS (5.2-x86_64). I get the folowing error
 when I launch tksurfer:
 surfer: ### redraw failed: no gl window open.
 The result is that no surface is shown.

 Any advice on how to solve the problem?

 Thanks,
 Elisa



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





-- 
Elisa Dell'Oglio, MS
Research Associate to Dr. Bakshi
Brigham  Women's Hospital, Harvard Medical School
Laboratory for Neuroimaging Research
One Brookline Place, Suite 602
Brookline, MA 02445, USA
Tel: 617-732-6977
Fax: 617-732-6540
Email: dellog...@bwh.harvard.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2009-04-01 Thread Pedro Paulo de Magalhães Oliveira Junior 
Try running glxgears

Can you post the output of *dmesg *command



2009/4/1 Elisa Dell'Oglio dellog...@bwh.harvard.edu

 Thanks you. I actually tried this already (I saw this solution was
 suggested to users that experienced the same problem). Unfortunately this is
 not working, I still get the error message:
 surfer: ### redraw failed: no gl window open

 Is there anything else that you would suggest to try?

 Thank you in advance,
 Elisa

 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 If you are using tcsh

 setenv doublebufferflag 1

 in bash

 export doublebufferflag=1

 ---
 Pedro Paulo de M. Oliveira Junior
 Diretor de Operações
 Netfilter  SpeedComm Telecom
 --- Novo Netfilter 3.0 www.netfilter.com.br



 On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio dellog...@bwh.harvard.edu
  wrote:

 Hi all,

 I am running freesurfer on CentOS (5.2-x86_64). I get the folowing error
 when I launch tksurfer:
 surfer: ### redraw failed: no gl window open.
 The result is that no surface is shown.

 Any advice on how to solve the problem?

 Thanks,
 Elisa



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





 --
 Elisa Dell'Oglio, MS
 Research Associate to Dr. Bakshi
 Brigham  Women's Hospital, Harvard Medical School
 Laboratory for Neuroimaging Research
 One Brookline Place, Suite 602
 Brookline, MA 02445, USA
 Tel: 617-732-6977
 Fax: 617-732-6540
 Email: dellog...@bwh.harvard.edu

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer error

2009-04-01 Thread Pedro Paulo de Magalhães Oliveira Junior 
I suggest you to migrate your virtual machine to VirtualBox:
http://www.virtualbox.org/
Have you tried setting the autoredraw on in tksurfer interface?
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter  SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br



2009/4/1 Elisa Dell'Oglio dellog...@bwh.harvard.edu

 I am indeed using a VMWare. I should probably check the VirtualBox version?
 Or is there another fix that I could try?
 Would you expect a different FPS (from glxgear)?

 Thank you very much for your time and patience.

 Elisa

 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 It seems that you are using running this Centos inside a VMWare.
 TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in
 current vmware

 ---
 Pedro Paulo de M. Oliveira Junior
 Diretor de Operações
 Netfilter  SpeedComm Telecom
 --- Novo Netfilter 3.0 www.netfilter.com.br



 2009/4/1 Elisa Dell'Oglio dellog...@bwh.harvard.edu

 Attached is the output of dmesg. I am not very familiar with evaluating
 the output of glxgear. Here is a sample of the frames per second that is
 printing:

 7920 frames in 5.0 seconds = 1569.891 FPS
 8280 frames in 5.0 seconds = 1654.312 FPS
 7920 frames in 5.0 seconds = 1576.902 FPS
 8520 frames in 5.0 seconds = 1688.239 FPS
 9000 frames in 5.0 seconds = 1789.300 FPS
 8520 frames in 5.1 seconds = 1683.927 FPS
 8359 frames in 5.1 seconds = 1650.856 FPS
 8280 frames in 5.0 seconds = 1653.440 FPS
 8280 frames in 5.0 seconds = 1643.529 FPS
 8040 frames in 5.0 seconds = 1599.484 FPS
 9227 frames in 5.1 seconds = 1825.203 FPS
 8760 frames in 5.1 seconds = 1732.738 FPS
 8160 frames in 5.0 seconds = 1630.169 FPS
 8400 frames in 5.0 seconds = 1677.716 FPS
 8520 frames in 5.0 seconds = 1701.086 FPS
 8021 frames in 5.1 seconds = 1587.792 FPS

 thanks,

 Elisa


 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 Try running glxgears

 Can you post the output of *dmesg *command



 2009/4/1 Elisa Dell'Oglio dellog...@bwh.harvard.edu

 Thanks you. I actually tried this already (I saw this solution was
 suggested to users that experienced the same problem). Unfortunately this 
 is
 not working, I still get the error message:
 surfer: ### redraw failed: no gl window open

 Is there anything else that you would suggest to try?

 Thank you in advance,
 Elisa

 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior 
 p...@netfilter.com.br

 If you are using tcsh

 setenv doublebufferflag 1

 in bash

 export doublebufferflag=1

 ---
 Pedro Paulo de M. Oliveira Junior
 Diretor de Operações
 Netfilter  SpeedComm Telecom
 --- Novo Netfilter 3.0 www.netfilter.com.br



 On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio 
 dellog...@bwh.harvard.edu wrote:

 Hi all,

 I am running freesurfer on CentOS (5.2-x86_64). I get the folowing
 error when I launch tksurfer:
 surfer: ### redraw failed: no gl window open.
 The result is that no surface is shown.

 Any advice on how to solve the problem?

 Thanks,
 Elisa



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





 --
 Elisa Dell'Oglio, MS
 Research Associate to Dr. Bakshi
 Brigham  Women's Hospital, Harvard Medical School
 Laboratory for Neuroimaging Research
 One Brookline Place, Suite 602
 Brookline, MA 02445, USA
 Tel: 617-732-6977
 Fax: 617-732-6540
 Email: dellog...@bwh.harvard.edu





 --
 Elisa Dell'Oglio, MS
 Research Associate to Dr. Bakshi
 Brigham  Women's Hospital, Harvard Medical School
 Laboratory for Neuroimaging Research
 One Brookline Place, Suite 602
 Brookline, MA 02445, USA
 Tel: 617-732-6977
 Fax: 617-732-6540
 Email: dellog...@bwh.harvard.edu





 --
 Elisa Dell'Oglio, MS
 Research Associate to Dr. Bakshi
 Brigham  Women's Hospital, Harvard Medical School
 Laboratory for Neuroimaging Research
 One Brookline Place, Suite 602
 Brookline, MA 02445, USA
 Tel: 617-732-6977
 Fax: 617-732-6540
 Email: dellog...@bwh.harvard.edu

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Tksurfer Error

2005-02-24 Thread Kevin Teich 
tksurfer: error while loading shared libraries: libglut.so.3: cannot
open shared object file: No such file or directory.
Do you have glut installed? If you are running a Red Hat box, you can 
check by:

$ rpm -qa | grep glut
Or just looking for libglut* in /usr/lib or /usr/local/lib.
--
Kevin Teich
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer