Re: [Freesurfer] Freeview ERROR: label name '3rd-Ventricle' is duplicated (FSv6.0.0 with updated Freeview)

[Wang, Ruopeng]

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Have you tried the latest Mac build of freeview? This has been fixed recently.

On Jul 30, 2023, at 11:02 AM, Ha Manh Luu 
mailto:hal4...@med.cornell.edu>> wrote:


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From: Ha Manh Luu
Sent: Thursday, July 20, 2023 10:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freeview ERROR: label name '3rd-Ventricle' is duplicated

Hello FreeSurfer Developers,

This is a follow up email.

I have installed FreeSurfer v6.0.0 in my MacOS 12.6.7 but I got Freeview 
crashed due to PETSC error (which has been fixed in FreeSurfer v7.1.1).

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/12bN_GdNSv2Ik7XN85oA3_ALo3usTg2uRRXhq5huLnfPJALe1wLKA90W0nYTXQzBkMMMwXkhalWdkNKtttdZX4VO3IoecjP2n6ZQWnSsBJ-6pm3IHgDJfJYL58MYAFgT3LsHo-h56WBWKPtYjLnw_wekGT0Qv4-jLor4uRE63YStSaxcmR3FtakpVstY5GyYhdTdzuH7uP9hKMgcognzvGVhOIRxWlcyOAAAhnqWsSZbJukpw8dUY4rsYc0VYbiGqQyZwhV2ayV7SEmRzn5BQ_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel6downloads

For the consistency with my previous work, I do not want to upgrade to 
Freesurfer V7.x in my MAC.

I updated freeview from this website:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1R1MsBHl0X1wmxG2J-0IPMwdJZBuAorLiw5witdVKJsjxWOZiITWTedjvVSJZKn77jLGiK-KnLbqBu-HZty6oFViZgp3LXnDX123uG1tZV3BcVMfkdh7_uzrjaV1xre6RQ6UXMd7nNbS7A_ObSs5vG13dWPOvfBA6XiZaJQoIjqLPOCMwVxM6iV24-fmDg4BXkuv32160p54tWtG4O08qgz7apm7Xj4zxBXINk-NpVE8iI_cqKLvZmMJPOgwL1ER5Xj__AIbu4RPSypij-LBwHw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview

After updating the Freeview, it works for me but it still shows the following 
error:
ERROR: label name '3rd-Ventricle' is duplicated! ERROR: label name 
'3rd-Ventricle' is duplicated! CTABfindDuplicateNames: 1 duplicate names found 
in: 
/private/var/folders/4w/c9v2n39j3hd_4rb1bmyrftqwgt/T/FreeSurferColorLUT.txt

I cat the file and see that '3rd-Ventricle' has 2 lablels in the file. I also 
see that the FreeSurferColorLUT.txt file is not identical to the 
FreeSurferColorLUT.txt in FreeSurfer home folder.

Can you tell me what is the file FreeSurferColorLUT.txt for and the issue is 
serious or not? If so, how to fix this?

  1.  Freesurfer version:  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0

2)  Platform: MacOS Darwin 12.6.7

  1.  freeview:  ERROR: label name '3rd-Ventricle' is duplicated! ERROR: label 
name '3rd-Ventricle' is duplicated! CTABfindDuplicateNames: 1 duplicate names 
found in: 
/private/var/folders/4w/c9v2n39j3hd_4rb1bmyrftqwgt/T/FreeSurferColorLUT.txt
  2.  FreeSurferColorLUT.txt: see attached

Thanks,

Ha
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Re: [Freesurfer] freeview error....

[fsbuild]

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Hello Gonzalo,
If you have not already done so, then I suggest installing the .deb 
installer package for 7.3.2 from,
surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer_ubuntu18-7.3.2_amd64.deb
- by cd’ing to where you downloaded the above file to on your machine and then 
running,
$ sudo apt install ./freesurfer_ubuntu18-7.3.2_amd64.deb
Then test the environment with,
$ export FREESURFER_HOME=/usr/local/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
$ which freeview$/usr/local/freesurfer/7.3.2/bin/freeview
… check freeview comes up with an empty window …
$ freeview
… then quit and try viewing an example volume …
$ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz
- R.

On Jul 27, 2023, at 10:15, Gonzalo Rojas Costa 
gonzalo.rojas.co...@gmail.com 
wrote:External Email - Use 
CautionHi: I have Ubuntu 
18.04.4 LTS and freesurfer release 
freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. When I run freeview, I 
got the error:"This application failed to start because no Qt platform plugin 
could be initialized. Reinstalling the application may fix this 
problem.Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, 
offscreen, vnc, wayland-egl, wayland, webgl, xcb." How can I correct 
it? Sincerely,Gonzalo Rojas 
Costa___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] freeview error....

[Gonzalo Rojas Costa]

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Hi:

  I have Ubuntu 18.04.4 LTS and freesurfer release
freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. When I run
freeview, I got the error:

"This application failed to start because no Qt platform plugin could be
initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl,
offscreen, vnc, wayland-egl, wayland, webgl, xcb."

  How can I correct it?

  Sincerely,


Gonzalo Rojas Costa
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Re: [Freesurfer] Freeview error

[Huang, Yujing]

Hi,

It shows that T1.mgz is empty.

How did you run recon-all? Can you do ‘ls -l /Users/results/sub-101/mri/’? Can 
you send recon-all.log in attachment? Does it work for your other subjects?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of tsengyuheng1...@gmail.com
Sent: Wednesday, March 15, 2023 8:31 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview error


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Hi Yujing,

It shows “-rw-rw-r--  1 username staff  0 Mar 15 09:44 T1.mgz” and “error: 
mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error”.

Best,

Y. Z.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 15, 2023 at 20:17
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview error
Hi,

Can you check if the path is correct?  What does ‘ls -l 
/Users/results/sub-101/mri/T1.mgz’ show?

If you do ‘mri_info /Users/results/sub-101/mri/T1.mgz’, does it report anything?

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of tsengyuheng1...@gmail.com<mailto:tsengyuheng1...@gmail.com>
Sent: Tuesday, March 14, 2023 11:05 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freeview error


External Email - Use Caution
Hi,

I met some errors when showing recon -all results in Freeview. I could not open 
the brainmask.mgz or the T1.mgz via the terminal or Freeview GUI. But they 
worked well with MRIcron. Could you please give me some advice on it?

The errors:
error: mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error
MRIread failed: Unable to read from /Users/results/sub-101/mri/T1.mgz

Thank you for the help!

Best,

Y. Z.
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Re: [Freesurfer] Freeview error

[tsengyuheng1...@gmail.com]

External Email - Use CautionHi Yujing, It shows “-rw-rw-r--  1 username staff  0 Mar 15 09:44 T1.mgz” and “error: mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error”. Best, Y. Z.  From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Huang, Yujing Date: Wednesday, March 15, 2023 at 20:17To: Freesurfer support list Subject: Re: [Freesurfer] Freeview errorHi, Can you check if the path is correct?  What does ‘ls -l /Users/results/sub-101/mri/T1.mgz’ show? If you do ‘mri_info /Users/results/sub-101/mri/T1.mgz’, does it report anything? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu  On Behalf Of tsengyuheng1...@gmail.comSent: Tuesday, March 14, 2023 11:05 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] Freeview error External Email - Use CautionHi, I met some errors when showing recon -all results in Freeview. I could not open the brainmask.mgz or the T1.mgz via the terminal or Freeview GUI. But they worked well with MRIcron. Could you please give me some advice on it? The errors:error: mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /Users/results/sub-101/mri/T1.mgz Thank you for the help! Best, Y. Z.
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Re: [Freesurfer] Freeview error

[Huang, Yujing]

Hi,

Can you check if the path is correct?  What does ‘ls -l 
/Users/results/sub-101/mri/T1.mgz’ show?

If you do ‘mri_info /Users/results/sub-101/mri/T1.mgz’, does it report anything?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of tsengyuheng1...@gmail.com
Sent: Tuesday, March 14, 2023 11:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freeview error


External Email - Use Caution
Hi,

I met some errors when showing recon -all results in Freeview. I could not open 
the brainmask.mgz or the T1.mgz via the terminal or Freeview GUI. But they 
worked well with MRIcron. Could you please give me some advice on it?

The errors:
error: mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error
MRIread failed: Unable to read from /Users/results/sub-101/mri/T1.mgz

Thank you for the help!

Best,

Y. Z.
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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 
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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] Freeview error

[tsengyuheng1...@gmail.com]

External Email - Use CautionHi, I met some errors when showing recon -all results in Freeview. I could not open the brainmask.mgz or the T1.mgz via the terminal or Freeview GUI. But they worked well with MRIcron. Could you please give me some advice on it? The errors:error: mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /Users/results/sub-101/mri/T1.mgz Thank you for the help! Best, Y. Z.
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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 
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Re: [Freesurfer] Freeview error

[Kumar, Avnish]

Hi,

This error suggests that your cluster instance is not able to find the swrast 
drivers:
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
swrast is a software renderer. It is provided by libgl1-mesa-dri library. If 
the library is not installed, you can install it - though the exact 
installation steps would depend on your OS. I'd advice to contact the 
maintainers of your compute cluster for this error.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Estephan Moana Filho 

Sent: Friday, March 10, 2023 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freeview error


External Email - Use Caution

Hi, I'm trying to open freeview in a linux node in my institution's computing 
cluster and an error is coming up consistently - see below. Can you please 
advise? Thank you.

agc01:~ moana004$ module list
No Modulefiles Currently Loaded.
agc01:~ moana004$ module load freesurfer/6.0.0
agc01:~ moana004$ 
study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \
> subjID_list="20005 10015 11012"; \
> for subjID in ${subjID_list}; do freeview 
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/brainmask.gcuts.mgz:colormap=heat
>  
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/T1.mgz:opacity=0.5;
>  done
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC<http://secure-web.cisco.com/1xBVMH7lnCEhUq9J5hsq5IuQWk3qEq0TYSuhzQe5BEwAIcoo_Ph2jMDpJW_bezKEUUHzz2fK7dDhSW-8id6Oueij27SJdAkDwBYIzlcFoGyiueE_dDjwDmC8QsYLEzRzKJaqJbvS-bSde41-Qb-iRAR4E_QYNC7Vr4rQztWhIKfMAMsp0fVxhLNiJAJcy2CLdAamFubSkH5DzggwUbrtTL-dR9xM5y1GVB9dYuSejFn4Tc7Kd4uAaso_mjMivlvhIymCnKQD1ZK-RPcczxUc8pjQaIItJqR6ivhNv_2RnyAaoBL8wqxRydIJ-5dSy6q3y/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal%5B0%5DPETSC>
 ERROR: or try MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://valgrind.org<http://secure-web.cisco.com/1koEldMN_Nux-AKyw6PB_HunrQTVcL6gNek0fymq4gNBgw_YlwUMFxL-HyUhOj8Y1H1Q1fZOnwvnWg9pYU3FNe6PP_Br-JPQM-PbaDqHdx7n2uMOFpFQhbtXbQwdTqXM6F_Y-_S5b79yCDLf4wpTVf26VqQwJgd7wwahUBtPXI_IJo7FdAqAbKynBkix5oLK_DYGI67GqYJC3PmALEekgeRYfuXueJqL_VbtuS15bXwKoDCjgKmLRhXqWp5fb6mVozKd5pXpXH4X_ZN9DWSal7bTva3ln5LI01McljU-CpxN-JqrVPmilgUFw1oFiHM1p/http%3A%2F%2Fvalgrind.org%2F>
 on linux or man libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri Mar 10 
11:22:48 2023
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugge

[Freesurfer] Freeview error

[Estephan Moana Filho]

External Email - Use Caution

Hi, I'm trying to open freeview in a linux node in my institution's
computing cluster and an error is coming up consistently - see below. Can
you please advise? Thank you.

agc01:~ moana004$ module list
> No Modulefiles Currently Loaded.
> agc01:~ moana004$ module load freesurfer/6.0.0
> agc01:~ moana004$
> study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \
> > subjID_list="20005 10015 11012"; \
> > for subjID in ${subjID_list}; do freeview
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/brainmask.gcuts.mgz:colormap=heat
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/T1.mgz:opacity=0.5;
> done
> libGL error: unable to load driver: swrast_dri.so
> libGL error: failed to load driver: swrast
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXbinUuAdIwcI0iRqe6KosyMKzWJq_kkReHZMfQMDhUHX3sHlUgUCEkU4XEOVVn-u2KtOf9LJ4sVNsGrNoauhQO_onuf_mvcuPTFxx8o39H4zCrl3lYXguL-r0BVaoORQIfA7PHqlLGpQ6qwCRVzlLs7A8q_mmDyyBbnpSu-VuQ5AtLTNeBRL5wKhCcIzIM4cSYpsztm9q1QVbHUuobd8L4mlLPi8jdsfTbOr0AiELvxbRPWPA_17c3xezx4gOAo7leN4se5Lw_dJq88bFxbg/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal[0]PETSC
>  ERROR:
> or try 
> http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwPz-rO-J1FzW6RPFhzjZ_DXULTjfDx7Tl3HkIFUWssfo_12FO0ZDaoyOkaJJ9NA3KDFT-WUV0Vs02nlPzcZsSaxemALkmavfAuE5-faK5-MEB5BmObdCUTf9A-8aEVtc3hW_Pd4BapjsUgSwXmzP5SIr4EIvObSju9mketw_eQ6rgURbuk78DM5GPWoKe1RErdc8mN8OMlJQXHLLfcPHZppsgwx7JIiD6kyDjxXzidtVNKt5K8snPYU12Id4NiL_KDUUCsAAtaunRZcJC9Lv/http%3A%2F%2Fvalgrind.org
>  on linux or man libgmalloc on Apple to find
> memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri
> Mar 10 11:22:48 2023
> [0]PETSC ERROR: Libraries linked from
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> libGL error: unable to load driver: swrast_dri.so
> libGL error: failed to load driver: swrast
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXbinUuAdIwcI0iRqe6KosyMKzWJq_kkReHZMfQMDhUHX3sHlUgUCEkU4XEOVVn-u2KtOf9LJ4sVNsGrNoauhQO_onuf_mvcuPTFxx8o39H4zCrl3lYXguL-r0BVaoORQIfA7PHqlLGpQ6qwCRVzlLs7A8q_mmDyyBbnpSu-VuQ5AtLTNeBRL5wKhCcIzIM4cSYpsztm9q1QVbHUuobd8L4mlLPi8jdsfTbOr0AiELvxbRPWPA_17c3xezx4gOAo7leN4se5Lw_dJq88bFxbg/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal[0]PETSC
>  ERROR:
> or try 
> http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwPz-rO-J1FzW6RPFhzjZ_DXULTjfDx7Tl3HkIFUWssfo_12FO0ZDaoyOkaJJ9NA3KDFT-WUV0Vs02nlPzcZsSaxemALkmavfAuE5-faK5-MEB5BmObdCUTf9A-8aEVtc3hW_Pd4BapjsUgSwXmzP5SIr4EIvObSju9mketw_eQ6rgURbuk78DM5GPWoKe1RErdc8mN8OMlJQXHLLfcPHZppsgwx7JIiD6kyDjxXzidtVNKt5K8snPYU12Id4NiL_KDUUCsAAtaunRZcJC9Lv/http%3A%2F%2Fvalgrind.org
>  on linux or man libgmalloc on Apple to find
> memory corruption errors
> 

Re: [Freesurfer] Freeview error on centos7

[Wang, Ruopeng]

Would it be possible to send us the volume and the surface files so that we can 
try to replicate the issue?

Thanks,
Ruopeng

On Mar 14, 2022, at 12:01 PM, Wen Wen 
mailto:wenw2...@gmail.com>> wrote:


External Email - Use Caution

Dear Freesurfer experts,
I’m running Freeview on a centos7 computer and having the issue of loading 
surface data and 1mm volume data. The error message is Segmentation fault (core 
dumped). This issue remains no matter I work locally or remotely. However, 2mm 
volume data can be visualized successfully in either way.

I've tried running glxgears, which gave me a pop-up window showing 3 
interlocking wheels (red/green/blue).
Below is the graphic card information obtained from lspci | grep VGA if helps.
01:00.0 VGA compatible controller: NVIDIA Corporation GP102GL [Quadro P6000] 
(rev a1)
42:00.0 VGA compatible controller: ASPEED Technology, Inc. ASPEED Graphics 
Family (rev 41)

Thanks in advance for your help.

Best,
Wen
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___
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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] Freeview error on centos7

[Wen Wen]

External Email - Use Caution

Dear Freesurfer experts,

I’m running Freeview on a centos7 computer and having the issue of loading
surface data and 1mm volume data. The error message is *Segmentation fault
(core dumped).* This issue remains no matter I work locally or remotely.
However, 2mm volume data can be visualized successfully in either way.


I've tried running glxgears, which gave me a pop-up window showing 3
interlocking wheels (red/green/blue).

Below is the graphic card information obtained from lspci | grep VGA if
helps.

01:00.0 VGA compatible controller: NVIDIA Corporation GP102GL [Quadro
P6000] (rev a1)

42:00.0 VGA compatible controller: ASPEED Technology, Inc. ASPEED Graphics
Family (rev 41)


Thanks in advance for your help.


Best,

Wen
___
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] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

[fsbuild]

External Email - Use Caution

In your terminal window after you’ve sourced the freesurfer setup script you 
should be able to do,$ which freeview
… and it will show something like …
/usr/local/freesurfer/bin/freeview
So using whatever that absolute path is to freeview on your system, then do,
$ ldd /usr/local/freesurfer/bin/freeview | grep not
If you see output that says a library was not found, then something is not 
right with your system - which could explain the segfault. In that case I 
would try to find a way to download and install the freesurfer 7.2.0 Debian 
package installer as that should install any missing 
libraries.https://secure-web.cisco.com/17qbBdi-wXIfcvgJHoFSyqwZNNfccEzYQiqaLM3KKP1GfRbI3U94aISVOv9a0YGhQd-FCtmmbw7EmGlkXloHQKHGR5kQ0Ohxp0JGux2qcz8j5Rt8B1ctRfTvIV0UnaEl1nURjUsgCYtjC_sdG7KQX4ngvB3LSoCGEbOfNmi6oSxEaLWw_txh_79zUoOTNlVLgJDc-Aiw0gVqTJZNFknHkH8hauq6pkHSeBkQOXmK_JglhjC6WkKJ7lxYocce_WbdghbeaKkfQAYCYs_29qmOAYZN6dGIMzsWXk3nEcX4_2o-8BIcJbPHPV8yjzL-ug7MmedUYalixU7ncC7ps_gf7gA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz
If no libraries are reported as missing for freeview, then if you have not 
already tried the variations on setting DISPLAY listed at the end of this page, 
then I would do so, 
https://secure-web.cisco.com/1ZTeXQ90uTtWNjlyitGyKt3hbJVwUsSL_sYysu7DQgUWeVYEJ3df0g2306v_BSgfcZcf-O-h84P8FI1bM8w6NvXdRDfn8OmNn3Bd2V_G3xAgU6xj4cUCTfEb713wXDGFlgtPBlmY8DpBUgV5sW4LgTOtwmG4nrBFDvr7sTDlSADHJxgc65FfWf__QvgO9AXBeGjue8kk34zd9MWvvU4rcxgnyVLxMPmKN4iPYD0FXifn62v010k6baCbhiM-My8JXv-HZT-AtXOYDaZqqe6lpOJxP5BDg8rXv8rApcm1Xiy-kKg73gkr8CeS_jMpXPsNPuk9XGaMpHUUQWsSXV1Cbnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
  You may have to use your IP address and append :0 or :1 to it.
If that does not work, then send back your default setting for DISPLAY and I 
will check with other people who use the WSL setup.
- R.

On Nov 17, 2021, at 21:02, 许霄 xux...@xii.ac.cn 
wrote:External Email - Use 
CautionI downloaded a license 
file, and copied the content in it to a new filecreated in $HOME path, 
named the new file 'license.txt'. After that,reset the environment 
variables:$echo "export XDG_RUNTIME_DIR=$HOME/.xdg"  
$HOME/.bashrc$echo "export DISPLAY=:0"  $HOME/.bashrc$echo 
"export FREESURFER_HOME=/usr/local/freesurfer/7-dev"  
$HOME/.bashrc$echo "export FS_LICENSE=$HOME/license.txt"  
$HOME/.bashrc$echo "source 
/usr/local/freesurfer/7-dev/SetUpFreeSurfer.sh"  
$HOME/.bashrcMeanwhile, to test if Xming was running, I executed xeyes, and it 
worked. But the same error "Segmentation fault (core dumped)" still appeared. I 
found that there was no .xdg file under $HOME path,mentioned in the 
command"export XDG_RUNTIME_DIR=$HOME/.xdg"  $HOME/.bashrc". Please see 
the details in the attachment. What should I do to fix 
it?BestXiao-原始邮件-发件人:fsbuild 
fsbu...@contbay.com发送时间:2021-11-18 03:05:29 
(星期四)收件人:freesurfer@nmr.mgh.harvard.edu抄送:xux...@xii.ac.cn主题:Re:
 [Freesurfer] freeview error after installation: Segmentation fault(core 
dumped) / free( ): invalid pointer, Aborted(core 
dumped)External Email - Use 
CautionHello, Xuxiao,You need 
to go to this URL,MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1-AZrSjO8Cl_Hc1uoojvBIGTFics6sBFWG99iZ-P1u3LukFGKniPlUm-E-VGjcRE_b-5E-iOvjqEZNnuGOgCw2Pkg1-eC-UxfUhNvM4PC4oeD-yGP31_5V7cBwdiywW09KhcDihFjOvJSLlMoqKyKIkSMftWf7jNXb3CzOUgWTiSKzJ6V7cP5ooLjf7jC6_Z2fma3-7ssLtdEbEYZL3t9_hHSX43mODgn8iO_TikKgwbVAJLuq6_dxHjhTZd2oIhm1adZDW1MzIDHvFsP_f9Gx49oAoTHPuuFB7gACzq83ISkU93lG2zQlUZjeTqIoCu3Y65c2oY5Pd95FlbeLROCOg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html,
 fill out the form and agree to the terms of the freesurfer license. Then 
you will be able to download a license file.- R.On Nov 17, 2021, at 06:10, 许霄 
xux...@xii.ac.cn 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,According to your reply, I found thatxeyes worked, but 
there wasno license file. I thought the license file would be 
createdautomatically after installation of freesurfer, or by the command 
"echo "export FS_LICENSE=$HOME/license.txt"  $HOME/.bashrc". Do I need 
to create a license file manually?-原始邮件-发件人:fsbuild 
fsbu...@contbay.com发送时间:2021-11-17 10:16:00 
(星期三)收件人:freesurfer@nmr.mgh.harvard.edu抄送:xux...@xii.ac.cn主题:Re:
 [Freesurfer] freeview error after installation: Segmentation fault(core 
dumped) / free( ): invalid pointer, Aborted(core 
dumped)External Email - Use 
CautionHello Xuxiao,In a 
terminal window in Ubuntu running under WSL, please try just running a simple X 
windows program like xeyes to test that your X-server is running on 
Windows,$ xeyes(see attachment for what it should look like)Keep an eye 
out for a flashing X server icon at the bottom of your Window

Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

[fsbuild]

External Email - Use Caution

Hello, Xuxiao,
You need to go to this 
URL,https://secure-web.cisco.com/1crNBAUgLZ3m6E0Fhbayk9W3IGxcTGzIN3PT2acc3MXecoz7EIfOO6Q0hNAXwrCNyIC3FTtDN9X9CrdO3H-snKR37T_1NLT0l_EraP2yjzm3K90Y7hGw16I7LpL23Pek7c9uSh4mCvpdPrEH8nSRGa7grnWixIg5S5DMwL01cI6OGfrzy1ymB8qiPj56dCQcC-Wn1lSUnhqx2wsO0I_aplt9EYRsWohmJ42NGrsULJ6LR49MgGcO7D-V4btHSc8eXpER7BlNegXZjO1OuHyCAdqvL4Em7Ie56gTnAgzigvQr4IiviXDFdMe2pyAOI6I3C/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html,
 fill out the form and agree to the terms of the freesurfer license. Then 
you will be able to download a license file.
- R.

On Nov 17, 2021, at 06:10, 许霄 xux...@xii.ac.cn 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,According to your reply, I found thatxeyes worked, but 
there wasno license file. I thought the license file would be 
createdautomatically after installation of freesurfer, or by the command 
"echo "export FS_LICENSE=$HOME/license.txt"  $HOME/.bashrc". Do I need 
to create a license file manually?-原始邮件-发件人:fsbuild 
fsbu...@contbay.com发送时间:2021-11-17 10:16:00 
(星期三)收件人:freesurfer@nmr.mgh.harvard.edu抄送:xux...@xii.ac.cn主题:Re:
 [Freesurfer] freeview error after installation: Segmentation fault(core 
dumped) / free( ): invalid pointer, Aborted(core 
dumped)External Email - Use 
CautionHello Xuxiao,In a 
terminal window in Ubuntu running under WSL, please try just running a simple X 
windows program like xeyes to test that your X-server is running on 
Windows,$ xeyes(see attachment for what it should look like)Keep an eye 
out for a flashing X server icon at the bottom of your Windows desktop. 
You may have to click on that flashing icon for the xeyes X window to 
open. But if you can’t display something simple like xeyes with the X 
server on Windows 10, then freeview is not going to work.If you installed the 
Xming X-server on Windows, then you should see an X icon on your desktop that 
you can click on to start the X-server. And you can check you see the X 
icon in the “hidden” area at the bottom of the screen which shows the X server 
is running on Windows. See the bottom of this page for how to see Xming 
is running and then scroll up to see the X windows desktop 
icon,MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1H_CTeKTz6NdVgYALgwJR96KSB3QipiR_myHy5jIueygSel_x4GLb9Zq9vHPghJWsr7MoV1X-_is5sXf16kw02qUpMNnUKv8U5w73pYtcYl56NWQplhjLta26EhSBCliv8k9CVJu8DRtzSLjUnFTXzN1mt3-4fRCLOjMR8cXvgqgX10p0y3TxJ4zh3Eqjz1lbG5j1qWKKOeP3TXvY0O5xkcYWYDsldlNnG1588yU1DlZ5KCuIjZF9Ei9ckhf_qCC5hqOAIIqghJsWrziMAZeJ-LFE-O9BmzK3ksGsAmzVmXLOR2LfaZ9DGr-jnfMz618U/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xmingIf
 xeyes works, then check your freesurfer license file can be found. One 
way to do that is to set the environment variable FS_LICENSE to the absolute 
path to your license file. So you could for example call your license 
file “license.txt” and copy it into your home directory (denoted by the 
environment variable $HOME). You can also set FS_LICENSE in your shell 
init file.$ cd $HOME$ pwdoutput deleted$ ls license.txtlicense.txt$ 
export FS_LICENSE=$HOME/license.txt… check it can be read …$ cat 
$FS_LICENSEoutput deletedNow set FREESURFER_HOME, source the setup 
environment script as you did in the screenshot you sent below, and try running 
freeview with no arguments to see if a blank window opens.$ freeviewAnother 
thing to consider is to try and install the latest version of freesurfer 
(7.2.0) using the Ubuntu .deb package installer from 
https://secure-web.cisco.com/1ZL6MYJBHRf57DH2b32bhIZVsh9Do26VHKbPCwa6qZJKfjdsp_-OgjUDQZxzE1ROYseLI1evFFchaClql8VymfC7TLCW0G0VtPSzT6PbzO_UEtdKlmyyEIgmiSt1FpWxs-wP8sYoYEI4zWOhAC43OIZxmsmxjIlqOyLpwLw7JMlStTNjgxj1brei8JQlakSpgxcegE2gtDdIFJy1Qejybjmcff_g9tlU0j73sqgjKyRK10YivyH7TMMCbXfs9sxgW-etgcm9IdqlRlyxR2HvE3ATu0ZH-Dcqf0nQGpriBsEnIVHxuBqIkLGRdFZ2_U1Z0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer_7.2.0_amd64.deb
 and install it with,$ sudo apt-get install ./freesurfer_7.2.0_amd64.debThen 
you should see 7.2.0 installed as something like /usr/local/freesurfer/7.2.0 
which you would use for FREESURFER_HOME- R.On Nov 16, 2021, at 07:26, 许霄 
xux...@xii.ac.cn 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I can't access the website of archives, so I have to ask questions 
in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the 
tutorialsFS7_wsl - Free Surfer Wiki 
(harvard.edu)andFS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu).. 
After adding the license, when I tried to run the 'freeview' command to test if 
everything works well, an error popped out: Segmentation fault(core dumped). 
more information about my freesurfer environment is shown as attached. Could 
anyone help me figure it out? Thanks in

Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

[许霄]

External Email - Use Caution

Hello FreeSurfer Developers, According to your reply, I found that xeyes 
worked, but there was no license file. I thought the license file would be 
created automatically after installation of freesurfer, or by the command "echo 
"export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc". Do I need to create a 
license file manually?


-原始邮件-
发件人:fsbuild 
发送时间:2021-11-17 10:16:00 (星期三)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送: xux...@xii.ac.cn
主题: Re: [Freesurfer] freeview error after installation: Segmentation fault(core 
dumped) / free( ): invalid pointer, Aborted(core dumped)



External Email - Use Caution




Hello Xuxiao,



In a terminal window in Ubuntu running under WSL, please try just running a 
simple X windows program like xeyes to test that your X-server is running on 
Windows, 


$ xeyes


(see attachment for what it should look like)



Keep an eye out for a flashing X server icon at the bottom of your Windows 
desktop.  You may have to click on that flashing icon for the xeyes X window to 
open.  But if you can’t display something simple like xeyes with the X server 
on Windows 10, then freeview is not going to work.


If you installed the Xming X-server on Windows, then you should see an X icon 
on your desktop that you can click on to start the X-server.  And you can check 
you see the X icon in the “hidden” area at the bottom of the screen which shows 
the X server is running on Windows.  See the bottom of this page for how to see 
Xming is running and then scroll up to see the X windows desktop icon, 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1ysFQMH5-3PjGsAtjRCyqR6tLEu576gjQo1Oa6S4YqfU8M46EFmftbnJSYl-FgENkNOcglwUy2Xl9QGw3VvItHf1he2SjG05OXmjKAFLxfAnISkt8daucJVpXy-As3Rc0D2D8Va9jiKZUk6Psp1pVAMfS7i2J58rC__U6sE3YyBjuF3BOq6p3CDxJnRa5_bNvA6sV681TFEzjLrpin9jEBf7vFH2x6C5lDqoy7HwHet9kh_iDPQR8JHOZJ7Ar9yQqEmu99IkGov2WCOD4Sc7TMg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming


If xeyes works, then check your freesurfer license file can be found.  One way 
to do that is to set the environment variable FS_LICENSE to the absolute path 
to your license file.  So you could for example call your license file 
“license.txt” and copy it into your home directory (denoted by the environment 
variable $HOME).  You can also set FS_LICENSE in your shell init file.


$ cd $HOME
$ pwd


$ ls license.txt
license.txt
$ export FS_LICENSE=$HOME/license.txt


… check it can be read …


$ cat $FS_LICENSE



Now set FREESURFER_HOME, source the setup environment script as you did in the 
screenshot you sent below, and try running freeview with no arguments to see if 
a blank window opens.


$ freeview


Another thing to consider is to try and install the latest version of 
freesurfer (7.2.0) using the Ubuntu .deb package installer from 
https://secure-web.cisco.com/1vUB0SIgaD7Aa_vdzXHRIqptu1j91bTzpsQFynE-rpn8jtlbmWFgPyISNROG_qJ8dem80ftsxmCbMcDaNYkkwofPBMCsSJoFU_GgAlR5Wm4_8Tu0vSB2o9INcRCiPcoTfpjL2PaEG74OFXyxtMuznKOve4ZXqDmFZxJRYoBAiIzcQUxvahij6rnuzc6bFte271nbgV21-o4BGFQQbgXjZQvJxTrnNLTf57oW6xJHbmfZQgAh09PSnIey5MKTcUFBepNZfXwkrjkBhvT13UnkC0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer_7.2.0_amd64.deb
 and install it with,


$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb


Then you should see 7.2.0 installed as something like 
/usr/local/freesurfer/7.2.0 which you would use for FREESURFER_HOME



- R.


On Nov 16, 2021, at 07:26, 许霄  wrote:



External Email - Use Caution



Hello FreeSurfer Developers,

I can't access the website of archives, so I have to ask questions in this way. 
I installed freesurfer7-dev in Ubuntu18 in wsl according to the tutorials  
FS7_wsl - Free Surfer Wiki (harvard.edu) and FS7_wsl_ubuntu - Free Surfer Wiki 
(harvard.edu). After adding the license, when I tried to run the 'freeview' 
command to test if everything works well, an error popped out: Segmentation 
fault(core dumped). more information about my freesurfer environment is shown 
as attached. Could anyone help me figure it out? Thanks in advance.
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Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

[fsbuild]

External Email - Use Caution

Hello Xuxiao, 

In a terminal window in Ubuntu running under WSL, please try just running a 
simple X windows program like xeyes to test that your X-server is running on 
Windows,
$ xeyes
(see attachment for what it should look like)

Keep an eye out for a flashing X server icon at the bottom of your Windows 
desktop. You may have to click on that flashing icon for the xeyes X 
window to open. But if you can’t display something simple like xeyes with 
the X server on Windows 10, then freeview is not going to work.
If you installed the Xming X-server on Windows, then you should see an X icon 
on your desktop that you can click on to start the X-server. And you can 
check you see the X icon in the “hidden” area at the bottom of the screen which 
shows the X server is running on Windows. See the bottom of this page for 
how to see Xming is running and then scroll up to see the X windows desktop 
icon,https://secure-web.cisco.com/1OO6_69UmGU84poSsYr7cookfWG3oW-9wCm0t5GqC3v9O7oBDQ1q-WnvTuSyggGEXti5uKZRYBxxYV5HExtu-ppR4au6_6-1kSsXd5xeWH0sjzxSBuO6-s3ylLX-eJLXv1NNHetN8T5te2f5B3q060rJz-IQmOr89jBBZJfBNqXj8GUrK2T83vEHEBRR-ZlVr4-U17E-yJeJ06x8hYwESZHStmIrv4RbAt-bNeHlKime_YN42ioashCJBm8bIY5tW/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming
If xeyes works, then check your freesurfer license file can be found. One 
way to do that is to set the environment variable FS_LICENSE to the absolute 
path to your license file. So you could for example call your license 
file “license.txt” and copy it into your home directory (denoted by the 
environment variable $HOME). You can also set FS_LICENSE in your shell 
init file.
$ cd $HOME$ pwdoutput deleted
$ ls license.txtlicense.txt$ export FS_LICENSE=$HOME/license.txt
… check it can be read …
$ cat $FS_LICENSEoutput deleted
Now set FREESURFER_HOME, source the setup environment script as you did in the 
screenshot you sent below, and try running freeview with no arguments to see if 
a blank window opens.
$ freeview
Another thing to consider is to try and install the latest version of 
freesurfer (7.2.0) using the Ubuntu .deb package installer from 
https://secure-web.cisco.com/1WCN8dpJeL5ctI2hET4QOYyxIu9gxAiTFJ_bFQH-ZV0hRCjqsGZHNpUBr7HvDJ2INK5w7k91cHO7oBPHd64q3mvNAsHPJ9QFmPFEKWWtzkZH3_7iVstG3kkMiNrY-XBlJtFZorcEBGB4rCuzw0l8A027a6pwCRSri-93w44c0RChuRCxOtMqknl97IR92JwtYxqZYQcLrH34Oj-6z2qv85Y07CKJW55gvlskUyCKgF10a1ZtypLL50vtTImOx8hrE/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer_7.2.0_amd64.deb
 and install it with,
$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb
Then you should see 7.2.0 installed as something like 
/usr/local/freesurfer/7.2.0 which you would use for FREESURFER_HOME

- R.
On Nov 16, 2021, at 07:26, 许霄 xux...@xii.ac.cn 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I can't access the website of archives, so I have to ask questions 
in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the 
tutorialsFS7_wsl - Free Surfer Wiki 
(harvard.edu)andFS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu). 
After adding the license, when I tried to run the 'freeview' command to test if 
everything works well, an error popped out: Segmentation fault(core dumped). 
more information about my freesurfer environment is shown as attached. Could 
anyone help me figure it out? Thanks in advance.freeview-Segmentation 
fault.png___Freesurfer mailing 
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xeyes.png
Description: Binary data
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Re: [Freesurfer] Freeview Error

[fsbuild]

External Email - Use Caution

Hello Gian,
I suspect the freeview binary is not going to be able to run on Debian linux. 
We don’t build or test on Debian linux, but freeview/freesurfer should be 
fine on CentOS 6, CentOS7 and Ubuntu 18 for linux and also on Mac OS.
Maybe someone could help you look at the steps listed 
here,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67for 
running freeview in a virtual machine. The instructions there are for 
setting up the virtual machine to run on Windows and the Mac - but those 
instructions should also basically work on (Debian) linux. But you would 
need to have privileges to install VirtualBox, download some files and 
uncompress them, etc.
- R.

On Mar 24, 2020, at 14:20, Gian Marco Duma gianmarco.d...@phd.unipd.it 
wrote:External Email - Use 
CautionDear Freesurfer 
developers, I'm trying to use freeview but I'm having a lot of problems. I'm 
not an expert in freesurfer neither in linux programming.I followed all 
the instructions from the installation page of freesurfer, unfortunately when I 
try to open freeview I have a simple message, that is 'Abort'.I have Debian 
operative system.I truly don't know what to do to open freeview. Do you have 
any suggestion?thanksGian 
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[Freesurfer] Freeview Error

[Gian Marco Duma]

External Email - Use Caution

Dear Freesurfer developers, I'm trying to use freeview but I'm having a lot
of problems. I'm not an expert in freesurfer neither in linux programming.
I followed all the instructions from the installation page of freesurfer,
unfortunately when I try to open freeview I have a simple message, that is
'Abort'.
I have Debian operative system.
I truly don't know what to do to open freeview. Do you have any suggestion?
thanks
Gian Marco
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[Freesurfer] freeview error

[Ortug, Alpen]

Hello FreeSurfer Experts,

I'm attempting to install Freesurfer. I am trying to test my installation.


$>recon-all -i sample-001.nii.gz -s bert -all




$>recon-all -s bert finished without error at


Wed Mar 11 19:09:43 EDT 2020
done

However, after this I am getting an error message when I try to open in 
Freeview. It is attached. I've searched the list and no similar errors have 
been reported.
Does anyone have any thoughts on how to trouble-shoot this one?

1) FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform:Ubuntu 
19.10 3) uname -a: Linux antalya 5.3.0-40-generic #32-Ubuntu SMP Fri Jan 31 
20:24:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 4) error file: see attached

Many thanks

Best



Alpen ORTUG, PhD
Post-doctoral Research Fellow

Division of Newborn Medicine

Boston Children's Hospital
Harvard Medical School
401 Park Dr.

Boston, MA 02215, USA




error .odt
Description: error .odt
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Re: [Freesurfer] Freeview error: GLXBadContext

[fsbuild]

External Email - Use Caution

Hello Alek,
When you say you are running Ubuntu 14 via a Windows 10 PC, do you mean you are 
running the add-on windows subsystem for linux (known as WSL) that allows you 
run an Ubuntu shell on Windows 10?  And then when you say you are 
remotely viewing things, does that mean you are remotely logging into that 
Windows machine?
If you are in fact using WSL, then for X Window based GUI application like 
Freeview to run in WSL, you need to have an X server installed and running on 
the windows side, e.g., Xming. Then WSL can send X windows based graphics 
from the Linux shell back to Xming on the Windows side for rendering.. 
But Windows OS has to be able to handle rendering the graphics thru 
Xming using the drivers for whatever the graphics card/hardware is (which could 
include a GPU).
If you look at this thread for the same error you posted, but on a pure linux 
desktop,https://stackoverflow.com/questions/9769613/x-error-badalloc-glx-badcontext-on-intelsandybridge-intel-hd-graphics-3000,
 it reads to me like this may have been solved by updating the *mesa* libraries 
in linux which support displaying graphics (directly on the linux OS driving 
the graphics card). Translating this to the Windows WSL environment 
however - it would seem the same error could be from the graphics received by 
the X-server on the Windows side not being compatible/supported by the graphics 
drivers/hardware there. It might also have something to do with how the 
X-server is configured.
I don’t have much experience with WSL, but I would think that in the Ubuntu 
linux shell you’d want to set display for the console,
$ export DISPLAY=:0
Then it sounds like that /usr/bin/xeyes or other *simple* X programs already 
get displayed correctly,
$ /usr/bin/xeyes
Do you get the same error if you run a simple freeview command to open a single 
volume, e..g.
$ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz
I would trytheabove directly on the windows machine (not remotely 
logged in).
- R.
On Mar 11, 2020, at 10:46, Duvnjak, Aleksandar 
aleksandar.duvnja...@imperial.ac.uk 
wrote:External Email - Use 
CautionDear FreeSurfer 
experts,Version: Freesurfer version 6.0Platform: Ubuntu 14.04 (Via a Windows 10 
PC)Upon completion of our first FreeSurfer job, in which we ran an array 
on ~50 subjects, we have tried to view the basic outputs (e.g. T1.mgz) using 
both freeview -v and FSLview. Upon running freeview -v, the app opens but shows 
nodiscernibleimage (see screengrab below). Upon exiting the viewing 
platform the command line reads:X Error: GLXBadContext 150 
Extension:  143 (Uknown extension) Minor opcode: 5 (Unknown 
request) Resource id: 0x8000c8I have found reference to this error 
in the archives 
at:https://www.mail-archive..com/freesurfer@nmr.mgh.harvard.edu/msg30865.htmland
 much like with this original query, we are running freeview remotely via a 
high-performace-computing system, and when we type glxgears at the command line 
spinning gears do popup.Furthermore, (and although this does not relate 
directly to Freesurfer, it may provide additional useful information) upon 
trying to view the same T1.mgz file with FSLview rather than freeview we 
receive the message "missing header/image file" within the viewer but no error 
in the command line.We appreciate this may be a simple solution, however 
as it is our first time running FreeSurfer, it is difficult to know how to 
proceed. I have attached the recon-all report log for the subject attempting to 
be viewed in the screengrab below.pastedImagebase640.pngKind 
regards,Aleks 
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Re: [Freesurfer] Freeview error

[Ruopeng Wang]

Is your work disk full?

On 9/17/19 10:22 AM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution


I tried in the command window where I started freeview but nothing 
happened. This is the output


miguel@miguel-VirtualBox:~$ ls 
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz



El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang 
(mailto:rpw...@nmr.mgh.harvard.edu>>) 
escribió:


Can you run the command in the command window that you start
freeview?

Ruopeng


On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández
mailto:miguelrivasf...@gmail.com>> wrote:

External Email - Use Caution


Dear Ruopeng,

I put that command in the freeview command console and this is
the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
This is not a shell. Only freeview commands are supported. Type
'-h' for all the available commands.
 Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang
(mailto:rpw...@nmr.mgh.harvard.edu>>) escribió:

If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng

On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution

Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I
obtained this error:


mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
-1): could not open file
MRIread failed: Unable to read from
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
-1): could not open file

Any suggestion about what could be the problem?, maybe the
write permissons of the freesurfer folder?

I am using the
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
version that is installed in a Ubuntu 18.04 virtual machine.
It is very strange because few weeks ago everything it was
working correctly.

Thanks in advance.


Best regards,
-- 
*Miguel Ángel Rivas Fernández*


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*Miguel Ángel Rivas Fernández*

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--
*Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Freeview error

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

I tried in the command window where I started freeview but nothing
happened. This is the output

miguel@miguel-VirtualBox:~$ ls
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz



El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang ()
escribió:

> Can you run the command in the command window that you start freeview?
>
> Ruopeng
>
> On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández <
> miguelrivasf...@gmail.com> wrote:
>
> External Email - Use Caution
>
> Dear Ruopeng,
>
> I put that command in the freeview command console and this is the output
>
> [FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
> This is not a shell. Only freeview commands are supported. Type '-h' for
> all the available commands.
>
>
>
>  Best regards,
>
> El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (<
> rpw...@nmr.mgh.harvard.edu>) escribió:
>
>> If you run:
>>
>> ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>>
>> What does it show?
>>
>> Ruopeng
>> On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer devs,
>>
>> I tried to open the brainmask.mgz file in freeview but I obtained this
>> error:
>>
>>
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
>> not open file
>> MRIread failed: Unable to read from
>> /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
>> not open file
>>
>> Any suggestion about what could be the problem?, maybe the write
>> permissons of the freesurfer folder?
>>
>> I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> version that is installed in a Ubuntu 18.04 virtual machine. It is very
>> strange because few weeks ago everything it was working correctly.
>>
>> Thanks in advance.
>>
>>
>> Best regards,
>> --
>> *Miguel Ángel Rivas Fernández*
>>
>> ___
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>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> *Miguel Ángel Rivas Fernández*
> ___
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>
>
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-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Freeview error

[Ruopeng Wang]

Can you run the command in the command window that you start freeview?

Ruopeng

> On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández 
>  wrote:
> 
> External Email - Use Caution
> 
> 
> Dear Ruopeng, 
> 
> I put that command in the freeview command console and this is the output
> 
> [FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
> This is not a shell. Only freeview commands are supported. Type '-h' for all 
> the available commands.
> 
> 
> 
>  Best regards, 
> 
> El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang ( >) escribió:
> If you run:
> 
> ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
> 
> What does it show? 
> 
> Ruopeng
> 
> On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
>> External Email - Use Caution
>> 
>> Dear Freesurfer devs,
>> 
>> I tried to open the brainmask.mgz file in freeview but I obtained this error:
>> 
>> 
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could 
>> not open file
>> MRIread failed: Unable to read from 
>> /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could 
>> not open file
>> 
>> Any suggestion about what could be the problem?, maybe the write permissons 
>> of the freesurfer folder? 
>> 
>> I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
>> version that is installed in a Ubuntu 18.04 virtual machine. It is very 
>> strange because few weeks ago everything it was working correctly. 
>> 
>> Thanks in advance.
>> 
>> 
>> Best regards,
>> -- 
>> Miguel Ángel Rivas Fernández
>> 
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> ___
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> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
> 
> -- 
> Miguel Ángel Rivas Fernández
> ___
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Re: [Freesurfer] Freeview error

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Dear Ruopeng,

I put that command in the freeview command console and this is the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

This is not a shell. Only freeview commands are supported. Type '-h' for
all the available commands.




 Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (<
rpw...@nmr.mgh.harvard.edu>) escribió:

> If you run:
>
> ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>
> What does it show?
>
> Ruopeng
> On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
> Dear Freesurfer devs,
>
> I tried to open the brainmask.mgz file in freeview but I obtained this
> error:
>
>
> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
> not open file
> MRIread failed: Unable to read from
> /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
> not open file
>
> Any suggestion about what could be the problem?, maybe the write
> permissons of the freesurfer folder?
>
> I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> version that is installed in a Ubuntu 18.04 virtual machine. It is very
> strange because few weeks ago everything it was working correctly.
>
> Thanks in advance.
>
>
> Best regards,
> --
> *Miguel Ángel Rivas Fernández*
>
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[Freesurfer] Freeview error

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this
error:


mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
not open file
MRIread failed: Unable to read from
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
not open file

Any suggestion about what could be the problem?, maybe the write permissons
of the freesurfer folder?

I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
version that is installed in a Ubuntu 18.04 virtual machine. It is very
strange because few weeks ago everything it was working correctly.

Thanks in advance.


Best regards,
-- 
*Miguel Ángel Rivas Fernández*
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[Freesurfer] freeview error

[zhac looch]

External Email - Use Caution

Hello freesurfer team,

How can ı fix the problem?

Ubuntu-brain:~$ freeview
Could not set locale
No such file or directory
This application failed to start because it could not find or load the Qt 
platform plugin "xcb"
in "".

Reinstalling the application may fix this problem.
Aborted (core dumped)
Ubuntu-brain:~$

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Re: [Freesurfer] Freeview error

[Hoopes, Andrew]

Hi, this should be fixed now in the OSX dev distribution.

best,
Andrew


From:  on behalf of "Md. Mamun Al-Amin" 

Reply-To: FS Help 
Date: Saturday, September 22, 2018 at 1:15 AM
To: FS Help 
Subject: [Freesurfer] Freeview error


External Email - Use Caution
Dear Experts
I have been encountered a problem opening Freeview window in Mac Terminal.
Could you please help me troubleshooting this problem?
Here is the screenshot.

Thanks in advance.

--

Kind regards

Md. Mamun Al-Amin
--
PhD Candidate, Queensland Brain Institute
The University of Queensland
Building 79, St Lucia QLD 4072
https://qbi.uq.edu.au/profile/877/md-mamun-al-amin
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[Freesurfer] Freeview error

[Md. Mamun Al-Amin]

External Email - Use Caution

Dear Experts
I have been encountered a problem opening Freeview window in Mac Terminal.
Could you please help me troubleshooting this problem?
Here is the screenshot.

Thanks in advance.

-- 

Kind regards

Md. Mamun Al-Amin
--
*PhD Candidate, Queensland Brain Institute*

*The University of Queensland*
*Building 79, St Lucia QLD 4072*
*https://qbi.uq.edu.au/profile/877/md-mamun-al-amin
*
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Re: [Freesurfer] Freeview error

[Ruopeng Wang]

The error message says it:

ERROR: MRISread: file 
'/Users/schumman/Non-Inf_FS_5_3/0002_WIP_3DT1_SAG_SENSE_3_1.nii/surf/lh.area.pial'
 has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

You were not loading a correct surface file. lh.area.pial is a scalar data 
file. Maybe you wanted to load lh.pial?

Ruopeng

> On May 28, 2017, at 11:00 AM, Bruce Fischl  wrote:
> 
> actually the attachment doesn't have an extension, so I can't even look at 
> it. Can you just resend as text?
> 
> cheers
> Bruce
> On Sat, 27 May 2017, Schumman Resonance wrote:
> 
>> Attached is the full command line; as per a screen output Freeview quits.I
>> have not tested all surface files, but Freeview uploads fine pial, white,
>> inflated, orig, and sphere.
>> Thanks!
>> On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl 
>> wrote:
>> Can you send us the full command line and screen output?
>> Cheers
>> Bruce
>> On May 27, 2017, at 11:45 PM, Schumman Resonance 
>> wrote:
>> 
>>  Hi,
>> Newbie question.
>> When I try to upload a surface to Freview I get the following
>> error:
>>  
>> [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: User provided function() line 0 in unknown
>> directory unknown file
>> [unset]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> Thanks,
>> Kev
>> 
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>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Freeview error

[Bruce Fischl]

actually the attachment doesn't have an extension, so I can't even look 
at it. Can you just resend as text?


cheers
Bruce
On Sat, 27 May 2017, Schumman Resonance 
wrote:



Attached is the full command line; as per a screen output Freeview quits.I
have not tested all surface files, but Freeview uploads fine pial, white,
inflated, orig, and sphere.
Thanks!

On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl 
wrote:
Can you send us the full command line and screen output?
Cheers
Bruce

On May 27, 2017, at 11:45 PM, Schumman Resonance 
wrote:

  Hi,
Newbie question.

When I try to upload a surface to Freview I get the following
error:
 

[0]PETSC ERROR:


[0]PETSC ERROR: User provided function() line 0 in unknown
directory unknown file

[unset]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0


Thanks,
Kev

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Re: [Freesurfer] Freeview error

[Bruce Fischl]

I'll take a look, but in the future can you just send this as text 
embedded in the email instead of screen shots.


thanks
Bruce


On Sat, 27 May 2017, Schumman 
Resonance wrote:



Attached is the full command line; as per a screen output Freeview quits.I
have not tested all surface files, but Freeview uploads fine pial, white,
inflated, orig, and sphere.
Thanks!

On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl 
wrote:
Can you send us the full command line and screen output?
Cheers
Bruce

On May 27, 2017, at 11:45 PM, Schumman Resonance 
wrote:

  Hi,
Newbie question.

When I try to upload a surface to Freview I get the following
error:
 

[0]PETSC ERROR:


[0]PETSC ERROR: User provided function() line 0 in unknown
directory unknown file

[unset]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0


Thanks,
Kev

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Re: [Freesurfer] Freeview error

[Schumman Resonance]

Attached is the full command line; as per a screen output Freeview quits.
I have not tested all surface files, but Freeview uploads fine pial, white,
inflated, orig, and sphere.
Thanks!

On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl 
wrote:

> Can you send us the full command line and screen output?
> Cheers
> Bruce
>
> On May 27, 2017, at 11:45 PM, Schumman Resonance 
> wrote:
>
> Hi,
>
> Newbie question.
>
> When I try to upload a surface to Freview I get the following error:
>
>
> [0]PETSC ERROR: --
> --
>
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
>
> [unset]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
>
> Thanks,
> Kev
>
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> properly
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>
>


Freeview_error_May2017
Description: Binary data
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Re: [Freesurfer] Freeview error

[Bruce Fischl]

Can you send us the full command line and screen output?
Cheers
Bruce

> On May 27, 2017, at 11:45 PM, Schumman Resonance  wrote:
> 
> Hi,
> 
> Newbie question.
> 
> When I try to upload a surface to Freview I get the following error:
>  
> 
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> 
> Thanks,
> Kev
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[Freesurfer] Freeview error

[Schumman Resonance]

Hi,

Newbie question.

When I try to upload a surface to Freview I get the following error:


[0]PETSC ERROR:


[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file

[unset]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0


Thanks,
Kev
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[Freesurfer] freeview error (libpng12.so.0) on Ubuntu

[Jeffrey Crawford]

Hello all!

I know there are issues with freeview use on Ubuntu, but I hit a wall in fixing 
them.

I am currently getting this error when typing "freeview" into the command 
prompt:

"freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory"

My current version of Freesurfer is: 
freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a.tar.gz

>From the research I did online, first, I used these commands from this mail 
>archive
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43219.html

then installed what was supposed to fix something similar from the wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/Download by doing "sudo apt-get 
install libjpeg62"

Now I have been trying to install "libpng12.so.0" or some variation on that, 
but linux does not seem to be able to find it.

Any help?

-Jeff
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Re: [Freesurfer] Freeview error: Surface does not contain valid volume geometry information

[Bruce Fischl]

Hi Claudia

you need to send us your full command line and the various other 
information we ask for when reporting issues (operating system, etc..)


thanks
Bruce
On 
Tue, 20 Sep 2016, Claudia Dacquino wrote:



Hi all, after doing GLM analysis I'm trying to run freeview to see results,
but I get this warning:

Surface does not contain valid volume geometry information. It may not align
with volumes and other surfaces.


What's wrong?

I'm using 5.1 version.


Thanks to all.

Claudia
--

Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia

Laboratorio di Neuropsichiatria

Dipartimento di Neurologia Clinica e Comportamentale

IRCCS Fondazione Santa Lucia

via Ardeatina 306 - 00179 Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 51501575

web: http://www.neuropsichiatrialab.com




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[Freesurfer] Freeview error: Surface does not contain valid volume geometry information

[Claudia Dacquino]

Hi all,
after doing GLM analysis I'm trying to run freeview to see results, but I
get this warning:

Surface does not contain valid volume geometry information. It may not
align with volumes and other surfaces.


What's wrong?

I'm using 5.1 version.


Thanks to all.
Claudia
-- 

Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia

Laboratorio di Neuropsichiatria

Dipartimento di Neurologia Clinica e Comportamentale

IRCCS Fondazione Santa Lucia

via Ardeatina 306 - 00179 Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 51501575

web: http://www.neuropsichiatrialab.com

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[Freesurfer] freeview error:

[Alison Boos]

Hi FreeSurfer Team,
 
I am trying to edit longitudinal data using FreeView. The original timepoints 
were processed and edited using FreeSurfer 5.1. The longitudinal data was also 
ran using FreeSurfer 5.1. I am currently trying to edit the longitudinal data 
using FreeView, however FreeView seems to have updated with the OS X and is 
incompatible with FreeSurfer 5.1. When I try to view the longitudinal base 
using FreeView errors pop up that say "failed to load". I don't want to update 
to FreeSurfer 5.3 for this project because it has all been run in 5.1 thus far. 
Does anyone have any insight about this?
 
I'm using a MAC PRO (2009) with OS X 10.9.5
FreeSurfer Version: freesurfer-Darwin-leopard-i868-stable-pub-v5.1.0
FreeView Information:
Process: freeview.bin [29818]
Path:
/Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview.bin
Identifier:  freeview.bin
Version: ???
OS Version:  Mac OS X 10.9.5 (13F1911)
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[Freesurfer] Freeview error

[김현호]

Dear all

I installed freesurfer as supposed for linux of centos 7.

I have a problem with freeview error.

After install was copleteted, Tying the command : "freeview"

-> freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory

So, Installed libXScrnsaver-1.1.2.2-6.1.el7.i686.rpm (libXss.so.1) but the
result wasn't changed.

Searching for libXss.so.1 file, finded in 'usr/lib' not 'usr/lib64'

I want to Install libXss.so.1 usr/lib64 and solve the problem. How can I
get freeview to run?

Help would be appreciated

gushkr.
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Re: [Freesurfer] freeview error

[Ruopeng Wang]

What if you just load one surface:

freeview -f good_output/surf/lh.pial

Does it load?

Best,
Ruopeng

On 01/06/2015 03:23 PM, Hirsch, Gabriella wrote:


Hi,

I am trying to view surfaces in 3D using Freeview on my own subject 
data via this command (replacing the subject name);


freeview -f 
good_output/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \


good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 
\


good_output/surf/lh.inflated:visible=0 \

good_output/surf/lh.white:visible=0 \

good_output/surf/lh.pial

While Freeview loads correctly, I get an error message upon loading: 
“Failed to load Surface /surf/rh.pial”. I checked my subject file in 
/surf and the rh.pial is indeed there.  I get the same error for both 
hemispheres.


Any help would be greatly appreciated!

Thanks,

Gabriella



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[Freesurfer] freeview error

[Cooke, Gillian]

Hi All,

I was hoping that someone might be able to help me.
When I load a surface into freeview (e.g. 
/Applications/freesurfer/subjects/fsaverage/surf/lh.inflated), I get an error 
in my terminal:

Did not find any volume geometry information in the surface

When I go on to load in my multiple comparisons corrected image the entire 
surface turns yellow.

Any suggestions for a fix?

Many thanks,
Gill

_
Gillian Cooke, Ph.D.
Postdoctoral Research Associate
Lifelong Brain  Cognition Lab
Beckman Institute
University of Illinois, Urbana
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Re: [Freesurfer] freeview error {Disarmed}

[rujing cha]

Dear doug, bruce and others,
Previously I could not view 
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
 from the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis;.
The freeview did represent 3 images. But it reported a something about
no geomatric information and I couldnot configure the overlay(When I
clicked the configure overlay, it stopped without any response). My
OS is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE
GTX 650 and setup the NVIDIA driver. Freesurfer version is
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer
has 2G memory and 4 processors.
I need help to fix it.
If anyone have viewed sample data or other data(*.inflated,
*sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by
freeview just as above, would you please tell me some information? The
information I need is Freesurer version, Centos version(desktop or
others) and something in CentOS setup, graphic card version and its
driver, memory size.
Thanks very much, doug, brucen and others.
Any reply will be highly appreciated.
All the best.
Rujing Zha

2014/1/3, Rujing Zha charuj...@gmail.com:
 Dear Ruopeng,
 Thanks for your help, Ruopeng.I learned the groupanalysis by manu
 ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran
 this command on your tutorial data (buckner data). Would you please tell me
 where my hardware setup is inappropriate?
 Thanks.
 All the best.
 Rujing Zha




 Hi Bruce and others,
 Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup
 the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup
 the nvidia drivers completely. Then I tried to run this command:
 freeview -f
 $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
 . It did present the underlay(lh.inflated),overlay and annot, but it
 suspended when I click the button configure overlay. Then freeview were
 suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do
 but terminated it manually in the command console by ctrl + c.
 I want to know why I cannot configure overlay. Is it a poor graphic card or
 CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is
 Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G.
 Thanks Bruce and others.
 All the best.
 2014-01-03



 Rujing Zha
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[Freesurfer] freeview error {Disarmed}

[Rujing Zha]

Dear Ruopeng,
Thanks for your help, Ruopeng.I learned the groupanalysis by manu 
ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this 
command on your tutorial data (buckner data). Would you please tell me where my 
hardware setup is inappropriate?
Thanks.
All the best.
Rujing Zha




Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup 
the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the 
nvidia drivers completely. Then I tried to run this command:
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
. It did present the underlay(lh.inflated),overlay and annot, but it suspended 
when I click the button configure overlay. Then freeview were suspended. The 
CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it 
manually in the command console by ctrl + c.
I want to know why I cannot configure overlay. Is it a poor graphic card or CPU 
or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) 
Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G.
Thanks Bruce and others.
All the best.
2014-01-03



Rujing Zha___
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[Freesurfer] freeview error

[charujing]

Dear Ruopeng,
Thanks for your help, Ruopeng.I learned the groupanalysis by manu 
ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this 
command on your tutorial data (buckner data). Would you please tell me where my 
hardware setup is inappropriate?
Thanks.
All the best.

2014-01-01



charujing___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] freeview error

[Rujing Zha]

Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup 
the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the 
nvidia drivers completely. Then I tried to run this command:
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
. It did present the underlay(lh.inflated),overlay and annot, but it suspended 
when I click the button configure overlay. Then freeview were suspended. The 
CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it 
manually in the command console by ctrl + c. 
I want to know why I cannot configure overlay. Is it a poor graphic card or CPU 
or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) 
Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G.
Thanks Bruce and others.
All the best.
2013-12-30



Rujing Zha___
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] freeview error

[rujing cha]

Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and
setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz,
and I setup the nvidia drivers completely. Then I tried to run this
command:
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
. It did present the underlay(lh.inflated),overlay and annot, but it
suspended when I click the button configure overlay. Then freeview
were suspended. The CPU ran 100%,and memory ran 23%. There was
nothing to do but terminated it manually in the command console by
ctrl + c.
I want to know why I cannot configure overlay. Is it a poor graphic
card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT,
and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and
RAM is 2.00G.
Thanks Bruce and others.
All the best.
2013-12-30



Rujing Zha
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] freeview error

[Rujing Zha]

Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup 
the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the 
nvidia drivers completely. Then I tried to run this command:
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
. It did present the underlay(lh.inflated),overlay and annot, but it suspended 
when I click the button configure overlay. Then freeview were suspended. The 
CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it 
manually in the command console by ctrl + c. 
I want to know why I cannot configure overlay. Is it a poor graphic card or CPU 
or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) 
Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G.
Thanks Bruce and others.
All the best.
2013-12-30



Rujing Zha___
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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
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dispose of the e-mail.