subject:"\[Freesurfer\] Freeview segmentation fault"

Re: [Freesurfer] Freeview segmentation fault

2023-04-04 Thread fsbuild

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You can set the environment variable FS_LICENSE to point to your license file. 
 Some people set that in their shell init file, e.g., .bashrc, and keep 
the file license.txt in their home directory.  For example,
$ cd $HOME$ head -1 license.tx...@somedomain.com        
<—— email you used to register
$ export FS_LICENSE=$HOME/license.txt$ head -1 
$fs_licens...@somedomain.com        <—— email you used 
to registerStarting
 with the Freesurfer 7.3.2 release, the Mac build used Xquartz 2.8.2.   
If you are not already running 2.8.2 or newer then I would download and install 
the latest version of Xquartz 
from https://secure-web.cisco.com/1SXQ4X5w-vvi7X1Bgt8BsNVoSPV15hx0E9DHqE4AzHBeWFpbXe19vrRVHq0jZvuEAZSGcAOVja-z5FXSeuccHK59eEkRg4Y_ZHcxr0hv_rtLMvQwqwdh-tceBzo5XNQKvY-Ymtey-kSeu3DC-R5QIilO9CGP_xy15NW2-uLeWf114Dn32_WGKEcE4jN6LkoNHRdE6aHFFTT7TY-15KQOdgHop9U4JjR5f3yQxTw5hEZLmHe_FEcnOZggIGbKBE5uOjo6oGgwEhMCvGTiBi0P9HKdNuO7cpO2SYX50ftRvndXOaM1hhmmD9cKgsuhWu3gXCGuPC3-QqAprHWWFcO3_Pw/https%3A%2F%2Fwww.xquartz.org
- R.
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Re: [Freesurfer] Freeview segmentation fault

2023-04-04 Thread Wang, Ruopeng

No, I meant the freesurfer license file. Where is the file located on your hard 
drive?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of OSE KADIRI 

Sent: Tuesday, April 4, 2023 3:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview segmentation fault

External Email - Use Caution

Hello,

It was added to my ~/.bashrc file. Is this what you mean?

Thank you,
Ose

On Tue, Apr 4, 2023 at 7:57 AM Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>> wrote:
Where is your license file located?

On Apr 4, 2023, at 2:26 AM, OSE KADIRI 
mailto:osekad...@g.ucla.edu>> wrote:

External Email - Use Caution

Hello,

I am having some trouble using Freeview on my university cluster with my 
MacBook (macOS Monterey version 12.4). Freeview works fine from a Windows 
machine, but when I try to view images (using XQuartz on my Mac), I get 
"segmentation fault." It does not seem to be a memory issue and I'm not using 
multiple screens. I can successfully run MATLAB and gnuplot using XQuartz. Any 
help is greatly appreciated!

Thank you,
Ose

--
Ose Kadiri
Staff Research Associate, Deters Lab
Department of Integrative Biology & Physiology, UCLA
Pronouns: she/her
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--
Ose Kadiri
Staff Research Associate, Deters Lab
Department of Integrative Biology & Physiology, UCLA
Pronouns: she/her
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Re: [Freesurfer] Freeview segmentation fault

2023-04-04 Thread OSE KADIRI

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Hello,

It was added to my ~/.bashrc file. Is this what you mean?

Thank you,
Ose

On Tue, Apr 4, 2023 at 7:57 AM Wang, Ruopeng  wrote:

> Where is your license file located?
>
> On Apr 4, 2023, at 2:26 AM, OSE KADIRI  wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am having some trouble using Freeview on my university cluster with my
> MacBook (macOS Monterey version 12.4). Freeview works fine from a Windows
> machine, but when I try to view images (using XQuartz on my Mac), I get
> "segmentation fault." It does not seem to be a memory issue and I'm not
> using multiple screens. I can successfully run MATLAB and gnuplot using
> XQuartz. Any help is greatly appreciated!
>
> Thank you,
> Ose
>
> --
> Ose Kadiri
> Staff Research Associate, Deters Lab
> Department of Integrative Biology & Physiology, UCLA
> Pronouns: she/her
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-- 
Ose Kadiri
Staff Research Associate, Deters Lab
Department of Integrative Biology & Physiology, UCLA
Pronouns: she/her
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Re: [Freesurfer] Freeview segmentation fault

2023-04-04 Thread Wang, Ruopeng

Where is your license file located?

On Apr 4, 2023, at 2:26 AM, OSE KADIRI 
mailto:osekad...@g.ucla.edu>> wrote:


External Email - Use Caution

Hello,

I am having some trouble using Freeview on my university cluster with my 
MacBook (macOS Monterey version 12.4). Freeview works fine from a Windows 
machine, but when I try to view images (using XQuartz on my Mac), I get 
"segmentation fault." It does not seem to be a memory issue and I'm not using 
multiple screens. I can successfully run MATLAB and gnuplot using XQuartz. Any 
help is greatly appreciated!

Thank you,
Ose

--
Ose Kadiri
Staff Research Associate, Deters Lab
Department of Integrative Biology & Physiology, UCLA
Pronouns: she/her
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[Freesurfer] Freeview segmentation fault

2023-04-03 Thread OSE KADIRI

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Hello,

I am having some trouble using Freeview on my university cluster with my
MacBook (macOS Monterey version 12.4). Freeview works fine from a Windows
machine, but when I try to view images (using XQuartz on my Mac), I get
"segmentation fault." It does not seem to be a memory issue and I'm not
using multiple screens. I can successfully run MATLAB and gnuplot using
XQuartz. Any help is greatly appreciated!

Thank you,
Ose

-- 
Ose Kadiri
Staff Research Associate, Deters Lab
Department of Integrative Biology & Physiology, UCLA
Pronouns: she/her
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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 segmentation fault: 11 on MacOS 10.15.7

2021-10-28 Thread fsbuild

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Hello Emmanuel,
You could try the suggestions in this post from last month,
https://secure-web.cisco.com/1H6jl_CDKnKsqkQWb-ixQ370LPSa0jmM_IIgqtrwqvBfOr_MUx_C9GKKKDgEZPw7aSb8zfBIBDSpaWvCvcKN6CMkVjPWc2oq9nhdchm-2CQeI5PkVlun_dK0wcM4GhixSf5CPH9LdCfKOHsucbO4TUY8N7IjQcXd91DvFhH0ebCZRgXOVX53qxng5aIbXT5FigcVm5p8_HhieBh3rWbczNNuppaofqBGL31iaC18t9TW2ki3orMf4QaVtJYd2e3uzP9OIszPoz3oswEtSvQt4DQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70979.html
It’s not formatted too well through the mail list archive, so I will try and 
send it to your private email separately.
- R.

On Oct 28, 2021, at 10:36, Emmanuel Guizar Rosales 
 
wrote:External Email - Use 
CautionDear Freesurfer Team,I 
installed Freesurfer freesurfer-darwin-macOS-7.1.1-20200811-8b40551 and tried 
to view surface files in freeview. However, if I try to open surface files in 
freeview, it crashes.Note: I can open the Freeview.app, but as soon as I try to 
load a surface file, it crashes. If I try to start freeview from the terminal 
after runningexport FREESURFER_HOME=path/to/freesurfersource 
$FREESURFER_HOME/SetUpFreeSurfer.shfreeviewthe app won’t even start and return 
the following error in the 
terminal:/Applications/freesurfer/7..1.1/bin/freeview: line 2:  1202 
Segmentation fault: 
11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview 
"$@"Attached you will find the full problem report:Every help would be much 
appreciated!Best wishes,Emmanuel*
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Re: [Freesurfer] Freeview segmentation fault on Mac OS X High Sierra

2021-03-17 Thread fsbuild

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Hello Mikael.
I don’t see a crash report/attachment with your posting.  You could just 
cut and paste the error output from the terminal followed by a cut and paste of 
the first page of the crash report directly into the actual email - if you like.
- R.

On Mar 17, 2021, at 08:47, Mikael Novén  
wrote:External Email - Use 
CautionDear experts,I recently 
updated to FreeSurfer 7.1.1 but this caused Freeview to stop working. I can 
neither use the terminal command ”freeview” or open it through the .app in 
Finder. I get a ”Segmentation fault: 11”. I attach the crash report below. 
XQuartz works (I can run ”xclock” and similar programs). Any help with 
getting Freeview to work is much appreciated. Kind regards,Mikael 
Novén___Freesurfer mailing 
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[Freesurfer] Freeview segmentation fault on Mac OS X High Sierra

2021-03-17 Thread Mikael Novén

External Email - Use Caution

Dear experts,

I recently updated to FreeSurfer 7.1.1 but this caused Freeview to stop 
working. I can neither use the terminal command ”freeview” or open it through 
the .app in Finder. I get a ”Segmentation fault: 11”. I attach the crash report 
below. XQuartz works (I can run ”xclock” and similar programs).
Any help with getting Freeview to work is much appreciated.

Kind regards,
Mikael Novén

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[Freesurfer] freeview segmentation fault

2014-05-13 Thread Mark D. Strohm

Hello-

We’re having a problem with our Freesurfer 5.3 install:  freeview exits with a 
Segmentation fault.  No windows open, and there is no other other output.

  strohm::funcserv1:=>freeview
  Segmentation fault

All I have been able to find is that it appears to be making an inappropriate 
ioctl call to the freeview script.

This is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on openSUSE 12.3.  
Any help would be appreciated

Thank you.

-Mark-


8011  open("/space/raid/fmri/freesurfer/bin/freeview", O_RDONLY) = 3
8011  dup2(3, 16)   = 16
8011  close(3)  = 0

8011  read(16, "#!/bin/tcsh -ef\nsource $FREESURFER_HOME/bin/tcl_setup\nsource 
$FREESURFER_HOME/bin/vtk_setup\nsource $FREESURFER_HOME/bin/qt_setup\nif($#argv 
> 0) then\n  if(\"$argv[1]\" == \"-tkmedit\") then\ntkmeditfv 
$argv[2-$#argv]\nexit 0\n  endif\nendif\nfreeview.bin $argv\n", 8192) = 259
8011  lseek(16, 0, SEEK_CUR)= 259

8011  ioctl(16, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 
0x7fffe2b9a2f0) = -1 ENOTTY (Inappropriate ioctl for device)
[…]
8011  ioctl(16, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 
0x7fffe2b9a480) = -1 ENOTTY (Inappropriate ioctl for device)
8011  write(17, "Segmentation fault\n", 19) = 19
8011  exit_group(139)   = ?
8011  +++ exited with 139 +++


-- 
Mark D. Strohm, Ph.D.
System Administrator, UCLA, Semel Institute & Department of Psychology
Center for Cognitive Neuroscience (CCN) & Functional Neuroimaging Core (FUNC)
2567D Franz Hall, 1-310-206-5618, mstr...@ucla.edu


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Re: [Freesurfer] freeview: segmentation fault

2011-12-08 Thread Ruopeng Wang

Would be hard for us to diagnose if we can't replicate the issue. Is 
there any core dump file or some kind of log file that may provide any 
hint? From what you described, it seems freeview crashes right when it 
is about to render the loaded image. that's about as far as I can guess 
now. Is that computer the only one you can run freeview on? Can you try 
on a different system?

Ruopeng

On 12/08/2011 03:24 PM, Xin Zheng wrote:
> Hi,
>
> I have not used freeview before in any version. The images open in
> tkmedit. What can we do to diagnose this problem?
>
> Xin
>
> On Thu, Dec 8, 2011 at 3:16 PM, Ruopeng Wang  
> wrote:
>> I have no problem loading this file in freeview, in both old and new
>> versions. Have you used freeview before on the same system? Did it work?
>>
>> Ruopeng
>>
>> On 12/08/2011 02:33 PM, Xin Zheng wrote:
>>> Hi Ruopeng,
>>>
>>> It seems to be with all files. Attached is one of them.
>>>
>>> Thanks!
>>> Xin
>>>
>>> On Thu, Dec 8, 2011 at 2:22 PM, Ruopeng Wang
>>> wrote:
 Does it happen with just that file or with other files as well? Would it
 be possible to send us that volume file?

 Ruopeng

 On 12/08/2011 02:03 PM, Xin Zheng wrote:
> Hi,
>
> We are trying to open something using freeview (ie. freeview -v
> SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
> When we tried to open it directly from the freeview GUI, it will load
> to about 7% and segmentation fault would occur again. We're using
> Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the
> problem?
>
> Thanks,
> Xin
> ___
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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 Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
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 properly
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Re: [Freesurfer] freeview: segmentation fault

2011-12-08 Thread Xin Zheng

Hi,

I have not used freeview before in any version. The images open in
tkmedit. What can we do to diagnose this problem?

Xin

On Thu, Dec 8, 2011 at 3:16 PM, Ruopeng Wang  wrote:
> I have no problem loading this file in freeview, in both old and new
> versions. Have you used freeview before on the same system? Did it work?
>
> Ruopeng
>
> On 12/08/2011 02:33 PM, Xin Zheng wrote:
>> Hi Ruopeng,
>>
>> It seems to be with all files. Attached is one of them.
>>
>> Thanks!
>> Xin
>>
>> On Thu, Dec 8, 2011 at 2:22 PM, Ruopeng Wang  
>> wrote:
>>> Does it happen with just that file or with other files as well? Would it
>>> be possible to send us that volume file?
>>>
>>> Ruopeng
>>>
>>> On 12/08/2011 02:03 PM, Xin Zheng wrote:
 Hi,

 We are trying to open something using freeview (ie. freeview -v
 SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
 When we tried to open it directly from the freeview GUI, it will load
 to about 7% and segmentation fault would occur again. We're using
 Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the
 problem?

 Thanks,
 Xin
 ___
 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.
>>>
>

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Re: [Freesurfer] freeview: segmentation fault

2011-12-08 Thread Ruopeng Wang

I have no problem loading this file in freeview, in both old and new 
versions. Have you used freeview before on the same system? Did it work?

Ruopeng

On 12/08/2011 02:33 PM, Xin Zheng wrote:
> Hi Ruopeng,
>
> It seems to be with all files. Attached is one of them.
>
> Thanks!
> Xin
>
> On Thu, Dec 8, 2011 at 2:22 PM, Ruopeng Wang  
> wrote:
>> Does it happen with just that file or with other files as well? Would it
>> be possible to send us that volume file?
>>
>> Ruopeng
>>
>> On 12/08/2011 02:03 PM, Xin Zheng wrote:
>>> Hi,
>>>
>>> We are trying to open something using freeview (ie. freeview -v
>>> SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
>>> When we tried to open it directly from the freeview GUI, it will load
>>> to about 7% and segmentation fault would occur again. We're using
>>> Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the
>>> problem?
>>>
>>> Thanks,
>>> Xin
>>> ___
>>> 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.
>>

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Re: [Freesurfer] freeview: segmentation fault

2011-12-08 Thread Bruce Fischl

can you open it in tkmedit? Sounds like something is wrong with the file
On 
Thu, 8 Dec 2011, Xin Zheng wrote:

> Hi,
>
> We are trying to open something using freeview (ie. freeview -v
> SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
> When we tried to open it directly from the freeview GUI, it will load
> to about 7% and segmentation fault would occur again. We're using
> Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the
> problem?
>
> Thanks,
> Xin
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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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 Partners Compliance HelpLine at
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Re: [Freesurfer] freeview: segmentation fault

2011-12-08 Thread Ruopeng Wang

Does it happen with just that file or with other files as well? Would it 
be possible to send us that volume file?

Ruopeng

On 12/08/2011 02:03 PM, Xin Zheng wrote:
> Hi,
>
> We are trying to open something using freeview (ie. freeview -v
> SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
> When we tried to open it directly from the freeview GUI, it will load
> to about 7% and segmentation fault would occur again. We're using
> Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the
> problem?
>
> Thanks,
> Xin
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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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 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] freeview: segmentation fault

2011-12-08 Thread Xin Zheng

Hi,

We are trying to open something using freeview (ie. freeview -v
SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
When we tried to open it directly from the freeview GUI, it will load
to about 7% and segmentation fault would occur again. We're using
Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the
problem?

Thanks,
Xin
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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 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.

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