subject:"\[Freesurfer\] Freeview"

Re: [Freesurfer] freeview colormap for volumes

2024-07-09 Thread Wang, Ruopeng

You can create your own color table file and put it in ‘luts’ folder under your 
FS home directory. There are a few stock color table files in that folder. You 
can copy and modify one of them to your own. The current color table does not 
support transparency, though.

Ruopeng

On Jul 8, 2024, at 7:12 PM, Proulx, Jean Sebastien 
mailto:jspro...@mgh.harvard.edu>> wrote:

Hello,

This seems to be a longstanding issue, unless there is a post I miss.

How can one specify a custom colormap for a volume? Bonus point for how to 
specify an alpha channel for voxel-specific transparency.

My immediate goal: visualize angle data with a colorbar that wraps around a 
full circle (same color for values 0 and 2pi). That would be enough for now, 
but ultimately I want these angles to display with high transparency for voxels 
where the estimate is uncertain (low 2-d vector magnitude).

Thanks for the help and
Have a great day!
Sebastien
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[Freesurfer] freeview colormap for volumes

2024-07-08 Thread Proulx, Jean Sebastien

Hello,

This seems to be a longstanding issue, unless there is a post I miss.

How can one specify a custom colormap for a volume? Bonus point for how to 
specify an alpha channel for voxel-specific transparency.

My immediate goal: visualize angle data with a colorbar that wraps around a 
full circle (same color for values 0 and 2pi). That would be enough for now, 
but ultimately I want these angles to display with high transparency for voxels 
where the estimate is uncertain (low 2-d vector magnitude).

Thanks for the help and
Have a great day!
Sebastien
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Re: [Freesurfer] Freeview cannot be opened (MacOS)

2024-07-02 Thread fsbuild

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If you prefer to run the last stable release (7.4.1),
 then I suggest downloading and installing the Intel binary package 
installer, 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.pkg;
 To bypass some security prompts, right click on the package file and 
then choose "open will default ..."

You should check the path, but I think you would set things up in the (bash) 
shell as,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1... source the 
environment setup script ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

  

If you don't mind running the latest development build (which can be 
unstable), then you can try the native arm64 binary package installer 
via the link, 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev-20240327.pkg;
 Install the same way via right click as listed above. Then check the 
path, e.g,
$ export FREESURFER_HOME=/Applications/freesurfer/dev... source the environment 
setup script ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

  

Assuming you have your license file setup, e.g., to be read via 
FS_LICENSE environment variable with license.txt under your home 
directory,

$ export FS_LICENSE=$HOME/license.txt

  

- then it should work to run freeview. I would first try running 
freeview from the shell command line w/o any arguments to see if it opens an 
empty window.

$ freeview

  

Then exit and try it again with a known to be good volume, 

$ freevivew $SUBJECTS_DIR/bert/mri/brain.mgz

  

- R.



On 7/1/24 13:42, Melih Keskin (keskinmeli...@gmail.com) wrote:



  External Email - Use 
Caution
  Hi,
I am trying to open Freeview 
using my M1 Macbook (Monterey version 12.5). I am posting the error it 
gives me below. I followed the steps from the below thread but none of 
the solutions worked (mainly changing the privacy settings and getting a
 new Freesurfer 
license).https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70979.html

Is there a solution to this problem as of 2024?
Thank you in advance,Melih






2024-07-01
 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method 
userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It
 should not be used in new applications. Use convertRectToBacking: 
instead.
[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://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.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 darwin12. named Melihs-MacBook-Pro.local by 
keskin Mon Jul 1 20:41:01 2024
[0]PETSC ERROR: Libraries linked from 
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC
 ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 
--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

  

  
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[Freesurfer] Freeview cannot be opened (MacOS)

2024-07-01 Thread Melih Keskin

External Email - Use Caution

Hi,

I am trying to open Freeview using my M1 Macbook (Monterey version 12.5). I
am posting the error it gives me below. I followed the steps from the below
thread but none of the solutions worked (mainly changing the privacy
settings and getting a new Freesurfer license).

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70979.html

Is there a solution to this problem as of 2024?

Thank you in advance,
Melih

2024-07-01 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method
userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It
should not be used in new applications. Use convertRectToBacking: instead.

[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://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.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 darwin12. named Melihs-MacBook-Pro.local
by keskin Mon Jul  1 20:41:01 2024

[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt

[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=0 --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
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Re: [Freesurfer] Freeview problems

2024-04-17 Thread fsbuild

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You can check the post (quoted below) to verify the setup for the 7.4..1 
release.  Instead of running the freeview command as listed in the post, 
you can run the mri_info command with no arguments to get the help info about 
the command line options. If mri_diff runs and prints out the help 
output, then the issue is likely your command line arguments.
- R..
bash-3.2$ mri_info
USAGE: mri_info fname1 fname2 options

 --conformed : print whether a volume is conformed stdout
 --conformed-to-min : print whether a volume is conformed-to-min 
stdout
 rest of output deleted

SETUP ENVIRONMENT
https://secure-web.cisco.com/1-xQ9e5Z3VTlXilKkcSpNfmxzfXMzCk-PG0p40zknkFsd-OPflitvKnVBlbPqmZOOFVb9VAQ0M1PT82eJ-TQA5l5vXu3cxmiGQ_qMXFYiU6W_jXNSmGaqA3RbGU1beyO26DOuGjlunX7l_t7p3sBnlGCA8WPnPy5fmpsoKV4dY4ITrs3S59UCZ3IberbbCAyXNGPIhR261f_R6V7uFYU-YpjHa3r0hv9PElrVro7lKsGm-JNW6TmXBe6o5armcI5hCwbyu-rAezm9TjIL9J1eeRnkdiZvqDGt6oWMD0j9ILzFiiHj3UZbJHfsC8hr3mZDxdqSJlibJW8p2rTBT4emBQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76743.html

If you setup the Freesurfer environment ... here using bash and not zsh ...
hostname ~ bash
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$source 
$FREESURFER_HOME/SetUpFreeSurfer.shfreesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
 Setting up environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME /Applications/freesurfer/7.4.1FSFAST_HOME 
  /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR   
/Applications/freesurfer/7.4.1/subjectsMNI_DIR
 /Applications/freesurfer/7.4.1/mni
 and point FS_LICENSE to your license.txt file, e.g., in your $HOME 
directory 
$ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export 
FS_LICENSE=license.txt$ head -1 license.txt...@somewhere.com  
email you used to register
 then try running from the command line ...
$ freeview$SUBJECTS_DIR/bert/mri/T1.mgz
Please keep in mind you will need to change SUBJECTS_DIR to some other path, 
e.g., $HOME/subjects
$ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects
 and put files there if you want to write /modify subject files and data 
since /Applications/freesurfer/7.4.1/subjects is read only by default (not 
intended to be used to write data).
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Re: [Freesurfer] Freeview problems

2024-04-17 Thread Savoia, Alice (Stud. FPN)

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The thing is that I am specifying the image. I am using the latest version of 
freesurfer

Inviato da Outlook per 
Android<https://secure-web.cisco.com/1W7yKqhfJwWOUYl3f6U4jF_oYFNwM-CC21FOzRUbLSIPEBPoWwmd8-mxshlcJOSclq0tAlPTaIAdAsZq1pZNxBvMKYYu7Si7dhVSLlXC4THNVPUr5ZuxMnVCJSANKiPcCWFkUTSNUrMqzsaNXOQVRhwIM9rMUCxBRvKivRiAwgcz6ZVAUdhctB5r_Rq6Mm1P0c8dtBJ6nZ_LoMlz6PnxC5WilYWMlsa1V7k2vrtfK6NCqnviBLFrBjX-TxBxHwszt5ABV4IhkMrJvJRynXmYkgvehqcN0fjU-a-A22OmH1n-dvvgb8BXRHLWw3UkClctqChhJYVjYmctl8MnySJY0_Q/https%3A%2F%2Faka.ms%2FAAb9ysg>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Monday, April 15, 2024 5:27:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems


I don’t think you pass the arguments correctly to mri_info. You need to specify 
an input image – ‘mri_info input.mgz --voxel 0 0 0’.



This should be done after you have sourced Freesurfer environment correctly. 
Here are the instructions to setup your environment on Mac 
https://secure-web.cisco.com/1rDKNPfMnebEaPcslhVYc4x92ni2r-ZJVCYbzp7uAEUT-O0YTBClVlYZf0bHYMegbIlGHWaTIdnfTJ42kdx-8UKR_HIGpdFRxAmDuSl7tkkBbXHeD9iEISP8SYN9uLpCgJI5uXtjejWvgnCrZvqkFIrkSuIpD81J0gSUEp3DSBhDTc97ropCSJd3bR3T35KTGXjnLVjmieSllKI66mLpk7szdHpYmUpLZKWBMXKjfxT9AfO6yg2gh2WiQql7AVXjLNLH9JftKI_kPbHrnatXGyQ2VhI0Pu8xuE47UpXhcfQQMlTTEbLeuSfOry1ftLKNNC2SNGqguPewxh5hKzqAimw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Mac



Also, which version of Freesurfer you are using?



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 11:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems



External Email - Use Caution

Ok I tried again and when I inserted the mri_info... the output was "mri_info: 
could not parse extension from 0"



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>>
Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



Can you try ‘mri_info  --voxel 0 0 0’?   Just wanted to make sure 
the license file is read properly.



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 Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



External Email - Use Caution

Is in the freesurfer directory



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



Can you confirm where your license file is?



Ruopeng



On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:



External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.

Thank you for your help,

Best regards.

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Frees

Re: [Freesurfer] Freeview problems

2024-04-15 Thread Huang, Yujing

I don't think you pass the arguments correctly to mri_info. You need to specify 
an input image - 'mri_info input.mgz --voxel 0 0 0'.

This should be done after you have sourced Freesurfer environment correctly. 
Here are the instructions to setup your environment on Mac 
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac

Also, which version of Freesurfer you are using?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 11:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems


External Email - Use Caution
Ok I tried again and when I inserted the mri_info... the output was "mri_info: 
could not parse extension from 0"

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>>
Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems


Can you try 'mri_info  --voxel 0 0 0'?   Just wanted to make sure 
the license file is read properly.



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 Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



External Email - Use Caution

Is in the freesurfer directory



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



Can you confirm where your license file is?



Ruopeng



On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:



External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.

Thank you for your help,

Best regards.

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Re: [Freesurfer] Freeview problems

2024-04-15 Thread Savoia, Alice (Stud. FPN)

External Email - Use Caution

Ok I tried again and when I inserted the mri_info... the output was "mri_info: 
could not parse extension from 0"

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems

Can you try ‘mri_info  --voxel 0 0 0’?   Just wanted to make sure 
the license file is read properly.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution

Is in the freesurfer directory

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:

External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.

Thank you for your help,

Best regards.

___
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Re: [Freesurfer] Freeview problems

2024-04-15 Thread Huang, Yujing

Can you set the terminal output?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 11:03 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution
I think is not reading it properly because it gives an error, also I tried to 
setup the environment on the terminal but is not working either

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>>
Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems

Can you try 'mri_info  --voxel 0 0 0'?   Just wanted to make sure 
the license file is read properly.

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 Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution

Is in the freesurfer directory

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:

External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.

Thank you for your help,

Best regards.

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Re: [Freesurfer] Freeview problems

2024-04-15 Thread Savoia, Alice (Stud. FPN)

External Email - Use Caution

I think is not reading it properly because it gives an error, also I tried to 
setup the environment on the terminal but is not working either


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems


Can you try ‘mri_info  --voxel 0 0 0’?   Just wanted to make sure 
the license file is read properly.



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems



External Email - Use Caution

Is in the freesurfer directory



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



Can you confirm where your license file is?



Ruopeng



On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:



External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.

Thank you for your help,

Best regards.

___
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Re: [Freesurfer] Freeview problems

2024-04-15 Thread Huang, Yujing

Can you try 'mri_info  --voxel 0 0 0'?   Just wanted to make sure 
the license file is read properly.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems


External Email - Use Caution
Is in the freesurfer directory

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng


On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:

External Email - Use Caution
To whom it may concern,
I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.
Thank you for your help,
Best regards.
___
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Re: [Freesurfer] Freeview problems

2024-04-15 Thread Savoia, Alice (Stud. FPN)

External Email - Use Caution

Is in the freesurfer directory

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:

External Email - Use Caution

To whom it may concern,
I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.
Thank you for your help,
Best regards.
___
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Re: [Freesurfer] Freeview problems

2024-04-15 Thread Wang, Ruopeng

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:

External Email - Use Caution

To whom it may concern,
I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.
Thank you for your help,
Best regards.
___
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 .
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[Freesurfer] Freeview problems

2024-04-15 Thread Savoia, Alice (Stud. FPN)

External Email - Use Caution

To whom it may concern,
I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.
Thank you for your help,
Best regards.
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 crashes when trying to load volumes

2024-01-16 Thread Wang, Ruopeng

I would also check if the license file is installed properly.

On Jan 15, 2024, at 7:06 PM, fsbuild
mailto:fsbu...@contbay.com>> wrote:

External Email - Use Caution

- R.

On Jan 12, 2024, at 11:52, Ford, Jamie K
mailto:j.f...@imperial.ac.uk>> wrote:

External Email - Use Caution

Hello,

Please could I get some advice on my installation? I've downloaded version
7.4.0 using the same steps described in the installation video MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFile=get=installFS_demo.mp4

Everything seems fine until I try to load any sort of volume, e.g., a Bert MRI
file (like on the video). Freeview then crashes. This is the same for any
volume.

Could someone please advice? Any guidance would be greatly appreciated.

Many Thanks,

Jamie

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Re: [Freesurfer] Freeview crashes when trying to load volumes

2024-01-15 Thread fsbuild

External Email - Use Caution

It would help for us to know what your machine is running, e.g., linux or
MacOS (Intel or Silicon Mac) - and what the version is for the operating
system, e.g. Linux Ubuntu 22, MacOS 12, etc. If you are running Linux on
Windows thru either WSL or a VM then please mention that and if the Windows
host is running Win 10 or 11.
- R.
On Jan 12, 2024, at 11:52, Ford, Jamie K j.f...@imperial.ac.uk
wrote:External Email - Use
CautionHello,Please could I get
some advice on my installation? I've downloaded version 7.4.0 using the same
steps described in the installation videoMailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFiledo=gettarget=installFS_demo.mp4Everything
seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like
on the video). Freeview then crashes. This is the same for any
volume.Could someone please advice? Any guidance would be greatly
appreciated.Many
Thanks,Jamie___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Freeview crashes when trying to load volumes

2024-01-12 Thread Ford, Jamie K

External Email - Use Caution

Hello,

Please could I get some advice on my installation? I've downloaded version 
7.4.0 using the same steps described in the installation video 
https://secure-web.cisco.com/1f3eoE6wiYWgcSSn4HiWKsg1DLQo_L2RuFn8xDGE0ZoFRimONJZEkp8-nCLB4OnsKrI2FSNIwso-HPZj20_bADxRVhFeYBha6i4oHHyRTS8LPRFdTHua_LY22sNiIXdojO-4S8YCUCgmr3-CMwI-LKU7LdaZ5rMNbUIzzrG4n2cZ1HJ0DWFSlLzCjmUHOmyMlECyZv8nz5Srt1wVLQouavmp2UxD0RG46swER8LNwxSk7myPsk5Bk5HNWg_Hkv4N3CiQgrcCBz6sVv_p4bEvaJA_ZX9yn4zgV4S0bFx4bEhitZRTFfX_0jRo3xnalEbcV/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FDownloadAndInstall%3Faction%3DAttachFile%26do%3Dget%26target%3DinstallFS_demo.mp4

Everything seems fine until I try to load any sort of volume, e.g., a Bert MRI 
file (like on the video). Freeview then crashes. This is the same for any 
volume.

Could someone please advice? Any guidance would be greatly appreciated.


Many Thanks,

Jamie


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Re: [Freesurfer] Freeview keeps aborting.

2024-01-10 Thread Dong, Yilei

External Email - Use Caution

Thank you!

From: fsbuild 
Sent: Tuesday, January 9, 2024 4:56 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Dong, Yilei 
Subject: Re: [Freesurfer] Freeview keeps aborting.

I would check with your IT support staff about the error including asking if 
the machines in your cluster are setup to display X Windows sessions with image 
viewing applications like Freeview.   If the machines support remote graphics, 
they should be able to tell you what you need to set in your terminal session 
for it to work.   But it could be they expect programs like freeview to run on 
your local client machine and read the image files/data over the network via 
NFS, etc.

- R.

On Jan 9, 2024, at 18:52, Dong, Yilei  wrote:

External Email - Use Caution

Dear freesurfer help,

I have freesurfer installed on UCSD's Expanse HPC, which is on the Rocky Linux 
8 operating system. Every time I try to open freeview, it always keeps 
aborting. How should I fix this so that freeview's GUI can be shown? I have 
included the screenshot for reference on the error.
Thank you.

Sincerely,
Yilei

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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1Uu68lFIR2hSqWZLuS-hbNHfLOvDEPV_CkquQB3-Vzi4kF2Rc6SB1Q0K737GYwvltXFG9aEAvGqMr2kSSdkylcUP1qV2ILcaUFCWRfKRGnrxIuCinLSQpLTbcg_G7dadJL2R4u5JN2ktkYI6eJ5ejxCajtc7JgJHe9UeB5LcRcBY_FUE5HdZ0PdcPABEdqht28PGZ1TGyXkRVZUR9fq5NWXx2FH56RvxzYN6MLbbjT2rP7vzuhwtfmWTpKCw0SmrsqIc1sScmr1cXtLI-tTbIivlukfg-2NZYd8cQg5LUyokkzJ9cvHBFQcAaefj4a4pQj5N4L4y_3aWnIbp3FRv0sA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1oPt1GdACaupVvEPlmvoIux9ZhwSgrgXMEtyHZWhA9xJ0FBVvWm3ZEZ0yOoxB_fB3E2WP08jAqEDiKOuDxLR_fgpUgMrDLDchCM2aMKyt4ZQGCUwKyXvOAXboPaxz32UBXfKWVPRe9NYN9QldEsOp8xyb8roHOlOYPZ_cGdvXltbvxOhigWa_DPwjrfnm-hRHH1RPb6ZXl06hiy6NF3ev4JDlq6BCmK_jlyjrfi9HSUVu5f9k2v5yun9IdhHIlAOKTB9Td1N5lYebfz8rnZ9dVXwBngYk2oAM_v37NEaamv-Cdgh1wZzEKcRVWXFEfz9xnJpXtxteWuF4_8or3sRgLw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!LLK065n_VXAQ!hfPBrHNz34q-V6kyy8xPmu6gYunFc_AnEq6VkqUdqOmtX-ENaeyYSeDWbK2kXa_oc8ig7tsUPF7Kqr4xNZqZ$>

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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview keeps aborting.

2024-01-09 Thread fsbuild

External Email - Use Caution

I would check with your IT support staff about the error including asking
if the machines in your cluster are setup to display X Windows sessions with
image viewing applications like Freeview. If the machines support
remote graphics, they should be able to tell you what you need to set in your
terminal session for it to work. But it could be they expect
programs like freeview to run on your local client machine and read the image
files/data over the network via NFS, etc.
- R.

On Jan 9, 2024, at 18:52, Dong, Yilei yid...@health.ucsd.edu
wrote:External Email - Use
CautionDear freesurfer
help,I have freesurfer installed on UCSD's Expanse HPC, which is on the
Rocky Linux 8 operating system. Every time I try to open freeview, it always
keeps aborting. How should I fix this so that freeview's GUI can be shown? I
have included the screenshot for reference on the error.Thank
you.Sincerely,YileiScreen Shot 2024-01-09 at 3.47.14
PM.png___Freesurfer mailing
listfreesur...@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freeview not showing output

2024-01-04 Thread fsbuild

External Email - Use Caution

As Ruopeng said, even if simple X-Windows programs like glxgears run, that does 
not mean freeview will display graphics.
If freeview is not displaying images after X-ming (or a different) 
X-Windows server runs on the Windows host and displays graphics from 
glxgears, then there is likely something not right with the OpenGL drivers 
working with the graphics hardware on the Windows host. Usually the fix 
is to update to the latest OpenGL drivers on the Windows host.
If you have not read through or tried the steps on this Wiki page, then it 
might help, 
https://secure-web.cisco.com/12p37USRW5-RyLF2YXnbTAoizwyX5lHFSny043woIbJwaVA1Q6_A8YJxMdsz083PotIEQxfNhBetezn8unJ3bpT7arlesM-opVIvQ-jxqHg6UZaTwwFvbkIbzmvXhlHlC02MgLrOwtH-BShA0LaKafUr8T7AWZt5Dy1bKLSpvXObbJNND8nFFzU6ikjAOYv8JvCwMSODydsxNuBgPbsqak7GwjQ3Ap4BqUrQHcZN4UX_4jgm1-o9L_odJwgkN4z7eGgHh9wg2zsdJrbBiJSkETQeqnnIC58Lc8iamkihm7PokgUoRcCHqiEG0hpPWCb2tqimgLM9hYepeAUqcX8FTtA/https%3A%2F%2Ffreesurfer..net%2Ffswiki%2FFS7_wsl_ubuntu
If you are seeing graphics from glxgears then I would presume DISPLAY and 
XDG_RUNTIME_DIR are likely set OK in Linux.
- R.

On Jan 4, 2024, at 10:08, Wang, Ruopeng rwa...@mgh.harvard.edu wrote:It 
appears your system has some problem displaying OpenGL content properly. I’m 
not familiar with Xming. Can you try some other x display for Windows such as 
mobaxterm?https://secure-web.cisco.com/1KYKTifNL0XRk6k_SapoZX6CTHF_pDgzD6UKF0dkksoSBoqImuAD98rrLboBd_aYWt93uiZcob83wd88Crd8E4w6HbvVkhUVwS-CFa__hpvt-RsRpD40l9EbM2nCjm3OlP-ailtdAw2JpkXjxXQiLyTFabILi3agYXU2Jlj8KQ8U1mG56Pnrzu9EGa4BgFUvqu5fXNHC8JzXAm3Ktv-7W5FqCSV4yvg0ORKm7Jgt5fCYUzzQCBTvCdkJPxlX0KCk8gXd6N4W0BXKiNpFFX1N-2zy1vKf80kre0reP_cD6emR7ZsP_67hH_apBmofRuDaMT7PpM1pYGe2F2WunI4xJgw/https%3A%2F%2Fmobaxterm.mobatek.net%2FOn
 Jan 4, 2024, at 6:11 AM, Shawa, Zeena zeena.shawa...@ucl.ac.uk 
wrote:External Email - Use 
CautionHi Ruopeng,Thank 
you for your quick reply!When running glxgears I just see a blank 
window.Sincerely,Zeena 
ShawaFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfWang, RuopengSent:Wednesday, January 3, 2024 4:29 
PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] Freeview 
not showing output⚠Caution: External senderWhat if you run 
glxgears command? Do you see 3D spinning gears or just a blank 
window?RuopengFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Shawa, Zeena 
zeena.shawa...@ucl.ac.ukSent:Wednesday, January 3, 2024 9:17:00 
AMTo:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduSubject:[Freesurfer]
 Freeview not showing 
outputExternal Email - 
Use CautionHello FreeSurfer 
Developers and Community,Hope your day has been going well and happy new 
year!I'm attempting to visualise FreeSurfer outputs using freeview, as 
described on the “Introduction to Freesurfer Output” tutorial, under the 
“Viewing Volumes with Freeview” section (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1wzX4cge9MlMx5r_8jnAVeO8ue9DOKEESG6wS-RZbEzhXP-7pQaQgxBK8QyBF7hm-bqYBz_sBcNzsM9MxEQ-owoVqQmRLE8GKpOudIwJavI3EU6YF_Bs_uAcZfSLu7O8gR4W_mzt643W0rot3Z4yPSTE3IePMTVkJV27B2yH3OF6BwcPOoP1ZfXocrxR56_ANZV8XjyeQaOQ5D9BY7BRh1gcp_P57Orpb9r_0CgjBkFDZL9nBqKcNgdmgbNshaYmrvP5yk_fMjqkC87ych1b9nPkqMBOnxpXESn_d39nq6tSxFAIGSpeutQYRT9L5CNGoL4z5e5xLi2rNrI0cDiXNCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview%26nbsp;).
 The viewer launches fine and seems to load everything, but instead of showing 
any output it simply shows a black screen in the middle (screenshot attached). 
There is no error outputted in the command line either. The viewer seems to 
work fine otherwise, and I have completed the Xming X-server setup as described 
here:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/18qHMAU0T79b7NwnKw9Zpf5tUXLvkF9EnPH2_5X4-JibgPev_yLgH9bOmnOl9ki6tsL6KJAPJ89TBivch0oRDHLcHX9p2zemlApVOavfNMc-oVeLvXDLYMfg46MM5nK0UOFATMr9pJhI1-RGWNYv073vMPVhYUMtVYo0_C8Rdgsw4Fz5Pd9NcVLJBUFY7uHP2NMrO9f7Hj201yg7U7OmezaP47vYHFgVw_Um1LN2zKYmYZZtbOoGyxl--WMOdEZ6YE9BbwFADgcB6KRW3UVvjR55-8xnv8jsDNhhNH1cBrcEZPSpsUs6gxuHuJtDcu7LTvHS_ZIUJ7xLZjI51NjzLnQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming%26nbsp;.I've
 searched the archives and GitHub issues and cannot find a similar error. I 
would appreciate any feedback on how to troubleshoot this issue.Thank you very 
much for your understanding and help!FreeSurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460Freeview 
version:Version 3.0, June 14 2023 buildXming versions: Xming fonts 
7.7.0.10, Xming 6.9.0.31Platform: WSL2 Ubuntu 22.04.3 LTSuname -a: Linux 
LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 
UTC 2023 x86_64 x86_64 x86_64 GNU/L

Re: [Freesurfer] Freeview not showing output

2024-01-04 Thread Wang, Ruopeng

It appears your system has some problem displaying OpenGL content properly. I’m 
not familiar with Xming. Can you try some other x display for Windows such as 
mobaxterm?

https://mobaxterm.mobatek.net/



On Jan 4, 2024, at 6:11 AM, Shawa, Zeena 
mailto:zeena.shawa...@ucl.ac.uk>> wrote:


External Email - Use Caution

Hi Ruopeng,

Thank you for your quick reply!
When running glxgears I just see a blank window.

Sincerely,
Zeena Shawa

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Wednesday, January 3, 2024 4:29 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview not showing output


⚠ Caution: External sender


What if you run glxgears command? Do you see 3D spinning gears or just a blank 
window?

Ruopeng

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shawa, Zeena 
mailto:zeena.shawa...@ucl.ac.uk>>
Sent: Wednesday, January 3, 2024 9:17:00 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freeview not showing output


External Email - Use Caution

Hello FreeSurfer Developers and Community,

Hope your day has been going well and happy new year!

I'm attempting to visualise FreeSurfer outputs using freeview, as described on 
the “Introduction to Freesurfer Output” tutorial, under the “Viewing Volumes 
with Freeview” section (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview<https://secure-web.cisco.com/1gxz0NYCFZQK8I7yoqBazXhNSxfbtas6xskrsStOsimpxep-CRHu-kt9xHa_jDMHycwgMGbK-R1EE1Wx1-27DmJLyMZMgFurBik3CudXcYGI6DBs8n9-VWwApw3DwaXmILbvsKW1f1OrgYxrhr5bIM9X2H_xDEw2Jo7W5d7sFmMKm4LVp9DSGKerrVezTrihKqSC6-52vVID3S1TVu-Tm4c7VR--K_GRqdcrQoyAHmZ5egxwViHpG3gE7FK5XeDFHQrZD2GqjUi7HNRyrGADz196SV1dcx3udIWduEStsQqmg1MXqOdGeq1UqDNtsoJjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview>
 ). The viewer launches fine and seems to load everything, but instead of 
showing any output it simply shows a black screen in the middle (screenshot 
attached). There is no error outputted in the command line either. The viewer 
seems to work fine otherwise, and I have completed the Xming X-server setup as 
described here: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FSL_wsl_xming<https://secure-web.cisco.com/12Wssvth0-cJDruIThEp84njg4hCdzZpcS7NBpfijyPxeJebO030r3OwPscWXgBNqe2XCpYhwoMiw-6XJnXeNSS6LsLtcxqrp2_U0hCa5Fvr4u5bu8-66-i16PnXQBV2TYic_r07skuoRAkLAd2pupjAQbArZZumqLreeL4GV-cfT8WQoBTN_TWwnOHDsFmX_HYhVeoiEbxPOKgQ10Ef1V-bszmAPXLBMPmCxbXIHCjOeigj0m6pzf14hmD6PjfYebcLiNUo3BSPRZVxCt7dE953_uTCZvyoobKGwzqnVvki1jlBhWGJFoc27s8Y-S9yh/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming>
 .

I've searched the archives and GitHub issues and cannot find a similar error. I 
would appreciate any feedback on how to troubleshoot this issue.
Thank you very much for your understanding and help!


  1.  FreeSurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
  2.  Freeview version: Version 3.0, June 14 2023 build
  3.  Xming versions: Xming fonts 7.7.0.10, Xming 6.9.0.31
  4.  Platform: WSL2 Ubuntu 22.04.3 LTS
  5.  uname -a: Linux LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP 
Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
  6.  specific command: freeview -v \

good_output/mri/T1.mgz \
good_output/mri/wm.mgz \
good_output/mri/brainmask.mgz \
good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f good_output/surf/lh.white:edgecolor=blue \
good_output/surf/lh.pial:edgecolor=red \
good_output/surf/rh.white:edgecolor=blue \
good_output/surf/rh.pial:edgecolor=red


Sincerely,
Zeena Shawa

Zeena Shawa
i4Health PhD Student
Alan Turing Institute – Roche Community Scholar
Research Group UCL Centre for Medical Image Computing


<https://secure-web.cisco.com/1btSHtYkkYjdXpDjgaSZRqJLvx8MmgkH1LViLzSFvV2UaKPIFkKz_qx4fM4S8H_JVWOCMLyJ7mM350kvRNKjXk7TCUSWYbfEmCUCNi86Wtxv7R-whPtR49byMyqYHzvzMLhS3GPzWbOT2t_reL5JjuiG8eyeA7gz8aUq1YQ1sFiNwYPclExyXO4V4dBbqyKULapviVphiYzeExtdqiAarVUNSv-d3XolybzGoI3Se5vh14atkhR9f36rQPBzcif61O1gzZXFLdQs7DgU38X-ZW_l6C4ooCzdwX2zdJ1kooNW6nxt7fMpD_LNQGmTJiXbY/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fzeena-shawa%2F><https://secure-web.cisco.com/10zA_WZOkmHp3Fh1W3Z_sjeqIo7FojuA9hL4g-JNcgF3m3JueOKwaQZYt89PE47C15EQNA19-aZMWJhuz1SmbzffKxD7sKNeXuQi8otqn_zmTQmTGqvmSD1lsSqCnttw6flVaDfEdaTxztGZU6lIfzBnus6XnN6fjFnw3

Re: [Freesurfer] Freeview not showing output

2024-01-04 Thread Shawa, Zeena

External Email - Use Caution

Hi Ruopeng,

Thank you for your quick reply!
When running glxgears I just see a blank window.

Sincerely,
Zeena Shawa

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wang, Ruopeng
Sent: Wednesday, January 3, 2024 4:29 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview not showing output


⚠ Caution: External sender

What if you run glxgears command? Do you see 3D spinning gears or just a blank 
window?

Ruopeng

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shawa, Zeena 
mailto:zeena.shawa...@ucl.ac.uk>>
Sent: Wednesday, January 3, 2024 9:17:00 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freeview not showing output


External Email - Use Caution

Hello FreeSurfer Developers and Community,



Hope your day has been going well and happy new year!



I'm attempting to visualise FreeSurfer outputs using freeview, as described on 
the “Introduction to Freesurfer Output” tutorial, under the “Viewing Volumes 
with Freeview” section (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1kiSOCERiGHmev9_ul_Wu2JKolOu65r8en_vwtW549oSXZKocnyTRUXEpA6M0OyJoJ-2zrXaxCKVDwsJYKmfWNE0hhLHbn97mQPs0qmXGPwIFulsRraF5GIhqVzo1GxVKsTAh0efsrZKd-YKfg9rbscCtooqgXdU0YOnG318Pf-TL30-VieapmgNEhfo1DXu2w1BuCSwEh6GxYXnojcAM0YKk9vxZgdGiXhBdSdawGSGvUi7d2OTMJK5UtI2cs6LSyzS7VoVmVN6-RdtA_dE3YhrCjUoCN4mheELwL7h2AzxwuYMQtVFO8ZLw6gNHRtvWMKnpFqInFvI3IbPLbCjNAw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview<https://secure-web.cisco.com/1gxz0NYCFZQK8I7yoqBazXhNSxfbtas6xskrsStOsimpxep-CRHu-kt9xHa_jDMHycwgMGbK-R1EE1Wx1-27DmJLyMZMgFurBik3CudXcYGI6DBs8n9-VWwApw3DwaXmILbvsKW1f1OrgYxrhr5bIM9X2H_xDEw2Jo7W5d7sFmMKm4LVp9DSGKerrVezTrihKqSC6-52vVID3S1TVu-Tm4c7VR--K_GRqdcrQoyAHmZ5egxwViHpG3gE7FK5XeDFHQrZD2GqjUi7HNRyrGADz196SV1dcx3udIWduEStsQqmg1MXqOdGeq1UqDNtsoJjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview>
 ). The viewer launches fine and seems to load everything, but instead of 
showing any output it simply shows a black screen in the middle (screenshot 
attached). There is no error outputted in the command line either. The viewer 
seems to work fine otherwise, and I have completed the Xming X-server setup as 
described here: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/15yf-nVjCI3PWceqysbwzCKgjF_R_yJOD5JvYkxcTY1tdV_KTiCTCK5Cs_VHB7NEDTfcWL0-M4r_w71LCXADyfo-7jXhPg5w71QZ3LEpbgHoqpUV8-xZvnMT-Bhg3he_eO73i-wAwLjKckpq3qQFD7N17dQDy66VKFjayBLUTVIGLyqC-FdRS3_cf-5OToJam39Xh3vw4V4wAM-PPGzOp_JZQPAq9NAPctP8CToK1TMmxE6PpZmXxh1Eq-qWqXdhuCykmtiKoaWp-gUHCuWQFUjdbbfAXl8fE6J1cEBKr9W6KyJh6oq4eHjzdMOFDLG-allMRAS8HF4jbmIDG-ZM4Gg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming<https://secure-web.cisco.com/12Wssvth0-cJDruIThEp84njg4hCdzZpcS7NBpfijyPxeJebO030r3OwPscWXgBNqe2XCpYhwoMiw-6XJnXeNSS6LsLtcxqrp2_U0hCa5Fvr4u5bu8-66-i16PnXQBV2TYic_r07skuoRAkLAd2pupjAQbArZZumqLreeL4GV-cfT8WQoBTN_TWwnOHDsFmX_HYhVeoiEbxPOKgQ10Ef1V-bszmAPXLBMPmCxbXIHCjOeigj0m6pzf14hmD6PjfYebcLiNUo3BSPRZVxCt7dE953_uTCZvyoobKGwzqnVvki1jlBhWGJFoc27s8Y-S9yh/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming>
 .



I've searched the archives and GitHub issues and cannot find a similar error. I 
would appreciate any feedback on how to troubleshoot this issue.

Thank you very much for your understanding and help!



  1.  FreeSurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
  2.  Freeview version: Version 3.0, June 14 2023 build
  3.  Xming versions: Xming fonts 7.7.0.10, Xming 6.9.0.31
  4.  Platform: WSL2 Ubuntu 22.04.3 LTS
  5.  uname -a: Linux LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP 
Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
  6.  specific command: freeview -v \

good_output/mri/T1.mgz \

good_output/mri/wm.mgz \

good_output/mri/brainmask.mgz \

good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \

-f good_output/surf/lh.white:edgecolor=blue \

good_output/surf/lh.pial:edgecolor=red \

good_output/surf/rh.white:edgecolor=blue \

good_output/surf/rh.pial:edgecolor=red





Sincerely,

Zeena Shawa



Zeena Shawa

i4Health PhD Student

Alan Turing Institute – Roche Community Scholar

Research Group UCL Centre for Medical Image Computing





[Title: LinkedIn - Description: image of LinkedIn 
icon]<https://secure-web.cisco.com/1btSHtYkkYjdXpDjgaSZRqJLvx8MmgkH1LViLzSFvV2UaKPIFkKz_qx4fM4S8H_JVWOCMLyJ7mM350kvRNKjXk7TCUSWYbfEmCUCNi86Wtxv7R-whPtR49byMyqYHzvzMLhS3GPzWbOT2t_reL5JjuiG8

Re: [Freesurfer] Freeview not showing output

2024-01-03 Thread Wang, Ruopeng

What if you run glxgears command? Do you see 3D spinning gears or just a blank 
window?

Ruopeng

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shawa, Zeena 

Sent: Wednesday, January 3, 2024 9:17:00 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freeview not showing output

External Email - Use Caution

Hello FreeSurfer Developers and Community,

Hope your day has been going well and happy new year!

I'm attempting to visualise FreeSurfer outputs using freeview, as described on 
the “Introduction to Freesurfer Output” tutorial, under the “Viewing Volumes 
with Freeview” section (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview<https://secure-web.cisco.com/1gxz0NYCFZQK8I7yoqBazXhNSxfbtas6xskrsStOsimpxep-CRHu-kt9xHa_jDMHycwgMGbK-R1EE1Wx1-27DmJLyMZMgFurBik3CudXcYGI6DBs8n9-VWwApw3DwaXmILbvsKW1f1OrgYxrhr5bIM9X2H_xDEw2Jo7W5d7sFmMKm4LVp9DSGKerrVezTrihKqSC6-52vVID3S1TVu-Tm4c7VR--K_GRqdcrQoyAHmZ5egxwViHpG3gE7FK5XeDFHQrZD2GqjUi7HNRyrGADz196SV1dcx3udIWduEStsQqmg1MXqOdGeq1UqDNtsoJjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview>
 ). The viewer launches fine and seems to load everything, but instead of 
showing any output it simply shows a black screen in the middle (screenshot 
attached). There is no error outputted in the command line either. The viewer 
seems to work fine otherwise, and I have completed the Xming X-server setup as 
described here: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FSL_wsl_xming<https://secure-web.cisco.com/12Wssvth0-cJDruIThEp84njg4hCdzZpcS7NBpfijyPxeJebO030r3OwPscWXgBNqe2XCpYhwoMiw-6XJnXeNSS6LsLtcxqrp2_U0hCa5Fvr4u5bu8-66-i16PnXQBV2TYic_r07skuoRAkLAd2pupjAQbArZZumqLreeL4GV-cfT8WQoBTN_TWwnOHDsFmX_HYhVeoiEbxPOKgQ10Ef1V-bszmAPXLBMPmCxbXIHCjOeigj0m6pzf14hmD6PjfYebcLiNUo3BSPRZVxCt7dE953_uTCZvyoobKGwzqnVvki1jlBhWGJFoc27s8Y-S9yh/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming>
 .

I've searched the archives and GitHub issues and cannot find a similar error. I 
would appreciate any feedback on how to troubleshoot this issue.

Thank you very much for your understanding and help!

  1.  FreeSurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
  2.  Freeview version: Version 3.0, June 14 2023 build
  3.  Xming versions: Xming fonts 7.7.0.10, Xming 6.9.0.31
  4.  Platform: WSL2 Ubuntu 22.04.3 LTS
  5.  uname -a: Linux LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP 
Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
  6.  specific command: freeview -v \

good_output/mri/T1.mgz \

good_output/mri/wm.mgz \

good_output/mri/brainmask.mgz \

good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \

-f good_output/surf/lh.white:edgecolor=blue \

good_output/surf/lh.pial:edgecolor=red \

good_output/surf/rh.white:edgecolor=blue \

good_output/surf/rh.pial:edgecolor=red

Sincerely,

Zeena Shawa

Zeena Shawa

i4Health PhD Student

Alan Turing Institute – Roche Community Scholar

Research Group UCL Centre for Medical Image Computing

[Title: LinkedIn - Description: image of LinkedIn 
icon]<https://secure-web.cisco.com/1btSHtYkkYjdXpDjgaSZRqJLvx8MmgkH1LViLzSFvV2UaKPIFkKz_qx4fM4S8H_JVWOCMLyJ7mM350kvRNKjXk7TCUSWYbfEmCUCNi86Wtxv7R-whPtR49byMyqYHzvzMLhS3GPzWbOT2t_reL5JjuiG8eyeA7gz8aUq1YQ1sFiNwYPclExyXO4V4dBbqyKULapviVphiYzeExtdqiAarVUNSv-d3XolybzGoI3Se5vh14atkhR9f36rQPBzcif61O1gzZXFLdQs7DgU38X-ZW_l6C4ooCzdwX2zdJ1kooNW6nxt7fMpD_LNQGmTJiXbY/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fzeena-shawa%2F>
 [Title: Twitter - Description: image of Twitter icon] 
<https://secure-web.cisco.com/10zA_WZOkmHp3Fh1W3Z_sjeqIo7FojuA9hL4g-JNcgF3m3JueOKwaQZYt89PE47C15EQNA19-aZMWJhuz1SmbzffKxD7sKNeXuQi8otqn_zmTQmTGqvmSD1lsSqCnttw6flVaDfEdaTxztGZU6lIfzBnus6XnN6fjFnw3zBYgwtDG-FV8ToeptaGEbgGd0x8cddnBQYWcOqriE19BW_3aBzCrmwWJlowhTJr5k6tRVNmm9kGO97QG7cj17ExkF4W9ef9-1pcdxSEkMaMKqWc5qvNdGptusYNVA7hudI6dyQGT0eG3mLud8bS2xAAwzdHb/https%3A%2F%2Ftwitter.com%2FShawaZeena>

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Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

2024-01-01 Thread Douglas N. Greve


Yes, that is correct

On 12/20/2023 2:07 PM, Edwards, Vincent wrote:


External Email - Use Caution

Hi,

I'm following up on my quick question from this time last week.

I have several brains that I sent through recon-all using Freesurfer 
7. If I wanted to use Freeview on Freesurfer version 5 to do 
pial/wm/and control point edits, would I be able to do recon-all 
through Freesurfer 7?  Years ago, someone asked if they could do 
recon-all in an older version of Freesurfer and edit in a newer GUI. 
Doug said that was fine. My question is basically the inverse of their 
problem. I assumed that since Freeview is a GUI, the version used 
shouldn't have any actual impact on things as long as we returned to 
version 7 to recon-all. I just want to confirm that my assumption is 
correct?


The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 
(recon-all for pial/wm/cp's)


Thanks,
Vincent Edwards

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___
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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 
 .

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

2024-01-01 Thread Douglas N. Greve


Yes, that is correct.

On 12/13/2023 3:01 AM, Edwards, Vincent wrote:


External Email - Use Caution

Hello,

I have several brains that I sent through recon-all using Freesurfer 
7. If I wanted to use Freeview on Freesurfer version 5 to do 
pial/wm/and control point edits, would I be able to do recon-all 
through Freesurfer 7? I assumed that since Freeview is a GUI, the 
version used shouldn't have any actual impact on things as long as we 
returned to version 7 to recon-all. That seemed to be the case when 
someone asked a similar question (the reverse) 
 , 
but that was many years ago so I wanted to confirm.


Thanks,

Vincent Edwards

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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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 
 .

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

2023-12-20 Thread fsbuild

External Email - Use Caution

The freesurfer 6.X and 7.x release release notes summarize some changes for
Freeview (listed below) since version 5 was released in 2013. If none of
the improvements in features/stability are relevant to what you are doing, then
I don’t see why you could not revert to the older 5.X software. But if
you run into issues with a now ~10 year old version of Freeview, we may tell
you to use the latest 7.4.1 release from June of 2023.
- R.
- - - - -

•New: interface for x virtual frame buffer (fsxvfb). When you run
freeview from fsxvfb, no X server is needed. This is good for taking a bunch of
pictures when you don't want freeview popping up allthe time. Eg, fsxvfb
freeview orig.mgz -ss mypic.png —quit
•The filled.mgz can now be edited instead of the wm.mgz. The
advantage to this is that filled.mgz is slightly further in the process and it
is more intuitive. The filled.mgz is actually a segmentation ofthe
subcortical mass. In Freeview, you can view it in outline mode, meaning that
the edges of the segmentations are actually the surface that you are editing.
After that, run recon-all with the -autorecon2-wm -autorecon3 options, just as
you would if you had edited the wm.mgz..Landmark-based repositioning of
surfaces. Did you ever want to just make the surface move through a certain
point? You can do that now by creating point sets in freeview. Create a
separate point set for each surface (lh, rh, white, and pial), then save it in
subject/surf with a file name repos.$hemi.$surf.json where $hemi is either lh
or rh and $surf is either white or pial. Then run recon-all with the
-autorecon2-surfonly -autorecon3 options. Note that you can do this
interactively inside ofFreeViewas well; look under
Tools-Resposition Surface. If you do it interactively, the surface may be
overwritten next time recon-all is re-run, but it gives you a chance to play
with the repositioning.freeview - can now load and visualize diffusion
orientation distribution function (ODF) data.FreeViewchanges: surfce path
and label editing, surface annotation editing, automatic segmentation assisted
by Geodesic Matting algorithm, displaying two time courses at the same time,
better support for Mac (petsc error fixed on Mac)

On Dec 20, 2023, at 14:07, Edwards, Vincent
vincent.edwa...@utdallas.edu
wrote:External Email - Use
CautionHi,I'm following
up on my quick question from this time last week.I have several brains
that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview
on Freesurfer version 5 to do pial/wm/and control point edits, would I be able
to do recon-all through Freesurfer 7? Years ago, someone asked if they
could do recon-all in an older version of Freesurfer and edit in a newer GUI.
Doug said that was fine. My question is basically the inverse of their
problem.I assumed that since Freeview is a GUI, the version used
shouldn't have any actual impact on things as long as we returned to version 7
to recon-all.I just want to confirm that my assumption is correct?The
pipeline would be: F7 (recon-all), F5 (edit with freeview),F7 (recon-all
for pial/wm/cp's)Thanks,Vincent
Edwards___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Freesurfer/Freeview Version Compatibility

2023-12-20 Thread Edwards, Vincent

External Email - Use Caution

Hi,

I'm following up on my quick question from this time last week.

I have several brains that I sent through recon-all using Freesurfer 7. If I 
wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point 
edits, would I be able to do recon-all through Freesurfer 7?  Years ago, 
someone asked if they could do recon-all in an older version of Freesurfer and 
edit in a newer GUI. Doug said that was fine. My question is basically the 
inverse of their problem. I assumed that since Freeview is a GUI, the version 
used shouldn't have any actual impact on things as long as we returned to 
version 7 to recon-all. I just want to confirm that my assumption is correct?

The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all 
for pial/wm/cp's)

Thanks,
Vincent Edwards
___
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[Freesurfer] Freesurfer/Freeview Version Compatibility

2023-12-13 Thread Edwards, Vincent

External Email - Use Caution

Hello,

I have several brains that I sent through recon-all using Freesurfer 7. If I 
wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point 
edits, would I be able to do recon-all through Freesurfer 7? I assumed that 
since Freeview is a GUI, the version used shouldn't have any actual impact on 
things as long as we returned to version 7 to recon-all. That seemed to be the 
case when someone asked a similar question (the reverse) 

  , but that was many years ago so I wanted to confirm.

Thanks,

Vincent Edwards
___
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Re: [Freesurfer] Freeview issue

2023-10-22 Thread fsbuild

External Email - Use Caution



The Qt graphics libraries may need virtualGl over a 
remote X connection. So try prefacing your freeview command with 
"vglrun". See the introductory text about vglrun and the install commands 
on this page, 
https://secure-web.cisco.com/1_jeLuB9K3YFX-_vkUZquNAqePEbWUSsW-inupVmdbjXlex4rhufV8pNS0NPj6_HwmfTXNTHj-f1VpwO5L1FxVZxjTuZd_jIKlPJYkhBZ0iXvHGrpj7gUiuE2Lt9vAZeu4ieazTNok61_W9Fp6jv7ukbRi4jmQb63yTPmjlf8IpULZuGieE0qGkioK4gcDBDplqwVm2PqqQMutUxdvd0z6GI-TTBv2AO2A7sAqo_dHWkHoPVMDaUl6alNIUg8L8JeYe3Rn_pHVqDrgHUhSpcXzqgCp6DA-cdBz0bQoVnRi_CXCU8BaXBwqbrOUYck_W1vMDl_8y3cgoynupChWihsJAmC-LOIkKi9YdqpiuqCh5U/https%3A%2F%2Fwww.starnet.com%2Fhelp%2Fvirtualgl%2F
Then once the remote display of images is working, you might run into an issue 
trying to map the display size to your
 remote screen resolution.

  

- R.



On 10/22/23 03:57, yunus soleymani (soleymani.yu...@yahoo.com) wrote:



  External Email - Use 
Caution
  I did the following codes 
respectively:cdwgetMailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/11GVLnIDWxo_vR8D2Oa9AP0rLkOmLrhl51L-g0K4pY8mWNpc25hCXYg5qw8EPIDzfeeqnv5cyYNzMcPC4QuvC50tzwwJorW1AfzALLGmEBRBXCgyXxcZc_hE7PwJ4tlnTT6sGRSjGObyGuLSiWR2CqZwl8RzH1BkEi9Ym8xXnYWGsmvBrglSgH16t-SgIKgF6aa5ME4NabctEizZwF8Z-I-2GkQcbaTmEQswaBOEXeplL7RIF-NDXzFrqplw2TJ5IOZ20pTaB80VCXGMqxLxT39ijfH-d0u5-loTVFRtTYIfeFpKjtCAO_Q304dRytXSKFjZ5De30yK8NnZkJ9fATbgdcDc9KYYSfx1p0yFs8GJQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
ls freesurfer_ubuntu22-7.4.1_amd64.deb
sudo apt-get update -y
sudo apt-get -y install ./freesurfer_ubuntu22-7.4.1_amd64.deb
export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1"  
$HOME/.bashrc
ls $FREESURFER_HOME
ls license.txt
echo "export FS_LICENSE=$HOME/license.txt"  $HOME/.bashrc
echo "export XDG_RUNTIME_DIR=$HOME/.xdg"  $HOME/.bashrc
echo "export DISPLAY=:0"  $HOME/.bashrc
echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh"  
$HOME/.bashrc
.
 The
 above codes all worked correctly and the software was installed 
successfully. Also, the software analyzes the subjects correctly by 
using parallel recon-all code. The only issue is that the Freeview 
interface doesn't work and the error mentioned above appears. Is it 
because of that I am using a remote desktop connection tool to connect 
to my institute servers?


Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 914 526 
9298






  



On Sunday, October 22, 2023 at 11:12:08 AM GMT+3:30, 
fsbuild fsbu...@contbay.com wrote:





External Email 
- Use CautionWondering
 if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package 
from the download page and installed it from your Downloads folder via,$ sudo 
apt install ./freesurfer_ubuntu22-7.4.1_amd64.debThe link for that file on the 
downloads pageMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1P6sJsKdfjhSOlm7uHbTXJ8nsEFCHNYGKzdj0djukhVoPCyG91EdBhVxbHi53kwpdQYCT-ByuHLRTukUzTBvHVUXJo03E4wEptjCsZFOVgHNqY15mUXlHsG7f_vvg0sAtr1BNs0Zq8iy1MDkYvqy_XHV1uXFLEzVBxejhxdjQTN5CXaz8hynqEdriY2-0tNSKP0TeFutwa5N8m6gYsk9nXS75QwEy1K3knJhXby-Pm_ZYQ_1LXXTArPv-7n0rrxguvS0zsbj-5MiODIlxB2KbSgy267kxc-qAcb_bj1_9j9MlCZjv_0PHnxJn8SSicHG5S2qZxz31VQe-xgh-gooxtMr4pSp0hF9d3j2pX8pAUVI/https%3A%2F%2Fsurfer.nmr.mgh.harvard..edu%2Ffswiki%2Frel7downloads%26nbsp;ishttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb-
 R.On Oct 22, 2023, at 02:19, yunus soleymani soleymani.yu...@yahoo.com 
wrote:External Email - Use 
CautionI have the same 
problem.I would greatly appreciate your help with 
this.Yunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner 
has detected a possible

Re: [Freesurfer] Freeview issue

2023-10-22 Thread yunus soleymani

External Email - Use Caution

I did the following codes respectively:> cd> wget 
https://secure-web.cisco.com/1aP0_Kx1EvY11b0NT6IxCZDi6qJ8ESnNx0MiHNLpkaZPFkc2atT4gkCWc3WkByTuDOEIqIhM9LAHtdegpZGTzMy4IURh53TQgiuOLIyTWU05XwMo5HiW7OA6Gj_FcIXBLb1PLtrzw1mtmYjESjmRYre-WGHAz9AVyOuzR_oG9a9OirPZ2Qh3BEvO4v8Loxp9XpAFS0MFB4a-zlusmSKJOJq8rJ1yITrGvkJi7wn2y1EEutTWfHU3HmKZbQGOVnMBMXv40daeRPvR-IEucGjGklk-zAvqWNsIfZ5vrjE8MhQOf30lJHr5amTQPOZgfmYHQ-8Yo2u9nRrZqG5AOxiw-IoNCNHaSeL3yg4hvhCe8oPU/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
> ls freesurfer_ubuntu22-7.4.1_amd64.deb
> sudo apt-get update -y
> sudo apt-get -y install ./freesurfer_ubuntu22-7.4.1_amd64.deb
> export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
> echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1" >> $HOME/.bashrc
> ls $FREESURFER_HOME
> ls license.txt
> echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc
> echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc
> echo "export DISPLAY=:0" >> $HOME/.bashrc
> echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> $HOME/.bashrc

...
 The above codes all worked correctly and the software was installed 
successfully. Also, the software analyzes the subjects correctly by using 
parallel recon-all code. The only issue is that the Freeview interface doesn't 
work and the error mentioned above appears. Is it because of that I am using a 
remote desktop connection tool to connect to my institute servers?

Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
soleymani.yu...@yahoo.com+98 914 526 
9298

On Sunday, October 22, 2023 at 11:12:08 AM GMT+3:30, fsbuild 
 wrote:  

External Email - Use Caution

Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package 
from the download page and installed it from your Downloads folder via,
$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
The link for that file on the downloads page MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/13ttr6Hme_2J70W8VLQfesRdjeVH11nPmGzfxDAMDQXWirIiYssEFIE06H69Zrpn8Z5KFzWA5Gr_xwcppidU_YClWa3g_aDJV-7e_RIC8rpD_6HhXUAYWk43Nd1YCAT-BVq5d9VMVaFvbM9zBBuMeIOCO1wEr0E03x8XvmI4j-Z4pu7LdmDuyKATu9hu_u_6z6RVxboUPTVE98Bpk0E3buwMAInG2qyxqncsHr8f2R3tqPloIW559z7uqmLQog66pR3qWdjhBl7-gjIqBCMJv9f9pxf4rudr1G7WhEvh9bfkoaGtiBHPGdDQBMeHn6cDx6HRKM9Xkmj6Gm74KbnSzM8-gsWXCsenld7RTyncONFw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
 is 
https://secure-web.cisco.com/1aP0_Kx1EvY11b0NT6IxCZDi6qJ8ESnNx0MiHNLpkaZPFkc2atT4gkCWc3WkByTuDOEIqIhM9LAHtdegpZGTzMy4IURh53TQgiuOLIyTWU05XwMo5HiW7OA6Gj_FcIXBLb1PLtrzw1mtmYjESjmRYre-WGHAz9AVyOuzR_oG9a9OirPZ2Qh3BEvO4v8Loxp9XpAFS0MFB4a-zlusmSKJOJq8rJ1yITrGvkJi7wn2y1EEutTWfHU3HmKZbQGOVnMBMXv40daeRPvR-IEucGjGklk-zAvqWNsIfZ5vrjE8MhQOf30lJHr5amTQPOZgfmYHQ-8Yo2u9nRrZqG5AOxiw-IoNCNHaSeL3yg4hvhCe8oPU/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
- R.

On Oct 22, 2023, at 02:19, yunus soleymani  wrote:

External Email - Use Caution

I have the same problem. I would greatly appreciate your help with this.
Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
soleymani.yu...@yahoo.com+98 914 526 
9298

On Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu 
 wrote:

External Email - Use Caution

Dear Expert,Recently I installed the latest version of freesurfer in Ubuntu OS 
22LTS.. Freesurfer is installed successfully, but freeview gives some errors 
which I pasted below. Please provide your suggestions. 

Thank YouRamesh

freeview 
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.

Aborted (core dumped)___
Freesurfer mailing list

Re: [Freesurfer] Freeview issue

2023-10-22 Thread fsbuild

External Email - Use Caution

Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer 
package from the download page and installed it from your Downloads folder via,
$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
The link for that file on the downloads 
pagehttps://secure-web.cisco.com/1_35_maf1qeyDwN-YbnCQ8jOb6jvY5lINnAzztz0hRLD0JseUsdcHLQQn-9oN4Xf-0aaTL-xA7oSZSleQrdE_yI-urkuo_8dbOO2aiY13AYtsJTRILkzHGZi1TGwCD8Ywi8woTfAO3wh_9v1Xgux9lnFhVCVb_XtZeAmupzyWe44oapIbnV7FxQ-SHiFFd6No6MeMtAV2bj4l_Tb0oyF4xPb51zNX2UW4sCtlr3XDT3E_jZWpa7Wfg9OutA3mWKZX-EwQZS83QmQEdq_lPlHr69Ck5qqSVMhCUnNw8b5MrCyOZpcPbS4WKnC6_OQaSXxyUhRdO_phUm9N6pB0UhdiYAatDutIdTKQI-qx-8lpM-g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%26nbsp;ishttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb
- R.

On Oct 22, 2023, at 02:19, yunus soleymani soleymani.yu...@yahoo.com 
wrote:External Email - Use 
CautionI have the same 
problem.I would greatly appreciate your help with 
this.Yunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 
914 526 
9298On
 Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu 
mgrameshbabu2...@gmail.com 
wrote:External Email - Use 
CautionDear Expert,Recently I 
installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is 
installed successfully, but freeview gives some errors which I pasted below. 
Please provide your suggestions.Thank YouRameshfreeviewThis 
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.Aborted (core 
dumped)___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1BZ4_HvToI5a6OuM5gIFWs2VyFinjkWLi8C5L5ny7WeSkoUPm5JKinKYGrfFLsEEF6vXjSSB20skB1EH-5lApynTVgrUWDRK6SYlzq7r_QITnqNOo7cdyNRDmeFg2IBypvUo11FF3iBvcCmldzGq4fUTBIXuuSU6A6hFQcj0jB-aOU055LyuED92RNGc3XyiZ5YqQI0p57CfVu0qZZlh-KwwTsUcpaxB0tdN7hR3-W5uhj2D2OK1GW5QBa4Dg9hc3fxMFboPH8PBvkJstq_3knPEMjnYxzfa0osNnEkqDYsyi_mQ01W0AvSIB65LMi-IKrNLcMNXAUF1tW-I5QZLaPvx6PAtiBikmWKoFykv5bRg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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
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this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview issue

2023-10-22 Thread yunus soleymani

External Email - Use Caution

I have the same problem. I would greatly appreciate your help with this.
Yunus
Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
soleymani.yu...@yahoo.com+98 914 526
9298

On Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu
wrote:

External Email - Use Caution

Dear Expert,Recently I installed the latest version of freesurfer in Ubuntu OS
22LTS.. Freesurfer is installed successfully, but freeview gives some errors
which I pasted below. Please provide your suggestions.

Thank YouRamesh

freeview
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.

Aborted (core dumped)___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1Xp0VKJZrWkw1axu7dNfRTVNW3J9WVWZwx0-XUhucp-IBwVdJ339tqn2xNaL3CDz5d6b_nu_ZGRer3K2q9U0wcUT95Lmbt4Trz8ROzMvg30ihH53XXfMbGi0suTDVjf9sjE2WWLcQBnKHXj43H3WmEfEhqLvW8CwfjX9QJOPRHndmOu-1HjCpsTQD7cXQ81JpbuTUfpDHkvG65T3peFrJCzKStBeEbqc07ueCAQHDUH9bWi0oWpx1-OITnxStpVy-Ub5B80dfZmNYtbzANoKeBxeiEfDhwfu8tMvnxynkDe_qZQEx9dbSbP-zOOyYQAmzdYBs7PoWLInSiquS6Dye2kqiWrH4edkWMp8ATHfxNQ4/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
___
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continue to communicate over unencrypted e-mail.

[Freesurfer] Freeview issue

2023-10-21 Thread Ramesh Babu

External Email - Use Caution

Dear Expert,
Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS..
Freesurfer is installed successfully, but freeview gives some errors which
I pasted below. Please provide your suggestions.

Thank You
Ramesh

freeview
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.

Aborted (core dumped)
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread Marina Fernández

External Email - Use Caution

Hi Andrei,

I was referring to .bashrc file located in these directories:
/root/.bashrc
/home/'your_user'/.bashrc
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread Andrei Bieger

External Email - Use Caution

Indeed, the /usr/local/freesurfer/.bashrc file is empty
Trying to set the FS_DISABLE_LANG to true or false also had no consequences.
But thank you, anyway.

Andrei

Em ter., 17 de out. de 2023 às 07:45, fsbuild 
escreveu:

>
> From what I can see, the freesurfer release 7 installers do not modify the
> shell init file, e.g., bashrc, and neither did the VM provided in the past
> with freesurfer 7.2.0 pre-installed have an entry with FS_DISABLE_LANG set
> in the bashrc file.
>
> - R.
>
> On Oct 17, 2023, at 06:04, Marina Fernández 
> wrote:
>
> External Email - Use Caution
>
> Hi Andrei and Freesurfer experts,
>
> We had the same problem in the past and we noticed there was an extra line
> in the .bashrc file of Ubuntu:
> export FS_DISABLE_LANG="true"
> Deleting this line solves the problem.
>
> The .bashrc file should contain only the following FS lines:
> #Freesurfer:
> export FREESURFER_HOME=/usr/local/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> Make sure you do this for home and root .bashrc files.
>
> Hope this helps.
>
> Best wishes,
> Marina
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1_NsSXXxHhSERQpz4d8OqS91y-OzK1aLH2u2j-m9x-L2BS5tKB_q-NZDjbc9lMdP_gBuTuDUkKyk74Da9_gJZzAbKBAijuDOfMcCXEvzgZ6o_nVNkXSbzBohduNmbC7RQcBrNesgWFsdHwikSiIgO7ypTMxfxAs3vLbfv4FhIIPS5TS-26NNIdsP6oieEjhrq355u42W7ykWO9k-6a2jzbXdcxsLLF9qLBHsjOYYtNfp7zKGKqCfjBuAIVvdXR7xh7sVy-B_tnbGdcjbtsUnsSKIm8-ntoU28eIixmne72J2gC1EEI5iFe9DQiaLF89Wv1nZkCiPSSzHjfVFt2jVI6g/https%3A%2F%2Fmail.nmr..mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
>

-- 
Andrei Bieger
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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 misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread fsbuild

External Email - Use Caution

From what I can see, the freesurfer release 7 installers do not modify the 
shell init file, e.g., bashrc, and neither did the VM provided in the past with 
freesurfer 7.2.0 pre-installed have an entry with FS_DISABLE_LANG set in the 
bashrc file.
- R.

On Oct 17, 2023, at 06:04, Marina Fernández 
marina.fdez.alva...@gmail.com 
wrote:External Email - Use 
CautionHi Andrei and Freesurfer 
experts,We had the same problem in the past and we noticed there was an extra 
line in the .bashrc file of Ubuntu:export FS_DISABLE_LANG="true"Deleting 
this line solves the problem.The .bashrc file should contain only the 
following FS lines:#Freesurfer:export 
FREESURFER_HOME=/usr/local/freesurfersource 
$FREESURFER_HOME/SetUpFreeSurfer.shMake sure you do this for home and root 
.bashrc files.Hope this helps.Best 
wishes,Marina___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu
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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 misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread Marina Fernández

External Email - Use Caution

Hi Andrei and Freesurfer experts,

We had the same problem in the past and we noticed there was an extra line
in the .bashrc file of Ubuntu:
export FS_DISABLE_LANG="true"
Deleting this line solves the problem.

The .bashrc file should contain only the following FS lines:
#Freesurfer:
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Make sure you do this for home and root .bashrc files.

Hope this helps.

Best wishes,
Marina
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 
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Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-16 Thread Andrei Bieger

External Email - Use Caution

I tried loading the files from the terminal and from freeview's GUI. They
all return the same issue with the surfaces.
And I just sent the files to your email.

Andrei

Em seg., 16 de out. de 2023 às 12:00, Wang, Ruopeng 
escreveu:

> Did you load everything from the command-line? Or did you load the surface
> first and then load the volume from the GUI.
>
> Again, would be very helpful if you can send us the exact volume and
> surface files so we can diagnose.
>
> On Oct 16, 2023, at 10:47 AM, Andrei Bieger 
> wrote:
>
> External Email - Use Caution
>
> Nice! Here it goes for lh.pial.
> Also, it is freesurfer v7.4.1 (freesurfer_ubuntu22-7.4.1_amd64.deb
> <https://secure-web.cisco.com/1r-pSD1Uu4XOpL1j1283yDyBECdR3MY-yLnamVWC7zbjI9MwmEPnTx5XTNx33ZNS3rJe7V4kGmvuAo0dcj8QOu8u6KMZmprx2r2fRc2CGI4jrbeqg8pu7hCAbSEExNH_1ztFoPjwTnqZraYzt7qTkomooGwrDC16fJvkmYRWcaP3CP2Inb7tNx4SutNfMbW7i0UZLw2GE2iSSXJt9wLp_pplOwq_Icds3GdlcJrSOWu-qjG5Vi8OCFDC6jZeFy4UBpzX9Di_ayI43HzDq4rlevthoF1FlSHXagTe2D6A5a7-Urhyi8Z-SbnkfagdULod5/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb>)
> running on Ubuntu 22.04.3 installed on a fresh VirtualBox VM running on an
> HP Intel-I7 laptop, running Windows 11 Pro.
>
> SURFACE INFO 
> type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
> num vertices: 132602
> num faces   : 265200
> num strips  : 0
> surface area: 108995
> vg.valid: 1
> AvgFaceArea  0.410993
> AvgVtxArea   0.821973
> AvgVtxDist   1.022856
> StdVtxDist   0.442829
> ctr : (-28.7116, -16.3092, 37.6244)
> original vertex space   : surfaceRAS
> vertex locs : surfaceRAS
> Volume Geometry (vg)
> volume geometry:
> extent  : (256, 256, 256)
> voxel   : ( 1.,  1.,  1.)
> x_(ras) : (-1.,  0.,  0.)
> y_(ras) : ( 0.,  0., -1.)
> z_(ras) : ( 0.,  1., -0.)
> c_(ras) : ( 5.6654, 26.6386, -17.9153)
> file:
> /mnt/A-NVME/mosaic-pd/neuroimagem/FS_OUTPUTS/11_I1473172/mri/wm.mgz
> Volume Geometry vox2ras
> -1.0   0.0   0.0   133.66544;
>  0.0   0.0   1.0  -101.36142;
>  0.0  -1.0  -0.0   110.08471;
>  0.0   0.0   0.0   1.0;
> Volume Geometry vox2ras-tkr
> -1.0   0.0   0.0   128.0;
>  0.0   0.0   1.0  -128.0;
>  0.0  -1.0   0.0   128.0;
>  0.0   0.0   0.0   1.0;
> cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments:
> mris_remove_intersection ../surf/lh.orig ../surf/lh.orig  ProgramVersion:
> 7.4.1  TimeStamp: 2023/08/30-23:36:58-GMT  BuildTime: Jun 14 2023 03:45:01
>  BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User:
> andrei  Machine: motox  Platform: Linux  PlatformVersion: 6.2.0-27-generic
>  CompilerName: GCC  CompilerVersion: 8.4.0
> mris_info
> creationtime 2023/10/16-14:40:04-GMT
> sysname  Linux
> hostname Ubuntu1
> machine  x86_64
> surfacefile surf/lh.pial
> hemicode0
> talairach_flag  0
> rescale 0.00
> nvertices   132602
> nfaces  265200
> total_area  108995.218750
> group_avg_vtxarea_loaded 0
> avgfacearea  0.410993
> avgvtxarea  0.821973
> avgvtxdist  1.022856
> stdvtxdist  0.442829
> vtx0xyz   -8.073509 -100.566986 17.722403
> num_intersecting_faces 0
>
> Em seg., 16 de out. de 2023 às 11:35, Huang, Yujing <
> yhuan...@mgh.harvard.edu> escreveu:
>
>> mri_info is for volumes. mris_info works with surfaces.
>>
>>
>>
>> Which version of Freesurfer are you using?
>>
>>
>>
>> Yujing
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Andrei Bieger
>> *Sent:* Monday, October 16, 2023 10:25 AM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Freeview misaligned surfaces "warning
>> matrixinverse failed"
>>
>>
>>
>> *External Email - Use Caution*
>>
>> The problem is, I'm having the same issue with the Bert sample that comes
>> with the freesurfer download.
>>
>> I'm not able to mri_info the pial surfaces as the function seems to work
>> only with volumes. When I use it with the brainmasks of my own project the
>> work just fine.
>>
>> Also, all files are being displayed just fine at my university desktop.
>> The problem is with my laptop, and I can't figure it out.
>>
>>
>>
>> Best,
>>
>> Andrei
>>
>>
>>
>

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-16 Thread Wang, Ruopeng

Did you load everything from the command-line? Or did you load the surface 
first and then load the volume from the GUI.

Again, would be very helpful if you can send us the exact volume and surface 
files so we can diagnose.

On Oct 16, 2023, at 10:47 AM, Andrei Bieger 
mailto:andreibie...@gmail.com>> wrote:


External Email - Use Caution

Nice! Here it goes for lh.pial.
Also, it is freesurfer v7.4.1 
(freesurfer_ubuntu22-7.4.1_amd64.deb<https://secure-web.cisco.com/1r-pSD1Uu4XOpL1j1283yDyBECdR3MY-yLnamVWC7zbjI9MwmEPnTx5XTNx33ZNS3rJe7V4kGmvuAo0dcj8QOu8u6KMZmprx2r2fRc2CGI4jrbeqg8pu7hCAbSEExNH_1ztFoPjwTnqZraYzt7qTkomooGwrDC16fJvkmYRWcaP3CP2Inb7tNx4SutNfMbW7i0UZLw2GE2iSSXJt9wLp_pplOwq_Icds3GdlcJrSOWu-qjG5Vi8OCFDC6jZeFy4UBpzX9Di_ayI43HzDq4rlevthoF1FlSHXagTe2D6A5a7-Urhyi8Z-SbnkfagdULod5/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb>)
 running on Ubuntu 22.04.3 installed on a fresh VirtualBox VM running on an HP 
Intel-I7 laptop, running Windows 11 Pro.

SURFACE INFO 
type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 132602
num faces   : 265200
num strips  : 0
surface area: 108995
vg.valid: 1
AvgFaceArea  0.410993
AvgVtxArea   0.821973
AvgVtxDist   1.022856
StdVtxDist   0.442829
ctr : (-28.7116, -16.3092, 37.6244)
original vertex space   : surfaceRAS
vertex locs : surfaceRAS
Volume Geometry (vg)
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1., -0.)
c_(ras) : ( 5.6654, 26.6386, -17.9153)
file: 
/mnt/A-NVME/mosaic-pd/neuroimagem/FS_OUTPUTS/11_I1473172/mri/wm.mgz
Volume Geometry vox2ras
-1.0   0.0   0.0   133.66544;
 0.0   0.0   1.0  -101.36142;
 0.0  -1.0  -0.0   110.08471;
 0.0   0.0   0.0   1.0;
Volume Geometry vox2ras-tkr
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments: 
mris_remove_intersection ../surf/lh.orig ../surf/lh.orig  ProgramVersion: 7.4.1 
 TimeStamp: 2023/08/30-23:36:58-GMT  BuildTime: Jun 14 2023 03:45:01  
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460  User: 
andrei  Machine: motox  Platform: Linux  PlatformVersion: 6.2.0-27-generic  
CompilerName: GCC  CompilerVersion: 8.4.0
mris_info
creationtime 2023/10/16-14:40:04-GMT
sysname  Linux
hostname Ubuntu1
machine  x86_64
surfacefile surf/lh.pial
hemicode0
talairach_flag  0
rescale 0.00
nvertices   132602
nfaces  265200
total_area  108995.218750
group_avg_vtxarea_loaded 0
avgfacearea  0.410993
avgvtxarea  0.821973
avgvtxdist  1.022856
stdvtxdist  0.442829
vtx0xyz   -8.073509 -100.566986 17.722403
num_intersecting_faces 0

Em seg., 16 de out. de 2023 às 11:35, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> escreveu:
mri_info is for volumes. mris_info works with surfaces.

Which version of Freesurfer are you using?

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 Andrei Bieger
Sent: Monday, October 16, 2023 10:25 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse 
failed"


External Email - Use Caution
The problem is, I'm having the same issue with the Bert sample that comes with 
the freesurfer download.
I'm not able to mri_info the pial surfaces as the function seems to work only 
with volumes. When I use it with the brainmasks of my own project the work just 
fine.
Also, all files are being displayed just fine at my university desktop. The 
problem is with my laptop, and I can't figure it out.

Best,
Andrei

Em seg., 16 de out. de 2023 às 08:37, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> escreveu:
How/when was your surface created?  Can you send mris_info output of your pial 
surface? I’m wondering if it has volume geometry information.

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 Andrei Bieger
Sent: Sunday, October 15, 2023 11:06 AM
To: fsbuild mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse 
failed"


External Email - Use Caution
Hello! Thank you for the reply.

I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date 
(apt update && upgrade), do

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-16 Thread Wang, Ruopeng

Would it be possible to send us the volume and the surface files? If the volume
geometric info from the surface is missing or wrong, it would be unlikely to
align with the volume.

Ruopeng

On Oct 15, 2023, at 11:06 AM, Andrei Bieger
mailto:andreibie...@gmail.com>> wrote:

External Email - Use Caution

Hello! Thank you for the reply.

I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date
(apt update && upgrade), downloaded and installed the
"freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the
bert/mri volume was displayed just fine on freeview. Yet when I add the
subject`s pial surfaces using freeview`s GUI, the same problem happened.
Please, see below.

Em dom., 15 de out. de 2023 às 00:23, fsbuild
mailto:fsbu...@contbay.com>> escreveu:

Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the
system versions. So if your setup is looking for or finding system versions
of those libraries, then freesurfer may be installed incorrectly and/or could
be finding the wrong Qt libraries via use of environment variables like
LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt
environment variables in your shell environment before source’ing the
freesurfer setup script).

I suggest you remove whatever freesurfer distribution you have on the machine
and do a clean re-install of 7.4.1 using the .deb package installer which you
can download via the link, MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu20-7.4.1_amd64.deb

If freesurfer was previously installed with the linux package tools then it
should work to uninstall it with,
$ sudo apt remove freesurfer
… answer y to all prompts ...

If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the
root freesurfer directory.

With the previous freesurfer installation removed, cd to where you downloaded
the freesurfer_ubuntu20-7.4.1_amd64.deb and try,

$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb
… wait for install to finish …

$ cd
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/7.4.1
FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects
MNI_DIR /usr/local/freesurfer/7.4.1/mni

$ which freeview
/usr/local/freesurfer/7.4.1/bin/freeview
$ freeview
… freeview should open an empty window …

… quit freeview and try opening this example volume …

$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz

If you see the attached image, then freeview/Qt is essentially working.

- R.

On Oct 14, 2023, at 14:14, Andrei Bieger
mailto:andreibie...@gmail.com>> wrote:

External Email - Use Caution

Hi, all!

I had to reinstall my VM where I had freesurfer running. Everything was running
fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows
laptop, where I'm running the version 7.4.1 of Freesurfer.
When I downloaded freesurfer it wouldn't run freeview, with the following
output: "Application failed to start because no Qt platform plugin could be
initialized. Available plugins are: (...)"

After some research, I tried "sudo apt install qt5-default" and freeview
started running. But the thing is, every time I try loading a subject, the
surfaces get completely misaligned with the volumes and the following messages
show on the terminal: "Warning: MatrixInverse failed" and "Did not find any
volume info". Please, see attached image.

I tried using Ubuntu 22 and previous versions of freesurfer but the problem
persisted. I also found a message with a similar issue on this list, but the
user stopped answering so a solution wasn't proposed. There is also a release
note from v5.3.0 saying that on Fedora this message would come up, but this is
not the case.
Any help with that?
--
Andrei Bieger
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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to

Re: [Freesurfer] freeview upgrade isn’t working/library issue

2023-09-19 Thread fsbuild

External Email - Use Caution

I don't think we can guarantee upgrading freeview will work with the 
existing libraries in a sufficiently old freeview distribution. I’m not 
sure what version of Ubuntu is running from the kernel listed below, but you 
could create a backup of your existing freesurfer tree (if you need to keep 
it), and then run the .deb freesurfer 7.4.1 installer matching your system 
(Ubuntu 18, 20, 22) which you can download from,
https://secure-web.cisco.com/1W5Z7do8RHfQJIQIHZ9EbWhe5GYVhLQ8shO8lqEwhsAE6gDaexj3KfFN5zXfZdCA7mfyFvRUV606uEVX8q8IDVG0LNCC0MZeeiPwAtx_-ZxvtEW4-pSlPhehcCbUhEw62kOvNMbYel7i60_-I4om9lr8wCgQc4VQO3UDbDmVYy7BHSKG7VWmKi_tDBsO0qgu5TkBA4znCgxcoZom8erNkPY1dTUq2y5hUZ73nRKztQ4HU7CbYVPgsEOkDiB0P7MIm4uK7VAY2YIXUAPB2HVffR_qC0byOa-k5I7Iw2kPda10T0X0yWknO4wH7-RH0OuZWCBOv1vPCtSOENEHGX5Zf0w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
- R.

On Sep 19, 2023, at 15:33, Hoptman, Matthew (NKI) 
matthew.hopt...@nki.rfmh.org 
wrote:External Email - Use 
CautionTO:freesur...@nmr.mgh.harvard.eduFROM:matthew.hopt...@nki.rfmh.orgSUBJECT:
 freeview upgrade isn’t working/library issueHello FreeSurfer 
Developers,I followed the instructions here to upgrade 
freeview:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewI am now getting the 
error:freeview: error while loading shared libraries: 
libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file 
or directoryI saw that it was recommended to install the package 
libvtk7.1, but that isn’t working:E: Unable to locate package libvtk7.1E: 
Couldn't find any package by glob 'libvtk7.1'Any help is appreciated. I 
am using:5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 
x86_64 x86_64 GNU/LinuxThanks,MattIMPORTANT NOTICE: This 
e-mail is meant only for the use of the intended recipient. It may contain 
confidential information which is legally privileged or otherwise protected by 
law. If you received this e-mail in error or from someone who was not 
authorized to send it to you, you are strictly prohibited from reviewing, 
using, disseminating, distributing or copying the e-mail.PLEASE NOTIFY US 
IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR 
SYSTEM. Thank you for your cooperation.IMPORTANT NOTICE: This e-mail is 
meant only for the use of the intended recipient. It may contain confidential 
information which is legally privileged or otherwise protected by law. If you 
received this e-mail in error or from someone who was not authorized to send it 
to you, you are strictly prohibited from reviewing, using, disseminating, 
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR 
BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your 
cooperation.___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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continue to communicate over unencrypted e-mail.

[Freesurfer] freeview upgrade isn’t working/library issue

2023-09-19 Thread Hoptman, Matthew (NKI)

External Email - Use Caution

TO: freesurfer@nmr.mgh.harvard.edu
FROM: matthew.hopt...@nki.rfmh.org
SUBJECT: freeview upgrade isn’t working/library issue

Hello FreeSurfer Developers,

I followed the instructions here to upgrade freeview:
https://secure-web.cisco.com/1Fr1m43dMDo6PfZjwvbGiKtV6gtUUqAq08NIpRJf8nkhbpl6t_xCxggb1kwbhGAFGwTRhGkv4sWJDCjuHWTgohXGwrq-nAIvtq0Nfdd0_tSvmjvKWkv0IlMgpiIVnUf21uW4udZFN11ePTzTN75eirFuiyPk5w32ox5i_idq8DjZL2rE1Lhw9aSRLi3dL4VfG-EQQoTkGSI8C9oJRQKc6GjfomWHQ9wZBHqlQ-up71hJye297HHynBTUWYmHHjdXxRE8hiF6oPiasyVgS3wzts8TCnn2zZEmlDUcp4aN9Vjx2Xj6vUXf5no1SeK6B6hk0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview

I am now getting the error:
freeview: error while loading shared libraries: 
libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file 
or directory

I saw that it was recommended to install the package libvtk7.1, but that isn’t 
working:
E: Unable to locate package libvtk7.1
E: Couldn't find any package by glob 'libvtk7.1'

Any help is appreciated. I am using:
5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 
x86_64 GNU/Linux

Thanks,
Matt


IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or otherwise protected by law. If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
from reviewing, using, disseminating, distributing or copying the e-mail.
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.




IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or otherwise protected by law. If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
from reviewing, using, disseminating, distributing or copying the e-mail. 
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview output viewing error

2023-08-23 Thread fsbuild

External Email - Use Caution

If you search the freesurfer mail archives for WSL you should find 
postings about how to setup an X-server on the windows host in order for 
Linux applications to run in WSL and use X-Windows to display images.  We 
provide some documentation, however we cannot guarantee these settings work 
with the current version of the 2nd iteration of WSL, i.e., WSL2, which you are 
running. 
See,https://secure-web.cisco.com/11H-L4FbGidKmZY-de-JntjYeQLAeVrQ1XgpdUHaMqg8CCouWlZ-csPc_4IeioBAVAqHhk45el9cRUZPv7wIb0Fa33nZc9N4PkjKI0dF1RPJVN-he9XBt1Ua6a4QSVeD_w5bZnfOLabOM5n15lkCAJOV069NjUvo7wvfKDC7ihp4tfFZRlqy04d4Ulv8M3XzFbXzHa3_X6PzLyLptMRW0DpSEH15MxILMfCaw2aXqyXv8WbtHT_dWkB1oPK8nKUInT_c31S6utPE9VzRLR2IkzwjB7r2AqOCZO1vkEd_sd-w--NZS1-g316PnttbIo3N5Ia8In0FQw1pQlYDew151jQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
Some people have found Moba X-term to be easier to setup and use compared to 
Xming for the 
X-server.https://secure-web.cisco.com/1wbbTwhirUX48Lj_j7Zcog0e6ACmMB4oLvaYMUSE6loHwKKH6rYEiMDQ_-1MsBcWWJ3dpd-OBkNiaLAOkgjmtSZ7JWjzkEua8MwktH6pGmclIPg9mYSOIZGoNJqa8TyOhIyULOcXHVCIwSrp1q7QmTmYGBmMt1RXf29SR5i7iBMuAElxCOfXtvqo5wRPR9HlFUq9YF3tI-JWR9ZV0DuGS-nlAMxp2FK8AZkA1JIcN9VK9U6c3gbDeHRkrBKUAB3cFvtv5i1SwGP3i-UzJh2-KSIxX1ezMDxvbg_rkI2XjKSvA8qTaTX0hmxVxg3O3Fd1B50G-W2xhwfmR-OPMEtPh0A/https%3A%2F%2Fmobaxterm.mobatek.net
Before trying to run freeview, check that simple X-windows programs like 
“xclock” or “glxgears” run directly from the terminal window inside linux, 
i.e., you should see a clock displayed,$ xclock… and spinning gears ...$ 
glxgears
An alternative to WSL is to run the VirtualBox VM we provide with freesurfer 
7.2.0 pre-installed running on Ubuntu 
18,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-sSQIXzdhv-YwluzAWgB4gG9phXhLQcVB_o2cNHMOGnK9Gp9XWPjB8FgTqezBrM26yU2u5N756v_OP8sEXvbixcSFk6pTTTGbu3wEJMe_5kxVgYIInMdlJVcY40F7nAa8KOLYdDPEcKUtp7gnSXtBSNLE4rpSwwlEQr2t1r_26eI3pnjxD9fv1Z2pFrryslOZVdLTsNVxs6jZcYOZZYcGKMTjoPot6uYkAjYPe0eKi-U441Xz0011uiNKcTTbbhPOQ4bs6_q6eY9BWkFuxm6JBvP1WaMMtWPal2bAZD488thEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
You can upgrade the VM from Ubuntu 18, to 20, etc…. Similarly you can 
uninstall freesurfer 7.2.0 and install the latest 7.4.1 rpm matching the Ubuntu 
OS you are running from the Freesurfer downloads 
page,https://secure-web.cisco.com/1m70yw-FWa8H1WUCpyYEQ2AgIFTjm9W5pcTX0PejadT4Xt5J_YSvLLKb8_hi0_CHsZkjcfaQJCEMoo1FR4a9GG9tUh6CWii4M9OYVfYi_14SBVGd6at8Lq4qJl4P52yuupYfLSlf4et8HVuNu-BSrFq_g6gQPHt7TDv0XpvqiAcUFOZflBvLAt77eCm7hGGXLN1fDoqdOUQwkVMKxE_fQKUtGggn2wVVcPGGKMn0c6cY2qTSjq4IujXwEdI3Q1R9TCQhHO3yRJUrQQ5_fmbPjy10RA6O0dq6U8snOAcvQBrLVHTurrJ96BgrBP2v5L89SDuPgaqSHlT1K2QIOorRFLA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
Advantages to the VM are it will run (thru Virtualbox) on most Linux, Mac, or 
Windows hosts and since the X-server is built into the VM, there is no need to 
install and configure a 3rd party X-server on a Windows host. Some users 
have switched to VirtualBox because they found it easier to use. 
See,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-sSQIXzdhv-YwluzAWgB4gG9phXhLQcVB_o2cNHMOGnK9Gp9XWPjB8FgTqezBrM26yU2u5N756v_OP8sEXvbixcSFk6pTTTGbu3wEJMe_5kxVgYIInMdlJVcY40F7nAa8KOLYdDPEcKUtp7gnSXtBSNLE4rpSwwlEQr2t1r_26eI3pnjxD9fv1Z2pFrryslOZVdLTsNVxs6jZcYOZZYcGKMTjoPot6uYkAjYPe0eKi-U441Xz0011uiNKcTTbbhPOQ4bs6_q6eY9BWkFuxm6JBvP1WaMMtWPal2bAZD488thEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
- R.


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Re: [Freesurfer] freeview (visualize pial and white surface)

2023-08-04 Thread DS

External Email - Use Caution

Hi experts,
I sent several images to troubleshot the problem by e-mail. But, I received an 
email saying that these files need approval from moderator. However, so far, I 
still did not get any reply from the moderator. I am not sure how to send you 
these files and how long it usually takes. Do I need to send a reminder to the 
moderator?
Thank you so much for help.
















At 2023-08-04 04:10:42, "Wang, Ruopeng"  wrote:

External Email - Use Caution

Would it be possible to send us the two surface files?
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of DS 
Sent: Thursday, August 3, 2023 3:30:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview (visualize pial and white surface)
 

External Email - Use Caution

Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.




../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.




But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized. 




Do you have any thoughts about this issue? Thank you so much for any 
suggestions.


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Re: [Freesurfer] freeview (visualize pial and white surface)

2023-08-04 Thread DS

External Email - Use Caution

Hi expert,
Yes, sure. I sent both lh.pial and lh.white files, but the automatic reply 
email showed "two files are being held until the list moderator can review it 
for approval". Hopefully, you will get both files soon. Please let me know if 
you did not receive these files. Thank you so much.













At 2023-08-04 04:10:42, "Wang, Ruopeng"  wrote:

External Email - Use Caution

Would it be possible to send us the two surface files?
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of DS 
Sent: Thursday, August 3, 2023 3:30:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview (visualize pial and white surface)
 

External Email - Use Caution

Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.




../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.




But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized. 




Do you have any thoughts about this issue? Thank you so much for any 
suggestions.


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Re: [Freesurfer] freeview (visualize pial and white surface)

2023-08-03 Thread Wang, Ruopeng

External Email - Use Caution

Would it be possible to send us the two surface files?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of DS 
Sent: Thursday, August 3, 2023 3:30:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview (visualize pial and white surface)

External Email - Use Caution

Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.

../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.

But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized.

Do you have any thoughts about this issue? Thank you so much for any 
suggestions.

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[Freesurfer] freeview (visualize pial and white surface)

2023-08-03 Thread DS

External Email - Use Caution

Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.




../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.




But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized. 




Do you have any thoughts about this issue? Thank you so much for any 
suggestions.


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Re: [Freesurfer] Freeview sudden termination

2023-08-02 Thread Wang, Ruopeng

External Email - Use Caution

.ctab is not an annotation file. Please try loading .annot files.

Ruopeng

On Aug 1, 2023, at 10:50 PM, Jacob Bunyamin
mailto:jacob.bunya...@monash.edu>> wrote:

External Email - Use Caution

Hi,

I am running freesurfer/7.3.2 and had an issue with freeview sudden
termination. The error message is

sub-002/label/aparc.annot.ctab
MRISreadAnnotationIntoArray: vertex index out of range: 538980362 i=2020300A,
in_array_size=132205
annot file:
/fs04/wr47/Project/Data/NIFTI/Freesurfer7.3.2/sub-002/label/aparc.annot.ctab
terminate called after throwing an instance of 'int'

It happened when I tried to load any annotation. I can load pial surfaces. I
worked in a cluster computer if that helps.

Thank you,

Kind regards,

Jacob
--
Jacob Bunyamin
PhD Student

Department of Neuroscience
Central Clinical School, Monash University
99 Commercial Road
Melbourne VIC 3004
E: jacob.bunya...@monash.edu
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.
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[Freesurfer] Freeview sudden termination

2023-08-01 Thread Jacob Bunyamin

External Email - Use Caution

Hi,

I am running freesurfer/7.3.2 and had an issue with freeview sudden
termination. The error message is


*sub-002/label/aparc.annot.ctabMRISreadAnnotationIntoArray: vertex index
out of range: 538980362 i=2020300A, in_array_size=132205*

*annot file:
/fs04/wr47/Project/Data/NIFTI/Freesurfer7.3.2/sub-002/label/aparc.annot.ctab*
*terminate called after throwing an instance of 'int'*

It happened when I tried to load any annotation. I can load pial surfaces.
I worked in a cluster computer if that helps.

Thank you,

Kind regards,

Jacob
-- 

*Jacob Bunyamin*

PhD Student


*Department of Neuroscience*

Central Clinical School, Monash University

99 Commercial Road

Melbourne VIC 3004

*E:* jacob.bunya...@monash.edu
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[Freesurfer] Freeview update for FS v6.0.0 on MacOS

2023-08-01 Thread Ha Manh Luu

External Email - Use Caution

Hello FreeSurfer Developers,



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).



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



I updated the latest freeview from this website:

https://secure-web.cisco.com/1GU54Krzar0viM1rYGXBq6dM7Sopf4ca6PYKueDS2-Ie8DsE96VUl5LU3kqCMNoKZeswnOMS0jLc5T-ucVsaRFDWnAIb0XlYokynDhdMEXB4vlwkfAsvfdaddpfTUoTIQnY7G0P8MnccLLGcpswqYbfshIcSdmpkgxmsOFHKfUW2V4cavb8aLnhsZiKwOAcm6BPUlTezu3gvNOR6eRFuP4fpaxoEI92VgCHTVqWQy7fjv2FVk52M2g4Aq7BJz0xZdbUP4MdopUiu0AHcm7Mh59a2d1mIWD8u3MOmxK3zWZUwOao4VRwJgLv8duxf6X3JuJfncqDznwRam8dWg-DBd5Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Ffreeview%2F


freesurfer-macOS-darwin_x86_64-dev-freeview.tar.gz
2023-07-29 08:52
37M





After updating the Freeview, it works for me but whenever I load a pial 
surface, I got this error message:


error: mincRead(): error reading volume from file 
/Applications/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc


I'm not sure this is serious or just relating to the rendering. Could anyone 
tell me how to fix this?



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

  2)  Platform: MacOS Darwin 12.6.7

  3)  freeview:  mincRead(): error reading volume from file 
/Applications/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc

  4)  FreeSurferColorLUT.txt: see attached



Thanks,

Ha

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

2023-07-31 Thread 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:


External Email - Use Caution



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....

2023-07-27 Thread 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....

2023-07-27 Thread 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 surface edgecolor overlay

2023-05-05 Thread Wang, Ruopeng

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This has been fixed in the dev build and the upcoming v7.4. You can update 
freeview following the instructions here:

https://secure-web.cisco.com/18RRIlfW8orAdONb8bSqGWriHwtoXhuC4U82129GHMM_ruuytXnN2a6KWWjlLZPYgJJgaLAPAebhHEwEu_enRieQsuAiHgjrI5TFZsd14HjyDNbjRBAyM-Aws2CLj3Qc-In25GKqI80tFV9ZKSvrKP41EjoO_0FpiAgX99Lr9RX60ZT1G9_XuvSCw4_-jtVNbsrstjnV2Cyp7B1dBgMPdkmKi9CgIiRD6zXUezj0PFPXt1ElXSg3AlcsfIitmFzODs15Dxo_ocqdHuKiUTxVhVQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview

Ruopeng

On May 5, 2023, at 3:54 AM, Dr. Cornelius Kronlage 
mailto:cornelius.kronl...@med.uni-tuebingen.de>>
 wrote:

   External Email - Use Caution

Dear freesurfer team,

in freeview, setting surface edgecolor in axial/saggital/coronal slices to the 
overlay color seems to have stopped working between 7.1.1 and 7.2.0 (and up 
until 7.3.2). This might have been fixed in the development version meanwhile, 
but I couldn't find anything on the list. To reproduce:

recon-all --version
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
cd $SUBJECTS_DIR
freeview -f 
fsaverage/surf/lh.pial:overlay=fsaverage/surf/lh.thickness:edgecolor=overlay 
--viewport axial
# edge color is color according to overlay data as expected

recon-all --version
freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
cd $SUBJECTS_DIR
freeview -f 
fsaverage/surf/lh.pial:overlay=fsaverage/surf/lh.thickness:edgecolor=overlay 
--viewport axial
# edge color is black

Best wishes
Cornelius



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[Freesurfer] freeview surface edgecolor overlay

2023-05-05 Thread Dr. Cornelius Kronlage

External Email - Use Caution

Dear freesurfer team,

in freeview, setting surface edgecolor in axial/saggital/coronal slices to the 
overlay color seems to have stopped working between 7.1.1 and 7.2.0 (and up 
until 7.3.2). This might have been fixed in the development version meanwhile, 
but I couldn't find anything on the list. To reproduce:
 
>recon-all --version
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
>cd $SUBJECTS_DIR
>freeview -f 
>fsaverage/surf/lh.pial:overlay=fsaverage/surf/lh.thickness:edgecolor=overlay 
>--viewport axial
># edge color is color according to overlay data as expected

>recon-all --version
freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
>cd $SUBJECTS_DIR
>freeview -f 
>fsaverage/surf/lh.pial:overlay=fsaverage/surf/lh.thickness:edgecolor=overlay 
>--viewport axial
># edge color is black

Best wishes
Cornelius



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Re: [Freesurfer] freeview rh and lh overlay_mask files both showing in the lh hemisphere

2023-05-01 Thread Wang, Ruopeng

External Email - Use Caution

Would it be possible to send us the surface and the overlay and mask files so I 
can replicate the issue?

Ruopeng

On Apr 16, 2023, at 9:18 PM, Jewelia Karina Yao 
mailto:jewelia...@stanford.edu>> wrote:

External Email - Use Caution

Hi FreeSurfer Developers,

I'm trying to use freeview to load the rh and lh inflated surfaces together 
with overlays and overlay masks. I'm able to this separately and successfully 
for each hemisphere, but when I try to load the hemispheres together, both of 
the overlay_mask files show up on the left hemisphere and not the right 
hemisphere. The following is the command I'm using:

freeview -f 
${SUBJECTS_DIR}/${SUBJECT}/surf/rh.inflated:curvature_method=binary:overlay=rh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/rh.ve_20pct.thresh.label
 \
-f 
${SUBJECTS_DIR}/${SUBJECT}/surf/lh.inflated:curvature_method=binary:overlay=lh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/lh.ve_20pct.thresh.label

I've tried running this with 7.1.1 and 7.2.0 on Mac 10.15.7 and Linux w/Ubuntu 
22.04 but still run into the same issue.

Let me know if there's something I'm missing or if there's a better way to 
troubleshoot.

Thanks!
Jewelia
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[Freesurfer] freeview rh and lh overlay_mask files both showing in the lh hemisphere

2023-04-16 Thread Jewelia Karina Yao

External Email - Use Caution

Hi FreeSurfer Developers,

I'm trying to use freeview to load the rh and lh inflated surfaces together 
with overlays and overlay masks. I'm able to this separately and successfully 
for each hemisphere, but when I try to load the hemispheres together, both of 
the overlay_mask files show up on the left hemisphere and not the right 
hemisphere. The following is the command I'm using:

freeview -f 
${SUBJECTS_DIR}/${SUBJECT}/surf/rh.inflated:curvature_method=binary:overlay=rh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/rh.ve_20pct.thresh.label
 \
-f 
${SUBJECTS_DIR}/${SUBJECT}/surf/lh.inflated:curvature_method=binary:overlay=lh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/lh.ve_20pct.thresh.label

I've tried running this with 7.1.1 and 7.2.0 on Mac 10.15.7 and Linux w/Ubuntu 
22.04 but still run into the same issue.

Let me know if there's something I'm missing or if there's a better way to 
troubleshoot.

Thanks!
Jewelia
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Re: [Freesurfer] Freeview segmentation fault

2023-04-04 Thread fsbuild

External Email - Use Caution

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 
fromhttps://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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--
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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

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  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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>  <
> https://secure-web.cisco.com/1kurZNq7_SQcUnJIvTCyEXe3KDuplqUnbEpAOqULdXyXBMK9B8lvT6614BUqzsneplVHKnov062Ve_bnks_dCGYeA5fFVDAGwjGphliCOybAwMTK_jBlgqv1vrY3WWCIpEhgKSTFwfgRy9EY30M6N0XcwISaRzwfXtz2yPula92357kCV2CDVRS0V-HzHFgwLo3nggAZaNn5AV89qxSezhIicyPMc5bNsjADAp7KOtrvkmQIrHatUcIVPZCFIzGcZr1kgllb2zSUkfij0pVFrduHPNITbWigZVFeLQMbZF1ZKUbCWic_2UMePaNdMWpQf63CkolD_IDKrSMqBrYA5kg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
> 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.
>


-- 
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

2023-04-04 Thread OSE KADIRI

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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Re: [Freesurfer] Freeview error

2023-03-15 Thread 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


External Email - Use Caution
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

2023-03-15 Thread 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

2023-03-15 Thread 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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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail.

[Freesurfer] Freeview error

2023-03-14 Thread 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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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 
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview error

2023-03-13 Thread 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

2023-03-10 Thread 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 Edit options restricted

2023-03-07 Thread Carlos Alcocer

External Email - Use Caution

Also is it possible to not archive or not include email signature on that
reply email. didn't mean to have my email signature on there

On Tue, Mar 7, 2023 at 12:30 PM Carlos Alcocer  wrote:

> Thank you for your prompt response. Yes, while it does not show the brush
> size and certain menu options being grayed out, when I hover the cursor
> over these options the cursor becomes grayed out and it does not let me
> click on any options. For example if I clicked the brush size nothing would
> happen.
>
> Thank you,
>
> Carlos
>
> On Tue, Mar 7, 2023 at 12:11 PM Wang, Ruopeng 
> wrote:
>
>> Recon Edit mode will disable a few options. But it looks to me the Brush
>> Size is not grayed out from your screenshot.
>>
>> To close the window, you can just switch to Navigate mode.
>>
>> Ruopeng
>>
>> On Mar 7, 2023, at 11:34 AM, Carlos Alcocer  wrote:
>>
>> External Email - Use Caution
>>
>> Hello,
>>
>> When I try to do recon-edit, it does not let me click on certain options
>> ie. changin the brush size. It additionally doesnt let me exit out of or
>> minimize it. I am running the most recent version of freesurfer (7.3.2) on
>> linux (wsl). I reinstalled/updated freeview but this did not resolve the
>> issue. I have attached screen shot below. You cant see cursor but if i were
>> to hover over brush size for example, the cursor would be a light gray and
>> not let mec change any of the options.
>>
>> 
>>
>> Thank you,
>>
>> Carlos
>>
>>
>>
>> ___
>> Freesurfer mailing list
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>>
>>
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>> Brigham Compliance HelpLine at
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>>  <
>> https://secure-web.cisco.com/1EVuiSbIS8ZB2ujtBmbigtVSQ3ljSq81_T8F1svQqansl3IPh-kT9rQ9gDjpgXlI2vEw-SVuHDG9_oTwoo9lukJyShICX62zHc5Nt6IeU2Kon1XRt6EzF84UZan2C0VFBNn6p46Fy4wjvUl-56NYPnr4jb6BLYLxGPHteTXQPVGCegSbZRUpNhuZWuPN6uvxQYXSTylRKUDySSlgCUnf6doB8BRsFHLEQryUlx7Hdde4t4rzRTwAeNCGYw5-cGdnYdNBwveNdmAoVVwF6ytqh31krOkGGquU-z26imF2coHIqhzaW3gQ8ktlSTf1V-OU3f8BSQE0dj2PVifWxMvZO1w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
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>>
>
>
>
>
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continue

Re: [Freesurfer] Freeview Edit options restricted

2023-03-07 Thread Carlos Alcocer

External Email - Use Caution

Thank you for your prompt response. Yes, while it does not show the brush
size and certain menu options being grayed out, when I hover the cursor
over these options the cursor becomes grayed out and it does not let me
click on any options. For example if I clicked the brush size nothing would
happen.

Thank you,

Carlos

On Tue, Mar 7, 2023 at 12:11 PM Wang, Ruopeng 
wrote:

> Recon Edit mode will disable a few options. But it looks to me the Brush
> Size is not grayed out from your screenshot.
>
> To close the window, you can just switch to Navigate mode.
>
> Ruopeng
>
> On Mar 7, 2023, at 11:34 AM, Carlos Alcocer  wrote:
>
> External Email - Use Caution
>
> Hello,
>
> When I try to do recon-edit, it does not let me click on certain options
> ie. changin the brush size. It additionally doesnt let me exit out of or
> minimize it. I am running the most recent version of freesurfer (7.3.2) on
> linux (wsl). I reinstalled/updated freeview but this did not resolve the
> issue. I have attached screen shot below. You cant see cursor but if i were
> to hover over brush size for example, the cursor would be a light gray and
> not let mec change any of the options.
>
> 
>
> Thank you,
>
> Carlos
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1Zv0JOGWoVT48_p01idKqhWA7fqj0bQj1bmD7aZ6f42ucpiWe2fLjfzZUetGyUtd3LakLSf7L3YMrMZMOdM9Zjx42F7Fn9U81gyNBVWdNkEdRy7355SOrf65f5Hjg8nVVQJDTlyGtUSxUTfwSBTB9f0c1CoOdGZD6gLJYd6UZf3q6IAzFk7KqLlMh965SmgiaKgvLvFTVbOOXDwhSmzbtRKpOkIBMaRX1oU8X6gVlav2uhRxWw6gQdTUg1dDsseA_GkPdQ5qC1U0Gej-DTyC-j_3Yj37QvssIR5Gb5JrSh4hfSJvgsrrAt7bTNk0c0DvfXTpr79hzOcMjW1d4G3s9zQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
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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://secure-web.cisco.com/1DJnG5jkc__W-1VLDfd-LdLL1-TBZriL4QP1zU-4_NSdxmfXoU6Wfj5voOZ7NGPiwdvC-pT9maE2ktFg2huJBH4SqNXyNRrZPqjX-nM2qhhVMQ-UvQzrrfUGGkjB4lVHedwHfC3kfC4YJysaDgEqwt53YcFm8NtNTku9sm5qHrBl3-lX-TYFgwwHRJPYd48VaD6tOb2gVnBwLms2i0m1eQFDAnydpHJytoCeLMeCemTJQDXhDn_eEkwITaZ4-2qrXb4mCf6DPtIarQgFju0tKMDYS_YXh0-ZL1mKCZ2nzPZekFhSChpown4hfcw3YbCMa3A25stcXq0Q90F90KJLezg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1DJnG5jkc__W-1VLDfd-LdLL1-TBZriL4QP1zU-4_NSdxmfXoU6Wfj5voOZ7NGPiwdvC-pT9maE2ktFg2huJBH4SqNXyNRrZPqjX-nM2qhhVMQ-UvQzrrfUGGkjB4lVHedwHfC3kfC4YJysaDgEqwt53YcFm8NtNTku9sm5qHrBl3-lX-TYFgwwHRJPYd48VaD6tOb2gVnBwLms2i0m1eQFDAnydpHJytoCeLMeCemTJQDXhDn_eEkwITaZ4-2qrXb4mCf6DPtIarQgFju0tKMDYS_YXh0-ZL1mKCZ2nzPZekFhSChpown4hfcw3YbCMa3A25stcXq0Q90F90KJLezg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
> 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.
>


-- 
Carlos Alcocer
B.A. Neurobiology and Behavior, Cornell University, 2019
818-746-0302
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 .
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 Edit options restricted

2023-03-07 Thread Wang, Ruopeng

Recon Edit mode will disable a few options. But it looks to me the Brush Size 
is not grayed out from your screenshot.

To close the window, you can just switch to Navigate mode.

Ruopeng

On Mar 7, 2023, at 11:34 AM, Carlos Alcocer 
mailto:cd...@cornell.edu>> wrote:


External Email - Use Caution

Hello,

When I try to do recon-edit, it does not let me click on certain options ie. 
changin the brush size. It additionally doesnt let me exit out of or minimize 
it. I am running the most recent version of freesurfer (7.3.2) on linux (wsl). 
I reinstalled/updated freeview but this did not resolve the issue. I have 
attached screen shot below. You cant see cursor but if i were to hover over 
brush size for example, the cursor would be a light gray and not let mec change 
any of the options.



Thank you,

Carlos



___
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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 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 Edit options restricted

2023-03-07 Thread Carlos Alcocer

External Email - Use Caution

Hello,

When I try to do recon-edit, it does not let me click on certain options
ie. changin the brush size. It additionally doesnt let me exit out of or
minimize it. I am running the most recent version of freesurfer (7.3.2) on
linux (wsl). I reinstalled/updated freeview but this did not resolve the
issue. I have attached screen shot below. You cant see cursor but if i were
to hover over brush size for example, the cursor would be a light gray and
not let mec change any of the options.

[image: image.png]

Thank you,

Carlos
___
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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.

Re: [Freesurfer] Freeview displaying images in the wrong orientation

2023-02-27 Thread Nathan Kindred (PGR)

External Email - Use Caution

That worked, thank you so much!

Best,
Nathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Date: Monday, 27 February 2023 at 15:38
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview displaying images in the wrong orientation
Freeview by default will display the image in its original pixel space, without 
re-sampling. You can try the -r flag to enable the resampling like this:

freeview foo.mgz -r -cubic

Ruopeng


On Feb 27, 2023, at 7:04 AM, Nathan Kindred (PGR) 
mailto:n.kindr...@newcastle.ac.uk>> wrote:

External Email - Use Caution

Hi,

Apologies for the delay, please find attached a screenshot of an example image 
in orient_mri and the same image in freeview.

Best,
Nathan

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Date: Wednesday, 22 February 2023 at 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview displaying images in the wrong orientation
⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Can you send us a screenshot or even better, a sample image file?

Ruopeng

> On Feb 22, 2023, at 7:34 AM, Nathan Kindred (PGR) 
> mailto:n.kindr...@newcastle.ac.uk>> wrote:
>
>External Email - Use Caution
>
> Hi,
>
> When I am displaying certain images in freeview the orientation does not 
> match what is displayed in both orient_mri and SPM. The coronal and 
> horizontal views seems to be okay but the midsagittal view is often wrong 
> with the front of the brain tilted up. How do I get freeview to display the 
> images in the correct orientation?
>
> Thanks,
> Nathan
>
>
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Re: [Freesurfer] Freeview displaying images in the wrong orientation

2023-02-27 Thread Wang, Ruopeng

Freeview by default will display the image in its original pixel space, without 
re-sampling. You can try the -r flag to enable the resampling like this:

freeview foo.mgz -r -cubic

Ruopeng

On Feb 27, 2023, at 7:04 AM, Nathan Kindred (PGR) 
mailto:n.kindr...@newcastle.ac.uk>> wrote:

External Email - Use Caution

Hi,

Apologies for the delay, please find attached a screenshot of an example image 
in orient_mri and the same image in freeview.

Best,
Nathan

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Date: Wednesday, 22 February 2023 at 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview displaying images in the wrong orientation
⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Can you send us a screenshot or even better, a sample image file?

Ruopeng

> On Feb 22, 2023, at 7:34 AM, Nathan Kindred (PGR) 
> mailto:n.kindr...@newcastle.ac.uk>> wrote:
>
>External Email - Use Caution
>
> Hi,
>
> When I am displaying certain images in freeview the orientation does not 
> match what is displayed in both orient_mri and SPM. The coronal and 
> horizontal views seems to be okay but the midsagittal view is often wrong 
> with the front of the brain tilted up. How do I get freeview to display the 
> images in the correct orientation?
>
> Thanks,
> Nathan
>
>
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Re: [Freesurfer] Freeview displaying images in the wrong orientation

2023-02-22 Thread Wang, Ruopeng

Can you send us a screenshot or even better, a sample image file?

Ruopeng

> On Feb 22, 2023, at 7:34 AM, Nathan Kindred (PGR) 
>  wrote:
> 
>External Email - Use Caution
> 
> Hi,
> 
> When I am displaying certain images in freeview the orientation does not 
> match what is displayed in both orient_mri and SPM. The coronal and 
> horizontal views seems to be okay but the midsagittal view is often wrong 
> with the front of the brain tilted up. How do I get freeview to display the 
> images in the correct orientation?
> 
> Thanks,
> Nathan
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Freeview displaying images in the wrong orientation

2023-02-22 Thread Nathan Kindred (PGR)

External Email - Use Caution

Hi,

When I am displaying certain images in freeview the orientation does not match 
what is displayed in both orient_mri and SPM. The coronal and horizontal views 
seems to be okay but the midsagittal view is often wrong with the front of the 
brain tilted up. How do I get freeview to display the images in the correct 
orientation?

Thanks,
Nathan


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continue to communicate over unencrypted e-mail.

[Freesurfer] Freeview Installation Error

2023-02-14 Thread Carlos Alcocer

External Email - Use Caution

Hi,

I have been trying to install FreeSurfer and I went to test out the
freeview command but received the following error.

freeview: error while loading shared libraries: libGL.so.1: cannot open
shared object file: No such file or directory

I am unsure how to proceed.

Thank you,

Carlos
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Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

2023-02-09 Thread fsbuild

External Email - Use Caution

When you say you are running Mojave, I think you probably meant to write
10..14.6 (not 10.16.6).
You could check you have the latest version of XQuartz (2.8.5) installed
from,https://secure-web.cisco.com/11eALbuyxL0_txSil8AchFZPgix3GCpAuJbqcYDFJFtJt6F-kBaf9JU5a338EKemH6N8VWFBwwDAwLWuuQJkh2SpdmbjcCUa76MdxUsBf1e_Cn3t1OtIUBfxrHP25IKD9WR6MAbUjPnX32kYdki8uhdNtqBeX1ROEXkPb3jlB_CZmEhuI3qIaYUx6FLN0oI9P6qQpP8MfUn1MD-hv2gomxH2sQkzNtqWuw6oLLHKAQxmo4cFHuvYa709L7ZZ0Qi89X11sEtAAVLwbOgucQ-Aon2ovVKDrSd9ZWLsERG05Q--yi2OKSN1wvIzUiHNQbzBQSeuSsxJ0-cy4wI8tCvNDwQ/https%3A%2F%2Fwww.xquartz.org%2F
You may need to reboot the machine after installing Xquartz.
Once back up, open a new terminal window and run the bash shell,
$ bash
Try putting your license file, e.g., license.txt. in your $HOME directory, and
then set the environment variable FS_LICENSE to its absolute path, e.g.
$ cd $HOME$ head -1 license.tx...@somewhere.org. —— email address you
used to register with
$ export FS_LICENSE=$HOME/license.txt$ head -1 $fs_licens...@somewhere.org.
—— email address you used to register with
Then the usual setup,$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$
source $FREESURFER_HOME/SetUpFreeSurfer.sh
Then try opening an empty Freeview window again,$ freeview
- R.
On Feb 8, 2023, at 14:28, Rankin McGugin rankin.mcgu...@gmail.com
wrote:freeview_2023-02-08-122744_Rankins-MacBook-Pro.crash
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Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

2023-02-09 Thread Wang, Ruopeng

Can you try the latest dev build from here?
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Ruopeng

On Feb 8, 2023, at 2:28 PM, Rankin McGugin 
mailto:rankin.mcgu...@gmail.com>> wrote:


External Email - Use Caution

of course, see attached



Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644


On Wed, Feb 8, 2023 at 1:22 PM Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>> wrote:
Would it be possible to send us the full crash report? You can find it in the 
Console app.

Best,
Ruopeng

On Feb 8, 2023, at 1:48 PM, Rankin McGugin 
mailto:rankin.mcgu...@gmail.com>> wrote:


External Email - Use Caution

Here is my error log:

Last login: Wed Feb  8 12:03:23 on ttys000
Rankins-MacBook-Pro:~ rankinmcgugin$ export 
FREESURFER_HOME=/Applications/freesurfer/7.3.2
Rankins-MacBook-Pro:~ rankinmcgugin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME   /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR   /Applications/freesurfer/7.3.2/mni
Rankins-MacBook-Pro:~ rankinmcgugin$
Rankins-MacBook-Pro:~ rankinmcgugin$ which freeview
/Applications/freesurfer/7.3.2/bin/freeview
Rankins-MacBook-Pro:~ rankinmcgugin$ freeview
/Applications/freesurfer/7.3.2/bin/freeview: line 2:  1592 Segmentation fault: 
11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Rankins-MacBook-Pro:~ rankinmcgugin$



Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644


-- Forwarded message -
From: Rankin McGugin mailto:rankin.mcgu...@gmail.com>>
Date: Wed, Feb 8, 2023 at 12:47 PM
Subject: Freeview 'quit unexpectedly' before opening
To: mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello,

I am a longtime FS user. I have read threads on this topic but no suggestions 
work in my case.  I have the license file in place. I removed my previous 
version of FS and have updated to 7.3.2.  However, now when I try to start 
Freeview, I get this problem report before the app even opens:

I have tried downloading the standalone Freeview, but get the same error.  I 
have restarted the computer, completely removed everything and redownloaded it, 
but still the same issue persists.
I am using macOS Mojave, 10.16.6
Are you able to guide me how to fix this and open Freeview?

Thank you!

Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644
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Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

2023-02-08 Thread Wang, Ruopeng

Would it be possible to send us the full crash report? You can find it in the 
Console app.

Best,
Ruopeng

On Feb 8, 2023, at 1:48 PM, Rankin McGugin 
mailto:rankin.mcgu...@gmail.com>> wrote:


External Email - Use Caution

Here is my error log:

Last login: Wed Feb  8 12:03:23 on ttys000
Rankins-MacBook-Pro:~ rankinmcgugin$ export 
FREESURFER_HOME=/Applications/freesurfer/7.3.2
Rankins-MacBook-Pro:~ rankinmcgugin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME   /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR   /Applications/freesurfer/7.3.2/mni
Rankins-MacBook-Pro:~ rankinmcgugin$
Rankins-MacBook-Pro:~ rankinmcgugin$ which freeview
/Applications/freesurfer/7.3.2/bin/freeview
Rankins-MacBook-Pro:~ rankinmcgugin$ freeview
/Applications/freesurfer/7.3.2/bin/freeview: line 2:  1592 Segmentation fault: 
11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Rankins-MacBook-Pro:~ rankinmcgugin$



Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644


-- Forwarded message -
From: Rankin McGugin mailto:rankin.mcgu...@gmail.com>>
Date: Wed, Feb 8, 2023 at 12:47 PM
Subject: Freeview 'quit unexpectedly' before opening
To: mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello,

I am a longtime FS user. I have read threads on this topic but no suggestions 
work in my case.  I have the license file in place. I removed my previous 
version of FS and have updated to 7.3.2.  However, now when I try to start 
Freeview, I get this problem report before the app even opens:

I have tried downloading the standalone Freeview, but get the same error.  I 
have restarted the computer, completely removed everything and redownloaded it, 
but still the same issue persists.
I am using macOS Mojave, 10.16.6
Are you able to guide me how to fix this and open Freeview?

Thank you!

Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644
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[Freesurfer] Freeview 'quit unexpectedly' before opening

2023-02-08 Thread Rankin McGugin

External Email - Use Caution

Hello,

I am a longtime FS user. I have read threads on this topic but no
suggestions work in my case.  I have the license file in place. I removed
my previous version of FS and have updated to 7.3.2.  However, now when I
try to start Freeview, I get this problem report before the app even opens:
[image: image.png]
I have tried downloading the standalone Freeview, but get the same error.
I have restarted the computer, completely removed everything and
redownloaded it, but still the same issue persists.
I am using macOS Mojave, 10.16.6
Are you able to guide me how to fix this and open Freeview?

Thank you!


*Rankin W. McGugin, PhD *Research Assistant Professor

Department of Psychology

Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu

work phone: (615) 322-4644
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Re: [Freesurfer] freeview: set file as read only (@Ruopeng)

2023-01-12 Thread Douglas N. Greve


Not that I know of. Ruopeng would know for sure.



On 1/7/2023 5:00 PM, Aaron Tanenbaum wrote:


External Email - Use Caution

Hello,
Is there a way to set a loaded volume as read only in freeview on the 
command line?


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Re: [Freesurfer] Freeview label thickness: making the label outline thicker?

2023-01-08 Thread Wang, Ruopeng

That edge thickness is for the intersecting outlines on the 2D slices. There is
no settings for outline thickness for labels.

Best,

Ruopeng

On Jan 8, 2023, at 10:58 AM, Greta Tuckute
mailto:gret...@mit.edu>> wrote:

Hi developers,
I am using Freeview to plot overlays on inflated surfaces with labels:
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=OVERLAY_NAME.mgh:overlay_color=colorwheel,inverse,truncate:overlay_threshold=1,5:label=lh.primary.label:label_outline=1:label_color=0,0,0
This command will nicely plot the left fsaverage surface with the overlay of
interest as well as the label in a black outline. My question is: the label
outline is incredibly thin. I can’t seem to find a command line flag that
adjusts this? In the Freeview GUI, there is a place to adjust “Edge thickness”
but no matter which value I try, it does not have any effect. Is there any way
to do this?
Attached Freeview screenshot and label file for reference.

Thanks so much for all your great work,
Greta

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Re: [Freesurfer] freeview: set file as read only

2023-01-07 Thread fsbuild

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You could try the usual file system commands to set permissions before opening, 
e.g., read only,
$ chmod 444 myvolume.mgz
Or on the command line prior to running freeview,

$ chmod 444 myvolume.mgz  freeview myvolume.mgz
You could put commands like those into a script with the file name as an 
argument.
- R.On Jan 7, 2023, at 17:00, Aaron Tanenbaum 
aaron.b.tanenb...@gmail.com 
wrote:External Email - Use 
CautionHello,Is there a way to 
set a loaded volume as read only in freeview on the command 
line?___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] freeview: set file as read only

2023-01-07 Thread Aaron Tanenbaum

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Hello,
Is there a way to set a loaded volume as read only in freeview on the
command line?
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Re: [Freesurfer] freeview quit unexpectedly on Mac OS M1

2023-01-03 Thread fsbuild

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Please try the following with the latest 7.3.2 release. The release page 
ishttps://secure-web.cisco.com/19K4NxhUlkogZZJ6mlyOImaI2Y4zmXjc6dwibN7nIQsfe_lWxinx40Flxvt9NeD5PMIt1r22ojFGIVQ1V-4Pb5nXsf43uRLNcvEq3QUVVNGyMjhCE8aoZmd-PLKwM9S0t5jcIBbw275wC0OF4OVV9QvWqkGRb65ofEj0Y3FuorMiG2bM8Gm1JDclitrKVNlGjXyOxE2G1wVVHF9W1ggVMQtkB7yooZle77Tp4dPP5Tq1ZpwXb5Zc46RWSryn1r55rnwlmfob_w_N5NBN8j878dj4Rak7e13PGX7hQWkR6Sr4sFdY_GuC7QWz6hN9eFpz0bppmyZdL01yljWsAOoQNfw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%26nbsp;and
 the link to the .pkg file 
ishttps://secure-web.cisco.com/1Wx2_5nhoR76Fau-VOEeMoQVIQIDXjamvDF-EFBcqQyt6f80bHsZHLkjkoNhP2bb53qYGAHwFjCvIC6OKEfTYiXngx9HRC8FN9UtODT1c6OVwjwITwjAKua7h0Hd76ZwrN9_2Qj8awhCLQiWAMNEWoOn5G-yf8uB6A-z_Hj2G7LkBEjutSbSzjUc8QN20QSPu_xsfCI0RZT1LaBN79_RH-Yqgux6hILnLhtWzJ1E2De_kR_rgHRiXPFg06OE-HIoau12weC-viiokCAojj4oGPoCdUS8oE58tnJ3nsSuMWTMhy587XGiS49N1qqe2XpzEyOXChssxytV28DzVSAO5Fg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer-darwin-macOS-7.3.2.pkg
1) Install the 7.3.2 release listed above. It will be installed as 
/Applications/freesurfer/7.3.2
2) Open a new terminal window and run the bash shell as,
$arch -arm64 /bin/bash
3) Set FS_LICENSE to point to the license.txt file you downloaded after 
registering via the online form at 
https://secure-web.cisco.com/12TyPaJsjD6Q9mekQ3_jITFFbb2NrPRGCuk6aPL36fn1jheifoCfpGcSh1bw_WNdv4w4aLnuF6w0RDVne_ZMB-wHfjj1UQVf3zoKRzSQ9cBy_KM4TWxF6LN0QDfvUFadZnhn9wQ_qcIb3gu0ObbL01LxCN-29321oF7Sf3_WMkF8pXPEJblhbNePWgZ0lVxwYUGhpEEgkBupUrQ_2oqaoNJOij-nG3eLVKYz-mJ58PxbTNBK536TrzWWSFAzrt2mJ4wUX97kn-995k2RSXhakecmfDVCHPAq-j1X7ph4CAW2sMitK-5JZtyhRumobhFbMt2yjXXE9QqNtAThYZkVPvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
 For example, it could be in your home directory as $HOME/license.txt. 
It can be anywhere but you just have to set FS_LICENSE to its absolute 
path and test it can be read.
$ ls $HOME/license.txt/Users/your userid/license.txt$ export 
FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou@youremail.something 
 — email you used to register with
4) Setup the environment,
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220803-878457d Setting up 
environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME/Applications/freesurfer/7.3.2FSFAST_HOME
  /Applications/freesurfer/7.3.2/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR  
/Applications/freesurfer/7.3.2/subjectsMNI_DIR  
  /Applications/freesurfer/7.3.2/mni
5) Try running freeview from the command line w/o any arguments to see if it 
opens an empty window,
$ freeview
6) If that worked, quit freeview and then run freeview from the command 
line again to open one of the provided volumes in the 7.3.2 release,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
7) If that worked, then try running freeview from the command line on one of 
your own volume or surface files.
- R.
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[Freesurfer] freeview quit unexpectedly on Mac OS M1

2023-01-03 Thread Philipp Klar

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Hello FreeSurfer Developers,

I am trying to run freesurfer which works fine up to a certain point. 
For example, starting freesurfer and loading a template works fine. But 
when I try loading a surface, freesurfer suddenly crashes after loading 
around 50% of the file.
Hence, freesurfer starts fine, I can play around with it (a bit), but 
when loading certain files (the files are fine), the same error below 
comes up over and over again.

ERROR: freeview quit unexpectedly. (see below for the full error.)

1) FreeSurfer version: 7.1.1 (the same problem occurs with the newest 
version
2) Platform: Macbook M1 Ventura 13.1 (22C65)
3) XQuartz 2.8.4
4) I ran export FREESURFER_HOME=/Applications/freesurfer/7.1.1
source $FREESURFER_HOME/SetUpFreeSurfer.sh
5) The lisence.txt is copied into /Applications/freesurfer/7.1.1

Thank you for any advice,
Philipp



-
Translated Report (Full Report Below)
-

Process:   freeview [1003]
Path:  
/Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview
Identifier:com.freesurfer.freeview
Version:   ???
Code Type: X86-64 (Translated)
Parent Process:launchd [1]
User ID:   501

Date/Time: 2023-01-04 06:40:59.8418 +0100
OS Version:macOS 13.1 (22C65)
Report Version:12
Anonymous UUID:6C794FA2-0A28-9E00-8C0F-C5F42E1E1D41


Time Awake Since Boot: 200 seconds

System Integrity Protection: enabled

Crashed Thread:19  ThreadIOWorker

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x7f8c8bff0e60
Exception Codes:   0x0001, 0x7f8c8bff0e60

Termination Reason:Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process:   exc handler [1003]

VM Region Info: 0x7f8c8bff0e60 is not in any region.  Bytes after 
previous region: 141495905  Bytes before following region: 15790496
   REGION TYPESTART - END [ VSIZE] 
PRT/MAX SHRMOD  REGION DETAIL
   MALLOC_TINY  7f8c8380-7f8c8390 [ 1024K] 
rw-/rwx SM=PRV
--->  GAP OF 0x960 BYTES
   MALLOC_LARGE 7f8c8cf0-7f8c94f0 [128.0M] 
rw-/rwx SM=PRV

Thread 0::  Dispatch queue: com.apple.main-thread
0  0x11512ea40 ???
1  0x11512f3c8 ???
2   libsystem_malloc.dylib0x7ff8004dd2d9 
nanov2_allocate_outlined + 246
3   libsystem_malloc.dylib0x7ff8004dd8e1 
nanov2_malloc_zero_on_alloc + 521
4   libc++abi.dylib   0x7ff80062c95a operator 
new(unsigned long) + 26
5   QtGui0x11eb09154 
QBrush::init(QColor const&, Qt::BrushStyle) + 276
6   QtGui0x11eb0992d 
QBrush::QBrush(Qt::GlobalColor, Qt::BrushStyle) + 45
7   QtGui0x11ea84557 0x11e934000 + 
1377623
8   QtGui0x11ea7b1ea 0x11e934000 + 
1339882
9   QtGui0x11ea7bbf9 0x11e934000 + 
1342457
10  QtGui0x11ea7b39c 0x11e934000 + 
1340316
11  QtGui0x11eaaadea 0x11e934000 + 
1535466
12  QtGui0x11eaae5db 
QTextDocumentFragment::fromHtml(QString const&, QTextDocument const*) + 
107
13  QtGui0x11eaa8411 
QTextCursor::insertHtml(QString const&) + 257
14  QtWidgets0x11dda7787 0x11dba7000 + 
2099079
15  QtWidgets0x11dd7f0a3 
QTextEdit::append(QString const&) + 83
16  freeview 0x1027533da 0x1025dc000 + 
1536986
17  freeview 0x102753bd7 0x1025dc000 + 
1539031
18  QtCore   0x11fe278cc 
QMetaObject::activate(QObject*, int, int, void**) + 3132
19  QtCore   0x11fe2f432 
QTimer::timerEvent(QTimerEvent*) + 98
20  QtCore   0x11fe1fcf6 
QObject::event(QEvent*) + 102
21  QtWidgets0x11dbb770d 
QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
22  QtWidgets0x11dbb8b12 
QApplication::notify(QObject*, QEvent*) + 594
23  QtCore   0x11fdf6564 
QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
24  QtCore   0x11fe4fb7f 
QTimerInfoList::activateTimers() + 991
25  libqcocoa.dylib  0x11f652472 0x11f61e000 + 
214130
26  CoreFoundation0x7ff80074bee1 
__CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
27  CoreFoundation0x7ff80074be90 
__CFRunLoopDoSource0 + 157
28  CoreFoundation

Re: [Freesurfer] Freeview crashes after installing the software

2023-01-02 Thread fsbuild

External Email - Use Caution

Please try the following with the latest 7.3.2 release if you are not already 
running 7.3.2. The release page 
ishttps://secure-web.cisco.com/1zn1v_OOPT0MJ0XxXSk4mw5hbeQD4yegZ0PSsCscJtOJcydo9vVD5VUmGTrY3Zm39hgoZoJ_8Fs2NC1-RrBhwU5MuYy9HC4Dbd4ac2pO6HAnEs5CSlKgV5PjQNwphnQywoCwpQernA1sX6t_5VhR7ERjh-Iekm87Ktmw0xZ_5vCsCwwGW1dK9OmM-KGf5KLRBH6NWZwqaDIiQzxbnWbXl6mUsuB9kO1XRw-SfV7jBhdBOfax_OHh-qMlNyYaEUe6nhnV-s82ew4TakMxRXAXAFLeMWRfdflhx3DXi0ZiW5eigN-rLr-FqSPRjBiCWjeEPb7e5FTpXW8780XCQKaaxPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%26nbsp;and
 the link to the .pkg file 
ishttps://secure-web.cisco.com/17qSx4asejqc1SOr4BdhhxtQLAqSTPmbMEBpF2VdcKKTR98MrDOL9cy-yE3A7C6FLelbOazGLW6N18QT9QaO7zsBaKl4a86erUCAyJXmUTekta6JWnkVIMZLtIgvw6lpoS43M_THMRxcy1wRA7ndKivihtwGSogIVUlpNHSWQGfhmunmWlkCO0ftj_Va4tL4M-iNbjTv4cZKt4G5v1vzHn6n4hHquNL5zEXUsPih5wCfoJUcmLBST0IK2tTGd6Hh_brtcyl5iy0__m9vSl4wTRWBHA3ZRH1mHX4XE0rZFjTasHUmrSB8MowJVNZ_1pmgqkD-FSrJeD0gY2Amt5N3cbg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer-darwin-macOS-7.3.2.pkg
1) Install the 7.3.2 release listed above. It will be installed as 
/Applications/freesurfer/7.3.2
2) Open a new terminal window and run the bash shell as,
$arch -arm64 /bin/bash

3) Set FS_LICENSE to point to the license.txt file you downloaded after 
registering via the online form at 
https://secure-web.cisco.com/1hvYfe1hO7ZqQEnaogRQmpJSBSH4ZqL7YpQWNvh19EOSXJMdv1bgCL6uZ9uIy0IVXOqhB-yyF3Sf07qUGdaf4MrLczgOfe-2HgOKVuwPyjhb4_ZGAuMxliNafufQMBnFsyYLGXd6F6YRKMX-3rVA_WZX-jJCrvE09W68XAnZbQp8tksFlLbP8RunEajsG_qiftGpWap9xtAHKfzuZXSNEhCtwlnsmpj2fDcvzyUkkKdZnsUNmDceyCfpXJZx6ZVDDanSr6Eg0LMk0CXI6kldUo1rjpwzB4YinsxqPSgaFFVQ_vSlssVpZhACzB1ZitvPKjwOuu8qboyc14euNBwq8uQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
 For example, it could be in your home directory as $HOME/license.txt. 
It can be anywhere but you just have to set FS_LICENSE to its absolute 
path and test it can be read.
$ ls $HOME/license.txt/Users/your userid/license.txt$ export 
FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou@youremail.something 
 — email you used to register with
4) Setup the environment,
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220803-878457d 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.3.2
FSFAST_HOME  /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR
/Applications/freesurfer/7.3.2/mni

5) Try running freeview from the command line w/o any arguments to see if it 
opens an empty window,
$ freeview
6) If that worked, quit freeview and then run freeview from the command 
line again to open one of the provided volumes in the 7.3.2 release,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
7) If that worked, then try running freeview from the command line on one of 
your own volume or surface files.
- R.
On Dec 30, 2022, at 12:55, Seyedeh Nasim Adnani sza0...@auburn.edu 
wrote:External Email - Use 
CautionHello,I have a 
MacBook Pro with Ventura 13.1 OS, 64 GB, SMC Apple M1 Max.I recently started 
installing the freesurfer software but unfortunately, a simple volume loading 
into the freeview crashes without displaying any image.I have tried installing 
various python versions (2,3) and modifying the PATH but nothing seems to help. 
Now, I wonder if the software is compatible with my mac. Is there any way I can 
make it work on my system? Many thanks in advance for your 
help.Best,Nasim 
Adnani,Sza0127@auburn.edu___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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 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 crashes after installing the software

2022-12-30 Thread Seyedeh Nasim Adnani

External Email - Use Caution

Hello,

I have a MacBook Pro with Ventura 13.1 OS, 64 GB, SMC Apple M1 Max.
I recently started installing the freesurfer software but unfortunately, a 
simple volume loading into the freeview crashes without displaying any image.
I have tried installing various python versions (2,3) and modifying the PATH 
but nothing seems to help. Now, I wonder if the software is compatible with my 
mac. Is there any way I can make it work on my system? Many thanks in advance 
for your help.

Best,
Nasim Adnani,
sza0...@auburn.edu
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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-20 Thread Wang, Ruopeng

After you load the image from the command-line, can you then load more images 
from the GUI?

Ruopeng

On Dec 20, 2022, at 3:23 AM, Addison, Reuben 
mailto:raddi...@mghihp.edu>> wrote:

The answer to this is question ‘ opening an image from the gui ‘ is yes. The 
image only opens when I open from the command line

Reuben A.

Get Outlook for iOS<https://aka.ms/o0ukef>

From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Tuesday, December 20, 2022 7:56:12 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Addison, Reuben mailto:raddi...@mghihp.edu>>
Subject: Re: [Freesurfer] Freeview quit unexpectedly


External Email - Use Caution


By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview GUI 
Open-> pull down menu that you get the core dump listed below, but it works 
when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from the command 
line in the terminal window?

The core dump shows a memory allocation error on MacOSX.  Some postings 
indicate setting MallocNanoZone to zero before running your program/command can 
remedy this,

$ bash
$ export MallocNanoZone=0 && freeview

- but this may not work.   I don’t see any other workarounds for this right 
now.  I have not seen this error before with freeview on older versions of 
MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben 
mailto:raddi...@mghihp.edu>> wrote:

I updated the Xquartz yet still same issue. Freeview only works with the 
command line but the gui is till crashing.

Gkxgears seems to work fine

I have attached images of both the crash report and the graphics information 
about my mac.

Reuben A



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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-20 Thread Addison, Reuben

The answer to this is question ‘ opening an image from the gui ‘ is yes. The 
image only opens when I open from the command line

Reuben A.

Get Outlook for iOS<https://aka.ms/o0ukef>

From: fsbuild 
Sent: Tuesday, December 20, 2022 7:56:12 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Addison, Reuben 
Subject: Re: [Freesurfer] Freeview quit unexpectedly

External Email - Use Caution

By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview GUI 
Open-> pull down menu that you get the core dump listed below, but it works 
when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from the command 
line in the terminal window?

The core dump shows a memory allocation error on MacOSX.  Some postings 
indicate setting MallocNanoZone to zero before running your program/command can 
remedy this,

$ bash
$ export MallocNanoZone=0 && freeview

- but this may not work.   I don’t see any other workarounds for this right 
now.  I have not seen this error before with freeview on older versions of 
MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben  wrote:

I updated the Xquartz yet still same issue. Freeview only works with the 
command line but the gui is till crashing.

Gkxgears seems to work fine

I have attached images of both the crash report and the graphics information 
about my mac.

Reuben A

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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-19 Thread fsbuild

External Email - Use Caution

By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,  $SUBJECTS_DIR/bert/mri/brain.mgz, using the freeview 
GUI Open- pull down menu that you get the core dump listed below, but it 
works when your run “freeview$SUBJECTS_DIR/bert/mri/brain.mgz” from 
the command line in the terminal window?

The core dump shows a memory allocation error on MacOSX. Some postings 
indicate settingMallocNanoZone to zero before running your 
program/command can remedy this,
$ bash$export MallocNanoZone=0  freeview
- but this may not work.  I don’t see any other workarounds for this 
right now. I have not seen this error before with freeview on older 
versions of MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben raddi...@mghihp.edu wrote:I 
updated the Xquartz yet still same issue. Freeview only works with the command 
line but the gui is till crashing.Gkxgears seems to work 
fineI have attached images of both the crash report and the graphics 
information about my mac.Reuben A
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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-16 Thread fsbuild

External Email - Use Caution

I would downloaded and install the latest Xquartz (X-Windows for MacOS) which
is version 2.8.3
fromhttps://secure-web.cisco.com/1opXWtR1b08TpiSxuOjmZYBoO9MYN5pgHsuKLDmoCgQvIQKCE3eLuXMzAhun8yJwDohErdmiN2RaG1_YIuaBUhEqyEnJTavnVvR5HbqS2OIlTNV_aVeIJTge1UvCSpI_itW2lL10W-8V13eDdK_QIOzAeCpiyBwovrfkjBbMkKRHtTbvQg8EvkYE5PXN0VxEqoAPLTUYxEj6y-wSVVShky5YYJjCGFll6x37tCPR245N1zBFv4VFCjqx9iF3A0ogRTe0k___etyob1p0uKc8kUONjzb3L8RpzAgn1rQAZ1U4SCAHbKMHgTqUB9bQSpwoD7ORGeHBOfYHmkcKvFyyk0g/https%3A%2F%2Fwww.xquartz.org%2F%26nbsp;
This was updated only a week ago and contains universal binaries.
After you install Xquartz open a new terminal window and type “glxgears”.
An X-Window should pop up showing the spinning gears.
% which glxgears
/opt/X11/bin/glxgears
% glxgears
303 frames in 5.0 seconds = 60.564 FPS
309 frames in 5.0 seconds = 61.607 FPS
…...
… close glxgears window to exit ...
Then at least your X-Windows graphics will be up to date (which might affect
the GUI). Then try your image again.
Do you see any warnings, error, info, etc., listed in the terminal window after
the freeview command? If so, please send that along.
Maybe you could send along a screenshot of what “about this mac” displays.
That would tell us if you are using a graphics card or the built-in
graphics - and also a screenshot of the freeview window.
- R.

glxgears.png
Description: Binary data
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview quit unexpectedly

2022-12-16 Thread Addison, Reuben

Please ignore the previous email. Apparently when I type the command it works 
but the issue is with using the gui

Reuben A.

Get Outlook for iOS<https://aka.ms/o0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Addison, Reuben 

Sent: Friday, December 16, 2022 10:02:56 AM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Freeview quit unexpectedly


Thank you.

I tried the steps and it worked once.



Now I try opening the file and it keeps crushing

The only file that opens now without crushing  is “freeview 
$SUBJECTS_DIR/bert/mri/brain.mgz”



Reuben A.



From: fsbuild 
Date: Thursday, December 15, 2022 at 12:14 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Addison, Reuben 
Subject: Re: [Freesurfer] Freeview quit unexpectedly

External Email - Use Caution



Please try the following:



1)  Open a new terminal window and run the bash shell as,



$ arch -arm64 /bin/bash



2) set FS_LICENSE to point to your license.txt file.  Say it is in your home 
directory, e.g., $HOME/license.txt.  It can be anywhere but you just have to 
set FS_LICENSE to its absolute path and test it can be read.



$ ls $HOME/license.txt

/Users//license.txt

$ export FS_LICENSE=$HOME/license.txt

$ head -1 $FS_LICENSE

you@youremail.something<mailto:you@youremail.something> <— email you used 
to register with



3) setup the environment



$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh



 freesurfer-darwin-macOS-7.3.2-20220803-878457d 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME   /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR   /Applications/freesurfer/7.3.2/mni

4) Try running freeview w/o any arguments to see if it opens an empty window.



$ freeview



5)  If that worked,  quit freeview and then try running freeview to open one of 
the provided volumes in the 7.3.2 release,



$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz



5) If that worked, then try running freeview on your file again.



- R.


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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-16 Thread Addison, Reuben

Thank you.
I tried the steps and it worked once.

Now I try opening the file and it keeps crushing
The only file that opens now without crushing  is “freeview 
$SUBJECTS_DIR/bert/mri/brain.mgz”

Reuben A.

From: fsbuild 
Date: Thursday, December 15, 2022 at 12:14 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Addison, Reuben 
Subject: Re: [Freesurfer] Freeview quit unexpectedly

External Email - Use Caution

Please try the following:

1)  Open a new terminal window and run the bash shell as,

$ arch -arm64 /bin/bash

2) set FS_LICENSE to point to your license.txt file.  Say it is in your home 
directory, e.g., $HOME/license.txt.  It can be anywhere but you just have to 
set FS_LICENSE to its absolute path and test it can be read.

$ ls $HOME/license.txt
/Users//license.txt
$ export FS_LICENSE=$HOME/license.txt
$ head -1 $FS_LICENSE
you@youremail.something<mailto:you@youremail.something> <— email you used 
to register with

3) setup the environment

$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-darwin-macOS-7.3.2-20220803-878457d 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME   /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR   /Applications/freesurfer/7.3.2/mni
4) Try running freeview w/o any arguments to see if it opens an empty window.

$ freeview

5)  If that worked,  quit freeview and then try running freeview to open one of 
the provided volumes in the 7.3.2 release,

$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz

5) If that worked, then try running freeview on your file again.

- R.

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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-14 Thread fsbuild

External Email - Use Caution

Please try the following:
1) Open a new terminal window and run the bash shell as,
$arch -arm64 /bin/bash

2) set FS_LICENSE to point to your license.txt file. Say it is in your 
home directory, e.g., $HOME/license.txt. It can be anywhere but you just 
have to set FS_LICENSE to its absolute path and test it can be read.
$ ls $HOME/license..txt/Users/your userid/license.txt$ export 
FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou@youremail.something 
 — email you used to register with
3) setup the environment
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220803-878457d 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.3.2
FSFAST_HOME  /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR
/Applications/freesurfer/7.3.2/mni

4) Try running freeview w/o any arguments to see if it opens an empty window.
$ freeview
5) If that worked, quit freeview and then try running freeview to 
open one of the provided volumes in the 7.3.2 release,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
5) If that worked, then try running freeview on your file again.
- R.

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[Freesurfer] Freeview quit unexpectedly

2022-12-14 Thread Addison, Reuben

I am trying to use freeview to load a volume. I am using freesurfer 7.3.2 on 
the new M1 mac pro with ios ventura.

Please view below the error report I am getting.  Is there any work around it? 
I have tried different volumes but same issues

Translated Report (Full Report Below)
-

Process:   freeview [2225]
Path:  
/Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview
Identifier:com.freesurfer.freeview
Version:   ???
Code Type: X86-64 (Translated)
Parent Process:launchd [1]
User ID:   501

Date/Time: 2022-12-14 22:18:58.4199 +
OS Version:macOS 13.0.1 (22A400)
Report Version:12
Anonymous UUID:4DD80B35-B000-767B-D8E0-4CF3002E053F

Sleep/Wake UUID:   305334BF-BD70-4E02-B20F-D4316B1A93BB

Time Awake Since Boot: 16000 seconds
Time Since Wake:   10255 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x36da55ddc150
Exception Codes:   0x0001, 0x36da55ddc150

Termination Reason:Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process:   exc handler [2225]

VM Region Info: 0x36da55ddc150 is not in any region.  Bytes after previous 
region: 59830335029585  Bytes before following region: 45241744899760
  REGION TYPESTART - END [ VSIZE] PRT/MAX 
SHRMOD  REGION DETAIL
  commpage (reserved)10-70   [384.0G] ---/--- 
SM=NUL  ...(unallocated)
--->  GAP OF 0x5f90 BYTES
  MALLOC_NANO  6000-6800 [128.0M] rw-/rwx SM=PRV

Kernel Triage:
VM - pmap_enter retried due to resource shortage
VM - pmap_enter retried due to resource shortage
VM - pmap_enter retried due to resource shortage


Thread 0 Crashed::  Dispatch queue: com.apple.main-thread
0   libobjc.A.dylib0x7ff80d3b0959 
objc_storeWeak + 188
1   AppKit  0x7ff810895aaa -[NSWindow setDelegate:] 
+ 199
2   libqcocoa.dylib  0x11d003d31 0x11cfe1000 + 
142641
3   libqcocoa.dylib  0x11cffd672 0x11cfe1000 + 
116338
4   libqcocoa.dylib  0x11cffd0fe 0x11cfe1000 + 
114942
5   QtGui   0x11d622eb7 
QWindowPrivate::create(bool, unsigned long long) + 151
6   QtWidgets  0x11c26d771 
QWidgetPrivate::create() + 1185
7   QtWidgets  0x11c26c414 
QWidget::create(unsigned long long, bool, bool) + 324
8   QtWidgets  0x11c27f81d 
QWidgetPrivate::setVisible(bool) + 189
9   freeview  0x100a60ded 0x1009f7000 + 433645
10  QtCore   0x11ece1b9f 
QObject::event(QEvent*) + 943
11  QtWidgets0x11c280e9a 
QWidget::event(QEvent*) + 4698
12  QtWidgets0x11c2459ea 
QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
13  QtWidgets0x11c246e11 
QApplication::notify(QObject*, QEvent*) + 497
14  QtCore   0x11ecb6a34 
QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
15  QtCore   0x11ecb7d79 
QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809
16  libqcocoa.dylib0x11d01b259 0x11cfe1000 + 
238169
17  libqcocoa.dylib0x11d01b9c8 0x11cfe1000 + 
240072
18  CoreFoundation   0x7ff80d7f1ef1 
__CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
19  CoreFoundation   0x7ff80d7f1ea0 
__CFRunLoopDoSource0 + 157
20  CoreFoundation   0x7ff80d7f1c6e 
__CFRunLoopDoSources0 + 212
21  CoreFoundation   0x7ff80d7f08c8 __CFRunLoopRun + 943
22  CoreFoundation   0x7ff80d7efe9f 
CFRunLoopRunSpecific + 560
23  HIToolbox  0x7ff817617bd6 
RunCurrentEventLoopInMode + 292
24  HIToolbox  0x7ff8176179e6 
ReceiveNextEventCommon + 679
25  HIToolbox  0x7ff817617723 
_BlockUntilNextEventMatchingListInModeWithFilter + 70
26  AppKit0x7ff81084db37 _DPSNextEvent + 909
27  AppKit0x7ff81084c9b8 -[NSApplication(NSEvent) 
_nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1219
28  AppKit0x7ff81083eff3 -[NSApplication run] + 586
29  libqcocoa.dylib

Re: [Freesurfer] FreeView cannot open any images

2022-12-01 Thread Fischl, Bruce R.,PHD

Hi Greta

Make sure you are in the "3D" view (the icon that looks like a little head next 
to the coronal/axial/sagittal ones)

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greta Tuckute
Sent: Thursday, December 1, 2022 6:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeView cannot open any images

Hello,

I am attempting to use FreeView (have used it successfully for a few years, but 
suddenly it stopped working — cannot identify any cause. Have not updated 
operating system or similar). 
The problem is that nothing is loaded or shown. I cannot load e.g., an inflated 
LH surface from fsaverage. Running:

❯ freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated

Only opens FreeView and shows the background. lh.inflated is shown under 
“Surfaces” in the upper left corner, but nothing is shown. Nothing changes with 
“Reset view”. I tried:

- Updating FreeView (did not help)
- Reinstalled FreeSurfer (did not help either)

Any idea what is going on? No error message. Other FreeSurfer commands work 
fine.

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg (FreeView: 
freesurfer-darwin-macOS-dev-freeview.tar.gz from 

Operating system: macOS Catalina, version 10.15.7 (19H1824)


Thanks so much,
Greta



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[Freesurfer] FreeView cannot open any images

2022-12-01 Thread Greta Tuckute

Hello,

I am attempting to use FreeView (have used it successfully for a few years, but 
suddenly it stopped working — cannot identify any cause. Have not updated 
operating system or similar). 
The problem is that nothing is loaded or shown. I cannot load e.g., an inflated 
LH surface from fsaverage. Running:

❯ freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated

Only opens FreeView and shows the background. lh.inflated is shown under 
“Surfaces” in the upper left corner, but nothing is shown. Nothing changes with 
“Reset view”. I tried:

- Updating FreeView (did not help)
- Reinstalled FreeSurfer (did not help either)

Any idea what is going on? No error message. Other FreeSurfer commands work 
fine.

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg (FreeView: 
freesurfer-darwin-macOS-dev-freeview.tar.gz from 

Operating system: macOS Catalina, version 10.15.7 (19H1824)


Thanks so much,
Greta




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Re: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

2022-11-15 Thread Wang, Ruopeng

You can run this command to clear the settings of freeview only:

rm ~/.config/Massachusetts\ General\ Hospital/freeview.conf

Ruopeng

On Nov 15, 2022, at 5:05 PM, Dierker, Donna 
mailto:do...@wustl.edu>> wrote:


External Email - Use Caution

This happens to me when I control-C in the terminal to quit freeview, instead 
of clicking the X in the upper right corner.
Doing this works for me:

rm -rf ~/.config/Massachusetts?General?Hospital

But this would blow away settings for other apps you might have that write to 
that subdir.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Drucker, Daniel 
mailto:ddruc...@mclean.harvard.edu>>
Date: Tuesday, November 15, 2022 at 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1
* External Email - Caution *
Hi,

If I do:
$ freeview -v myfile.nii.gz

If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview 
window pops up, the loading bar gets to 99%, then then nothing else happens. 
I'm not sure what to do to debug this further.



--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School




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