subject:"Re\: \[Freesurfer\] 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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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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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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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

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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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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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/Linuxspecific command:

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 
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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
 ). 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
 .

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

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Re: [Freesurfer] Freeview issue

2023-10-22 Thread fsbuild

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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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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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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 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 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 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 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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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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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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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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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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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 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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 .
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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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Re: [Freesurfer] Freeview ERROR: label name '3rd-Ventricle' is duplicated (FSv6.0.0 with updated Freeview)

2023-07-31 Thread Wang, Ruopeng

External Email - Use Caution

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

External Email - Use Caution

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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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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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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Re: [Freesurfer] Freeview segmentation fault

2023-04-04 Thread fsbuild

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You can set the environment variable FS_LICENSE to point to your license file. 
Some people set that in their shell init file, e.g., .bashrc, and keep 
the file license.txt in their home directory. For example,
$ cd $HOME$ head -1 license.tx...@somedomain.com
—— email you used to register
$ export FS_LICENSE=$HOME/license.txt$ head -1 
$fs_licens...@somedomain.com—— email you used 
to registerStarting
 with the Freesurfer 7.3.2 release, the Mac build used Xquartz 2.8.2.  
If you are not already running 2.8.2 or newer then I would download and install 
the latest version of Xquartz 
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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> risk and wish to continue to communicate over unencrypted e-mail.
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-- 
Ose Kadiri
Staff Research Associate, Deters Lab
Department of Integrative Biology & Physiology, UCLA
Pronouns: she/her
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Re: [Freesurfer] Freeview segmentation fault

2023-04-04 Thread Wang, Ruopeng

Where is your license file located?

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


External Email - Use Caution

Hello,

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

Thank you,
Ose

--
Ose Kadiri
Staff Research Associate, Deters Lab
Department of Integrative Biology & Physiology, UCLA
Pronouns: she/her
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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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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
 ERROR: or try MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
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 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 MailScanner has detected a possible

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
>>
>>
>>
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>>
>>
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>> Brigham Compliance HelpLine at
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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.
>>
>
>
>
>
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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
>
>
>
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> Freesurfer mailing list
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>
>
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> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
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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.
>


-- 
Carlos Alcocer
B.A. Neurobiology and Behavior, Cornell University, 2019
818-746-0302
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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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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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> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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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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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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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contains patient information, please contact the Mass General Brigham 
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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 
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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:


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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 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 
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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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Re: [Freesurfer] Freeview crashes after installing the software

2023-01-02 Thread fsbuild

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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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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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this message immediately.  Continuing to send or respond to e-mail after 
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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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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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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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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] 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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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 
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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-16 Thread fsbuild

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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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contains patient information, please contact the Mass General Brigham
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.
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continue communication over unencrypted e-mail, please notify the sender of
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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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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
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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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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 
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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 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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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 
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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 -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>>
 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>>
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




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

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

2022-11-15 Thread Dierker, Donna

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 
 on behalf of Drucker, Daniel 

Date: Tuesday, November 15, 2022 at 3:01 PM
To: 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



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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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 
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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 
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Re: [Freesurfer] Freeview on WSL in Windows 10

2022-11-03 Thread Dicamillo, Robert

Hello Monica,

The login page you display is not accessible to the public.   We have 
information about how to get started with WSL on the public wiki pages, e.g., 
https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wslWe talk about installing 
WSL version 1 and WSL version 2, though it reads like you already have a 
version of WSL up and running and a version of Linux installed.

With WSL running Linux, you should download the appropriate freesurfer binary 
linux .rpm or .deb installer and use that to install freesurfer.  Those are 
available per OS (CentOS 7, 8 and Ubuntu 18, 20, 22) via a link on the WSL 
pages above to here, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads.

For Freeview to display graphics, you need to install a 3rd party X windows 
server on your windows host.  We demonstrate using Xming but some users have 
not been able to get Xming to work but have had success with MobaXterm.

WSL is a work in progress and can change without notice when Microsoft 
automatically updates your Windows machine.  We cannot guarantee the current 
version of WSL, the 3rd party X-servers, and the specifics graphics 
card/hardware in your computer are all going to cooperate to allow X-windows 
graphics to work.

If WSL does not work for you, an alternative its to use a different 
virtualization technology like VirtualBox instead of WSL.   We have a 
pre-installed version of Freesurfer 7.2.0 inside an Ubuntu 18 VM that runs 
under Virtualbox.  That eliminates having to use/install an X-server on your 
Windows machine.  Information about installing VierualBox and running the 
Freesurfer Ubuntu 18 VM can be found under, https://freesurfer.net/fswiki/VM_67

- R.

On Nov 3, 2022, at 04:11, Monica Crotti 
mailto:monica.cro...@kuleuven.be>> wrote:

External Email - Use Caution

Dear Freesurfer developers,

I am writing to you with regard to two issue I would like to address:

1. I subscribe to the email list but when I am trying to access the page 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN
 I got the following error


2. I installed Freesurfer on a WSL2 environment on my computer Windows 10. 
Neverthless, I am unable to run the freeview command. I looked into web for 
solutions related to the error I got which is the following

freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: 
cannot open shared object file: No such file or directory

Following what I found on the web, I run the following commands

$sudo add-apt-repository ppa:ubuntuhandbook1/ppasudo

apt-get install qt4-dev-tools libqt4-dev libqtcore4 libqtgui4

and I get the following errors

base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer# cd bin/
(base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer/bin# ldd 'freeview.bin' 
| grep not
libvtkverdict.so.5.6 => not found
libvtkGraphics.so.5.6 => not found
libvtkmetaio.so.5.6 => not found
libvtkpng.so.5.6 => not found
libvtkzlib.so.5.6 => not found
libvtksqlite.so.5.6 => not found
libvtkImaging.so.5.6 => not found
libvtkFiltering.so.5.6 => not found
libvtkCommon.so.5.6 => not found
libvtksys.so.5.6 => not found
libvtkGenericFiltering.so.5.6 => not found
libvtkexoIIc.so.5.6 => not found
libvtkNetCDF.so.5.6 => not found
libvtkVolumeRendering.so.5.6 => not found
libvtkRendering.so.5.6 => not found
libvtkftgl.so.5.6 => not found
libvtkWidgets.so.5.6 => not found
libvtkHybrid.so.5.6 => not found
libvtkIO.so.5.6 => not found
libvtkDICOMParser.so.5.6 => not found

I was wondering if you could help me in solving this issue.

Thank you in advance,
Best regards

Monica
Monica Crotti, M.Sc. | PhD Student
Locomotor and Neurological Disorders Group
Department of Development and Regeneration
KU Leuven, Belgium

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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
Compliance

Re: [Freesurfer] Freeview: missing voxels in reconstructed surfaces

2022-10-18 Thread Wang, Ruopeng

This appears to be a rendering artifact that happens sometimes with remote 
display. Are you viewing remotely from a Windows machine?

Ruopeng

On Oct 18, 2022, at 9:45 AM, Sarah Lavelle 
mailto:lavel...@tcd.ie>> wrote:


External Email - Use Caution

Dear Freesurfer,

I have an issue when viewing my reconstructed surfaces on Freeview my linux 
version :
freesurfer-linux-ubuntu18_x86_64-dev
freesurfer 7-dev

The surfaces have a large number of empty voxels. This is not a problem with 
the recon-all function as I can see the same surface file perfectly on my Mac 
with the fully working mac version. It seems to be a problem with my Freeview.

Some additional information that may help finding the cause:
When I open Freeview from Ubuntu, I get the following errors:

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-lavells1'
QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major 
code: 146 (Unknown), minor code: 20
QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major 
code: 146 (Unknown), minor code: 20

There are no other errors in ubuntu after I load Freeview i.e. No errors in 
Ubuntu when I then load the surface.

I hope you can help me fix this issue as soon as possible. Many thanks,
Sarah





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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] Freeview does not show images

2022-10-07 Thread fsbuild

External Email - Use Caution

Did it say the driver was installed successfully?  I’m wondering if the 
driver did not install because it does not support your machines hardware for 
some reason. But it should tell you if it cannot be installed.

You can tell if the DCH driver is installed by following the instructions 
here,https://secure-web.cisco.com/1C5iHX14FwFkb0bd5IYlzilnGkZNKBRhHFB5E1e8VAvgm832QpAA9pmst0ZQuoC01uGEtlN0Qfoy-8iUOVAv0r83MvIFhsS80-v9aycte39pSTISKdutTDgKy-hUW2qUx7xQZlC_l0pzPpONAt9fSyazQZ1GnRIQAMDEESUBRNX0c-v5cahiYmnyhb-nCV1r0ZvrgDZ7ghyZbtWcGndQw6amYiwjrvnXcDvAMEq5qd7pU3QU8ZOl9LnfFOQ6-k-ZLWIW6e0Yi8IRtVSlJSwNiDgACgB4gBvastg8A-sPy18j6Cfqj7NAY_DRglVfDj6Q80iOZn7cNsef3V1nq15s3WA/https%3A%2F%2Fwww.intel.com%2Fcontent%2Fwww%2Fus%2Fen%2Fsupport%2Farticles%2F58296%2Fgraphics.html
There is more info about it 
here,https://secure-web.cisco.com/1OnUvmRVhRWfRd2WCZXsandn42tB-a7ROvNPXbkZSl_hqHPKINKCSHkLxTmBG52oxmFqNtZjYTJ4Ppsay9_RddV5-RNszenkWzdmp4HV-k_JjuxpBLReMrMuOZL81oKe1VYne_9XcnTCtTbwzqyk6E5zeTXMOjQLj9-LeBN1OjCg16d38W4e9brBF4IQ4m5PdQjQQKLE5dak8O_fvzZ6AbMssGWmc3vnGyQFRuvfHgDq6SzzD5T2doFTIUemiQkSfxIMt4N5QyFpPyk5A1dbQcglJ1XctZd5C9TUn8KHtL_PYtauBGmPBHy7agS-rlu3q/https%3A%2F%2Fwww.intel..com%2Fcontent%2Fwww%2Fus%2Fen%2Fsupport%2Farticles%2F58295%2Fgraphics.html
- R.
On Oct 7, 2022, at 06:05, Justina Lee justinale...@gmail.com 
wrote:External Email - Use 
CautionHi Ruopeng,I tried 
to run the glxgears command in the WSL Ubuntu subsystem, but it doesn't show me 
the gears. I am having the same issue as this thread linked 
here:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1NxVL-emVuHw_jOzG4gXfcbpKLhoo9hS4C5IwCTkrb4Ge9RJeQgNfYxUY1b8UhVCwRwafISyQbYMLx5-0RvvSU6ZggG_ziHWkZu0dtETp0bWIPD2HpbN6cd9K0jyPv1EBAwomGF2psP-nMqtKFGOakonOE6Q_h5y-kwI5W6pz9NkKkFvaiUlrprN5Kw4EXmO6JNwQEEw8dt3jPlAlFb2GTb8v7sMcKcBtvKJX5-yZ1wcnQudjQkqYOv4-1MPtgi-cUNyFr_ZXvY5rkay6B-wM9gX5K9w7EmXiyuHWMwtAcDEuN9kXbDMGWjIX1ffOkkcs218lhqcGDyQ2a1ZisDYd_w/https%3A%2F%2Fgithub.com%2Fmicrosoft%2Fwslg%2Fissues%2F654
 I followed the advice and downloaded the latest Intel Graphics Driver, but 
this did not seem to fix the issue for me.I also looked at the 
corresponding debian package installer in accordance with my ubuntu version, 
and the same error occurs. How can I add a 3D accelerator or GPU acceleration 
so that the glxgears command can show me the gears?Thanks for your help and 
time.Sincerely,JustinaOn Thu, Oct 6, 2022 at 3:39 PM Wang, Ruopeng 
rwa...@mgh.harvard.edu wrote:Are you able to run glxgears command? Do 
you see spinning gears?RuopengOn Oct 6, 2022, at 4:28 AM, Justina Lee 
justinale...@gmail.com 
wrote:External Email - Use 
CautionTo whom this may concern 
and can help,I am currently trying to run Freeview under the 
WindowsSubsystem Linux System. I can successfully download and open 
images, but nothingseems to be showing onmy end (see image attached 
at the end).In order to find out what is preventing the X-server from 
correctly displaying graphics, I have tried to run the $ xeyes command and the 
eyes pop up, meaning that the X-windows server is working fine.Upon checking 
the WSL Version, I am currently using the WSL version 2.I have entered the two 
commands as follows:$echo "export XDG_RUNTIME_DIR=$HOME/.xdg"  
$HOME/.bashrc$echo "export DISPLAY=:0"  $HOME/.bashrcThen I 
exited Ubuntu, and tried to run freeview again (attempting to open a data file 
T1.mgz.) This still did not produce any image in freeview, although it opened 
it up. I tried changing the window, contrast, and brightness but to no 
avail.Is there another solution?Terribly sorry and thank you so much for 
your time.Sincerely,JustinaFreeview image 
display.png___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/1x2O2S2I-mf4HqnIK9_KstdCRE_wrCYlZRAFykGOfPQ3DzAXEq1u4VB41Wm4omVXkZJCypctowclP7mzCCA2g9I2ClLH90Xo_AbtFLWI5gGn9YP2wN3CVJqk2NY8Pe9Ynk0b_UjWkortSmdeEXQAfE8a95OtcNyWdR4Sa_oBIPly9uE-v-baM6cEJThYIjD1IaSulqOeIK-aqOVxZnjAG5dTRfco1tbGi8183-fAt19eY-cz8NSK-8mFGQCcj-seU8FULksI7FOc6rNUwR2BNff6QnUfh4BLFVaOgW-oy0122VupSftbfyne0EiipNUgA6XukNCc_4_bhLhyH8Cz2xQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
 mailing listfreesur...@nmr.mgh..harvard.eduMailScanner has detected a possible 
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Re: [Freesurfer] Freeview does not show images

2022-10-07 Thread Justina Lee

External Email - Use Caution

Hi  Ruopeng,

I tried to run the glxgears command in the WSL Ubuntu subsystem, but it
doesn't show me the gears. I am having the same issue as this thread linked
here: 
https://secure-web.cisco.com/1_nwpKy6edOMjc8Fb4TT_DQsKayIHq7yz6rjZXWYrhXvOMtkPtnDTAgvyHwlJknIz0NqjN44E48l9HTzHWpxTRB7K9qfWEddgLzY-N8DwQ9LJuanknR3cqBZCSGGybx3kfCwXL0JqnlBMKd4YPRiOBQ0tvJnklmkeHvAu0bOaW_5y3ABUG-9zqwhYo-JKOs-npIB2AdvV4eRkQ6-M0I8iPV2U8PHw1JoFhE100pzdpkEHDewV_Z7VJaoHYTWjJR4LPr_DMg2vecc2aM_SIu4Zgmk3bNNQ0II7UXChxgZatN8b6T1b4ayMSM8cKseJiDTbEG_czfPEz8ArXDVdM5yDMQ/https%3A%2F%2Fgithub.com%2Fmicrosoft%2Fwslg%2Fissues%2F654
 I followed the advice
and downloaded the latest Intel Graphics Driver, but this did not seem to
fix the issue for me.

I also looked at the corresponding debian package installer in accordance
with my ubuntu version, and the same error occurs. How can I add a 3D
accelerator or GPU acceleration so that the glxgears command can show me
the gears?

Thanks for your help and time.

Sincerely,
Justina

On Thu, Oct 6, 2022 at 3:39 PM Wang, Ruopeng  wrote:

> Are you able to run glxgears command? Do you see spinning gears?
>
> Ruopeng
>
> On Oct 6, 2022, at 4:28 AM, Justina Lee  wrote:
>
> External Email - Use Caution
>
> To whom this may concern and can help,
>
> I am currently trying to run Freeview under the Windows Subsystem Linux
> System. I can successfully download and open images, but nothing seems to
> be showing on my end (see image attached at the end).
>
> In order to find out what is preventing the X-server from correctly
> displaying graphics, I have tried to run the $ xeyes command and the eyes
> pop up, meaning that the X-windows server is working fine.
>
> Upon checking the WSL Version, I am currently using the WSL version 2.
>
> I have entered the two commands as follows:
>
> $ *echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc*
> $ *echo "export DISPLAY=:0" >> $HOME/.bashrc*
> Then I exited Ubuntu, and tried to run freeview again (attempting to open
> a data file T1.mgz.) This still did not produce any image in freeview,
> although it opened it up. I tried changing the window, contrast, and
> brightness but to no avail.
>
> Is there another solution?
>
> Terribly sorry and thank you so much for your time.
>
> Sincerely,
> Justina
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
>
> ___
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> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
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> Brigham Compliance HelpLine at
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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

Re: [Freesurfer] Freeview does not show images

2022-10-06 Thread Wang, Ruopeng

Are you able to run glxgears command? Do you see spinning gears?

Ruopeng

On Oct 6, 2022, at 4:28 AM, Justina Lee 
mailto:justinale...@gmail.com>> wrote:


External Email - Use Caution

To whom this may concern and can help,

I am currently trying to run Freeview under the Windows Subsystem Linux System. 
I can successfully download and open images, but nothing seems to be showing on 
my end (see image attached at the end).

In order to find out what is preventing the X-server from correctly displaying 
graphics, I have tried to run the $ xeyes command and the eyes pop up, meaning 
that the X-windows server is working fine.

Upon checking the WSL Version, I am currently using the WSL version 2.

I have entered the two commands as follows:

$ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc
$ echo "export DISPLAY=:0" >> $HOME/.bashrc
Then I exited Ubuntu, and tried to run freeview again (attempting to open a 
data file T1.mgz.) This still did not produce any image in freeview, although 
it opened it up. I tried changing the window, contrast, and brightness but to 
no avail.

Is there another solution?

Terribly sorry and thank you so much for your time.

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

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

Re: [Freesurfer] Freeview does not show images

2022-10-06 Thread fsbuild

External Email - Use Caution

I don’t think you told us what you installed for freesurfer in WSL.  The 
freesurfer installation should match the version of Ubuntu Linux that WSL 
installed.
You can check the Ubuntu OS version in the Ubuntu terminal window with,
$ cat /etc/os-releaseNAME="Ubuntu"VERSION="20.04..4 LTS (Focal Fossa)”. —- 
Ubuntu OS version = 20ID=ubuntuID_LIKE=debianPRETTY_NAME="Ubuntu 20.04.4 
LTS"VERSION_ID="20.04"HOME_URL="https://secure-web.cisco.com/1bVGj42N9EXVJFRZ7YL0IHj3ZYnjuVnNPLHNWkT-3uhiq6L7h9sN45hYiXV3Pd2V9J875qc-JBl9Tqt3UW2-YFbfENbpMYKffxCCGjQ06zKLwod7Q_JQGE4wByDfutTxeGYCmuIqtI7SzB9_uci0U9V-QpVsNxDUNY7O6guwj8kwphlSkuvBCTMIqfVNQGBtzzpsktGWscaG2P2EA1-qDf9FO8zMgdj_dAyVFJ9Im1k5JqsgNC7NsmMljgT3OXGo0Q7mPx-P0HD7xeLczNB1HHPTSPKpoLtCi8i2WDCK9BX5XQmIYzS7363K01hkUhjFoG8LeE6W-jm7kIAxmKjGU3g/https%3A%2F%2Fwww.ubuntu.com%2F"SUPPORT_URL="https://secure-web.cisco.com/12UtwR8986v4WnSkHQkzTHdLViFU2xy4D4gPieyqjFBGaUQm9SdqsxP46X32ln5PDRPOUrHicYocOH2L1hwKgbvD3w9U0VkIYbV4CTFhr6Hhf-nG5kKgj1fz-XIurMxIjURcu2gA5nuWphwwqE3ZkbtJc5Em2l6Em2rXM_Mv2hlsMTS9P3WR48Y5nkdBMkONJI824C3CsoHWluEVdL9mvzacA_M_i3BmabrSeQ0AZC_TY8_0tDgQZqLLYdI_FxemGPuGNG-8rZABngQkDjtZPbJW3yTUJrCgc-4EjIAKfaQvkA4H6wSmXbofi1e_KkuSD7R5KDW-hESL1Nqp-d1DwcA/https%3A%2F%2Fhelp.ubuntu.com%2F"BUG_REPORT_URL="https://secure-web.cisco.com/1ovllB_ySt3ww3AwjGhOIt_eu_N2HW4iWf5szA8QTOw55-PRuQZz3ZLpB4w7cxz3FrFMPPMH71GXeyyhNfXl0hvfucoA6lByiy6VU0_Gn61wilEzNPto1d7gUKGm-FIqG_iL-dlTfQuvVXqPPKNw15envffK_8vXlgDXKfU9B5sk_LqGtaSy_NnUMLobghmWkoB4fSLI-71vWMhOX15rguf4LkRNf7ZqZVdNI9J7TGLb1_FBxbcP97TQ4FnBmJqor_EUOvgjx3_ccpTyAAkjZYElwWzaVpz_v0ic0PZp9tPRitW-jqkrRYbI1AA21Dq6dFUzU2eMRjvYs8ZrtIZNnEA/https%3A%2F%2Fbugs.launchpad.net%2Fubuntu%2F"PRIVACY_POLICY_URL="https://secure-web.cisco.com/1gsSaM6y5sGY58Zoe__dEZ5uF1C7Q91HlD5GBMyNhKdRRciBtH5S1o48IydYVZJpfO4VDzGHjpxNm7cN_weTNNjndXUe-Wt_ExcsnbGitQtWH41HzTXNEr9kjBYnAC21Avcq_bECC792lqQO97bDGdh-X1ogJo4RvcMSzJzQFDLD0C1uGdANIb0skCCrS-1UaA6QcE0C2stQTchmfJpw0zqIS5VrVYWD8FSQqS4bC_EX01eSUdSmeLvv0pPOjv9ajiICZozd_7e2cjaCOH-CqfxTYt38iRuXKoA8P8vMD-HTZSfBrDTG-q4oTH2-yZkRzAN0VxYTZfe1jxneAvbnvGA/https%3A%2F%2Fwww.ubuntu.com%2Flegal%2Fterms-and-policies%2Fprivacy-policy"VERSION_CODENAME=focalUBUNTU_CODENAME=focal
With the above version info, you can use the debian package installer (.deb 
file), e.g., from 
https://secure-web.cisco.com/1suBrY-ijWwnSebRIO5a6tmmiUPrI9YyHka5F3mVaW4EnbxeV7rRdvWIOMgbVvcZqj1zwLYm7MmIFr6q5tJwIbAg1f3RqAwcy6uPcrMadB7sC3jFtmy9Qx-Rk9wWABvuRmD6mYZdeowemlWPRRwxOO1v4Voh0hsTf_JphGDQ9UPmUtm_Bc31ftltQ2ZPxaMtRKNBbFEdtYbxDMrbYxkTA51NhX5PNWukbYyKXQ6iCm5VWhzPLL6cnFnPXhqMhUu21GttqYVbuyuuyqesW1KpjInNTju23w21vzESLlu4dN3lp8IMm4SmXcUWBHJ4YoXeM/https%3A%2F%2Fsurfer..nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads,
 that matches your version of Ubuntu. For Freesurfer 7.3.2 the choices 
are:
freesurfer_ubuntu18-7.3.2_amd64.debfreesurfer_ubuntu20-7.3.2_amd64.debfreesurfer_ubuntu22-7.3.2_amd64.deb
For the output above, you would choose freesurfer_ubuntu20-7.3.2_amd64.deb to 
match the version of Ubuntu Linux.
… cd in Ubuntu linux to where you downloaded or copied in the 
freesurfer_ubuntu20-7.3.2_amd64..deb file …… and install it with ...$ sudo apt 
install ./freesurfer_ubuntu20-7.3.2_amd64.deb
… and if the install succeeds then freesurfer would be installed under 
…/usr/local/freesurfer/7.3.2
… and to remove the install above you would do …$ sudo apt remove freesurfer
If you didn’t use the “apt install” command above to install freesurfer, then I 
would remove your current copy of the ./freesurfer tree, and do the “apt 
install”. Then you could source the freesurfer setup script and try 
running freeview again.
Microsoft can change the WSL environment without notice when your Windows 
machine updates. The version of Ubuntu linux installed in WSL depends 
upon when you set it up on your machine. We try to troubleshoot issues 
users report back to us, but we can’t always remotely debug every interaction 
between WSL, different X servers (X-ming, Moba Xterm) and your machines 
graphics card.  We have written up some of workarounds at the bottom of 
this 
page,https://secure-web.cisco.com/1Wk9iTNOO9n-TGjUWv3BghCeFjAi82pV6d2_DiVsToobAk3JeVZwflclvI4UX-bexunNh4zfn2cUTgKsbqsCcQyA3h8A5mlBqdKhRa_w2nbR0RK13SVjyUWKuomeXRYT5EWIHJGYShx2_sV6OWd1zwMfUPGEPRUL0VThpkdKxzwUjFd-0s4uyLwMFszqKkVgB8Tvt8QKbllUDLHMXJarF6XeboFO1uhE5diy294c_TItL24tIgwITgkUl_uHG5bXQ3KY-U6TcyjlSQpj--lZMhaGdLlYpAlSUlDwbP-JuuN_V9-zo2Ku_9AJk2UyCNV-MKaZDfBg97tIyMeDNKtm4Ag/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
  But some users are not able to get a 3rd party X-server running on 
Windows to work with every graphics application they run in WSL.  A 
simpler alternative is to use the VirtualBox VM as it has both freesurfer and 
an X-server pre-installed matching the OS provided in the VM.
- R.
On Oct 6, 2022, at 04:28, Justina Lee justinale...@gmail.com 
wrote:External Email - Use 
CautionTo whom this may concern 
and can help,I am currently trying to

Re: [Freesurfer] Freeview does not display image

2022-10-04 Thread fsbuild

External Email - Use Caution

With regards to WSL, there is probably something preventing the X-server from
correctly displaying graphics. Instead of running freeview you could try
a simpler command to test X-window graphics. One command is “xeyes” which
you can look for and try running in the Ubuntu terminal window by typing,
$ which xeyes/usr/bin/xeyes$ xeyes

If a window does not open displaying something like a pair of eyes then the
X-windows server is not working correctly.
There are 2 different versions of WSL, i.e. version 1 and 2. The setup
for the X-server can be different depending upon which version you are running.
You can try to find the version by typing the following command at the
Windows command prompt. The number under VERSION should be the version of
WSL you are running.
C:\Users\sam wsl -l -v NAME STATE
VERSION* Ubuntu Running 2 — means you are
running WSL version 2
Down the bottom of this page are some instructions for setting up the Ubuntu
shell environment for
WSL,https://secure-web.cisco.com/1iKRwZpgN3zDuJlFspVtdJXrVV6ghp3nndYFCB19UUv0S_ZDUd_LyQflWBXOV2Ec9k9oguJAS9Wfh1JxC7S9wxuFfXpCUILrH9-cexgQn92l463Ch5Gr2lQn-XHFXD9dE6p6QUlj5oaIRqS2lWhFg--xR_sftxNpLbn21muMopMfiIkPPlS4f0pw2UGvA7-UFydNYWfu1-QRwV7b39O4-J2Qw2bkZ61RTVmdM9kLDq72IwZhIGJ7lH-lBHNqLjTtqdSgXCAZ8aBjKzGRyvB5ZCivTW5z6NzirccbCJLj-IJDFJqQAQ5JbMxd6E9ts3Wwh/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
If you have not already run these 2 commands, then I would do so,
$echo "export XDG_RUNTIME_DIR=$HOME/.xdg"
$HOME/.bashrc$echo "export DISPLAY=:0" $HOME/.bashrc
Then exit your Ubuntu terminal window and start a new one so those settings
take effect. Then try running the “xeyes” command again to see if it
works. If it does work, then try running freeview again.

With regards to trying to use the VM, if uncompressing the image is crashing
then you may be running out of disk space. You should check there is at
least 40 Gig of free disk space in the location where you are trying to open
the zip file.
- R.

On Oct 4, 2022, at 03:11, Justina Lee justinale...@gmail.com
wrote:External Email - Use
CautionHello R,Sorry I wasn’t
so clear on my part. I am using ubuntu linux on the windows subsystem linux
(WSL). I followed these instructions atMailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wslto download the WSL,
X-server, and the freesurfer.Is it still possible to fix the problem here
internally or should I follow the instructions sent from the link previously to
download Virtual Box and run freesurfer in this way? I have been trying to open
the zip file Ubuntu compressed image but it seems to keep crashing as I load
it. I will keep trying if the first way aforementioned is not
possible.Thank you and hope this has become alittle
clearer.Sincerely,JustinaOn Mon, Oct 3, 2022 at 8:35 PM fsbuild
fsbu...@contbay.com
wrote:External Email - Use
CautionHello Justina,We need to
know what your setup is on Windows for running Linux in order to help with
running freeview. It reads like you are not using VirtualBox to run the
Linux Ubuntu OS,I do not have VirtualBox installed So it’s not clear
to me how you are currently running Ubuntu Linux on your Windows machine in
order to run freeview or other freesurfer commands. Are you running
Ubuntu linux with the Windows Subsystem for Linux (WSL)? Maybe you are
connecting remotely to a linux machine via VNC or the like from your Windows
machine ?If you don’t mind running freesurfer 7..2.0 (instead of the
newest 7.3.2 release), there is a smaller version of the VM to download
fromMailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to
behttps://secure-web.cisco.com/1pDNeyyXnoU0PIQ7-rMdLh5tom581Kv0B3Mn8Rs7MprnKn-uT1AsFMEXN1z6iQArgATy5KV7HFg2cGHq78q-g3VX9AinZ7V0Bxa4EIXQiO3UdAQDoa00Zs7HZRkZ9XkzwKxYLtNBM0S4mZV54KcjnKyyDKFDQgBLezEsQS2ZD50o1zs_hbB9fcTqsw3suSoDAwWsZ3fcar4GR8SUP9KKhs1Kqpmd0xOsvsFUxzls5Y-u3lryPzutEkuO0Vcz4-4FjqP-8u0Rzp5fygoIJ0Dmk-Wrk1VE-QvdMCIMM67fFazyTCcyyYB3iMB4zcygRcD8Y/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67%26nbsp;
with setup instructions under that link. But you would still need
to download and install VirtualBox on your Windows machine and then download
and install the Freesurfer Software.- R.On Oct 3, 2022, at 09:35, Justina Lee
justinale...@gmail.com
wrote:External Email - Use
CautionTo whom that can provide
any insight,I am currently using Ubuntu on windows to open freeview to show
some data. My issue at hand is that freeview does not show any images, despite
changing the window levels (contrast and brightness). Using the command
freeview -v works, and I am able to run it smoothly.. When I try to open an mgz
file, it runs fine, but I am unable to see anything.I do not have
VirtualBox installed and tried to take this advice from previous but I ran

Re: [Freesurfer] Freeview does not display image

2022-10-04 Thread Justina Lee

External Email - Use Caution

Hello R,

Sorry I wasn’t so clear on my part. I am using ubuntu linux on the windows
subsystem linux (WSL). I followed these instructions at
https://secure-web.cisco.com/1p8Cin-EJEpeRx1cZi8s231xYYwEa73Ljn6cCDVMGOudNzx-clBR6sZUCDMeSmSC85H7RtRtyEHdxO6j7DqYMFXEEle0HWR03qo71o_mjxHnvDmseEhe6KVuhPF3a9EM59Nka9FTcsYt1gVTr_HvvTbhHKoEmZ7oV9i3KeY7rIQGCvfTf9bQme8kx7TWvoWnm5VKZSHSvq48kfOuo2C6lIY_MAf92M9I1KgyaWazv2MhWZWGikJgOV2nw4QC69vFLjpH3ctxn4UIMJLn7bY8klGzGH6U_lmVmi2m4Q1eV11REMBdDeMc-XzcjqJYUvXvg-Th-bs5WT8twMoaIT9Yw2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
 to download the WSL,
X-server, and the freesurfer.

 Is it still possible to fix the problem here internally or should I follow
the instructions sent from the link previously to download Virtual Box and
run freesurfer in this way? I have been trying to open the zip file Ubuntu
compressed image but it seems to keep crashing as I load it. I will keep
trying if the first way aforementioned is not possible.

Thank you and hope this has become alittle clearer.

Sincerely,
Justina


On Mon, Oct 3, 2022 at 8:35 PM fsbuild  wrote:

> External Email - Use Caution
>
>
> Hello Justina,
>
> We need to know what your setup is on Windows for running Linux in order
> to help with running freeview.  It reads like you are not using VirtualBox
> to run the Linux Ubuntu OS,
>
>  I do not have VirtualBox installed 
>
>
> So it’s not clear to me how you are currently running Ubuntu Linux on your
> Windows machine in order to run freeview or other freesurfer commands.  Are
> you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?  Maybe
> you are connecting remotely to a linux machine via VNC or the like from
> your Windows machine ?
>
> If you don’t mind running freesurfer 7..2.0 (instead of the newest 7.3.2
> release), there is a smaller version of the VM to download from *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be* 
> https://secure-web.cisco.com/1paaB_cgPVQ7btidlPguZcJsmtliH8F8hjmenNiwMMKj6psPWB7PbCzz88mGy5PUxJ4_RYJHEnEgzOrASI38A31sVxjVmfxfUSo9L9FoxfPo2Av_MQ6ngrK-iKSLjkEbUggeuaoXemH1U78dhZuZM2A4CAL_oLkIUIFvyvWpHvLbzriR6DhJXh-EgzZuO82YSUqI3pVfRIQ1T5aFoSn8Y-hAXTf-f5_IS6TEMtEMFUpxxu98IMgpvc-KXmk-Wzm8NyBtiXkhuju9KJHm65VHaV7mHETaWMKcy3_JUxpNDLu3RFKJJlU9p2uLb6LOYUMWA_NvQjUVmIQKA27QoJS_YzA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
> 
> with setup instructions under that link.   But you would still need to
> download and install VirtualBox on your Windows machine and then download
> and install the Freesurfer Software.
>
> - R.
>
> On Oct 3, 2022, at 09:35, Justina Lee  wrote:
>
> External Email - Use Caution
>
>
> To whom that can provide any insight,
>
> I am currently using Ubuntu on windows to open freeview to show some data.
> My issue at hand is that freeview does not show any images, despite
> changing the window levels (contrast and brightness). Using the command
> freeview -v works, and I am able to run it smoothly. When I try to open an
> mgz file, it runs fine, but I am unable to see anything.
>
>  I do not have VirtualBox installed and tried to take this advice from
> previous but I ran across the problem of downloading the course Virtual
> Machine. I do think that I do not need to download the VirtualBox and can
> continue using Ubuntu on Windows.
>
> What could be the issue with this? Should I be downloading the Virtual
> machine to run Freeview?
>
> Thank you so much for your time and I hope that my issue is not too big of
> a problem to solve.
>
> Sincerely,
> Justina
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1XBB9mVISZMBi-_VRhIEm62UucxuNsrx0F-92EzExHgsYK_1D4N3Dg9If49qUFuo11Cdn9sLRgmZ46jVvgxo6jP2o7lsQu7bhK6-Kmis1M884MqF9f3CYVJizJM92RHyc69rt33Kug3_Ex5lc4S1Lwy1cldPGDcO_12gxyVoS4xQ-hQmsLuMF7olr9OaTaR26WjwJWv4kYz5JakPSmgFQy7NhpuCBXaLebRmKHa1vfKdNlLrIUghVJSKuVtEfHAnLhlbZo47AY4-dhZ8SMj_Rj1aC0lyrwn1GLDDeTFoQpIZAmkO-44ho_t6mBBm3YoPQ8xfugoEGeHNuUuP6rwOAXw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>

Re: [Freesurfer] Freeview does not display image

2022-10-03 Thread fsbuild

External Email - Use Caution

Hello Justina,
We need to know what your setup is on Windows for running Linux in order to
help with running freeview. It reads like you are not using VirtualBox to
run the Linux Ubuntu OS,
I do not have VirtualBox installed ...
So it’s not clear to me how you are currently running Ubuntu Linux on your
Windows machine in order to run freeview or other freesurfer commands.
Are you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?
Maybe you are connecting remotely to a linux machine via VNC or the like
from your Windows machine ?

If you don’t mind running freesurfer 7.2.0 (instead of the newest 7.3.2
release), there is a smaller version of the VM to download
fromhttps://secure-web.cisco.com/1YWO9PWAWb2dUg45HhJ8-Uf5BVRKini-Plt5R0ZzrEI56U73eIIqsvtOabP978uAZGbMguO6zYQXj2qmsPJoTTh7XQB1Lfjd_GAeMNqapxT92fvVsg3gtB6o_K_TGqYKm52s7ec5nvDnfb305SkZY5SoJ35m3yTBjgDCFLbXXPxXkheXpgZ_WR53HyCMzoKJTA3AY00j28VO95fGeTZ7uWfvDvLe8v_Og6PX24DOCLRBZTaLzr9cWE2lBsMd6N0avVNQetV_emJ79GF0lrvGJSxK2kaC87ydb09ZWR2FVyUPprRlBNZm7zdFvyF1pcMsa/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67%26nbsp;
with setup instructions under that link. But you would still need
to download and install VirtualBox on your Windows machine and then download
and install the Freesurfer Software.
- R.

On Oct 3, 2022, at 09:35, Justina Lee justinale...@gmail.com
wrote:External Email - Use
CautionTo whom that can provide
any insight,I am currently using Ubuntu on windows to open freeview to show
some data. My issue at hand is that freeview does not show any images, despite
changing the window levels (contrast and brightness). Using the command
freeview -v works, and I am able to run it smoothly. When I try to open an mgz
file, it runs fine, but I am unable to see anything.I do not have
VirtualBox installed and tried to take this advice from previous but I ran
across the problem of downloading the course Virtual Machine. I do think that I
do not need to download the VirtualBox and can continue using Ubuntu on
Windows.What could be the issue with this? Should I be downloading the Virtual
machine to run Freeview?Thank you so much for your time and I hope that my
issue is not too big of a problem to
solve.Sincerely,Justina___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview quitted unexpectedly

2022-08-28 Thread fsbuild

External Email - Use Caution

Hello Danesh,
Try putting your license.txt file into your home directory and setting the 
environment variable FS_LICENSE to point to it.
$ export FS_LICENSE=$HOME/license.txt$ cd $HOME$ cat $FS_LICENSE… you should 
see your email address used to register for the license plus other license code 
…
Then try source’ing the Freesurfer script to setup the environment,
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ 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

Then try running freeview with no arguments and it should bring up an empty 
window,$ which freeview/Applications/freesurfer/7.3.2/bin/freeview$ freeview
- R.
On Aug 23, 2022, at 10:36, Danesh kajbaf daneshkaj...@gmail.com 
wrote:External Email - Use 
CautionDear support team,After 
installing Freeview, I tried to load a volume, while checking how it works with 
samples, from the subject folder in the Freesurfer folder. Unfortunately after 
choosing the file, Freeview crashed out and popped up an error message 
“Freeview quitted unexpectedly!”. I tried with other files and the same 
happened again, while all these files could be loaded by FSLeyes, so the 
problem was not with data. I run Apple Diagnostics to find if the problem was 
with the hardware or OS and there was no issue.Attached is the text file of the 
error as I copied and pasted it so it might help to tackle the problem.Freeview 
2.0 is installed ,via the Freesurfer 7.3.2 package installer, on macOS Catalina 
10.15.7, and my MacBook Pro’s part number is A1706.Regards,DaneshError 
txt.rtf___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur

2022-08-15 Thread fsbuild

External Email - Use Caution

Hello Sara,
You could try running bash shell and putting a copy of your license file as 
license.txt in your home directory and then set the environment variable 
FS_LICENSE to point to it, e.g.
$ bash$ cd $HOME… copy in your license file here as license.txt ...$ export 
FS_LICENSE=$HOME/license.txt… make sure it is there …$ cat $FS_LICENSE… should 
see contents of your license file ...

… then setup the freesurfer environment as usual …$ export 
FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreesurfer.sh… output deleted …$ which 
freeview/Applications/freesurfer/7.3.2/bin/freeview… see if you can just bring 
up freeview displaying an empty window …$ freeview
There are various postings reporting that MacOS BigSur running on machines with 
dual monitor settings have issues including when they wake up from the screen 
saver or the machine has goner to sleep - as in the machine crashes.
Some reports recommend turning off the screensaver, and making sure the machine 
energy saver settings are not set to put the machine to sleep.
- R.
On Aug 15, 2022, at 17:08, Addison, Reuben raddi...@mghihp.edu 
wrote:Sara, do you have a double screen by any chance ?Reuben A. 
GetOutlook for iOSFrom:freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sara Sanchez-Alonso 
sanchez.alonso.s...@gmail.comSent:Monday, August 15, 2022 5:07:01 
PMTo:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.eduSubject:[Freesurfer] Freeview quits 
unexpectedly on macOS Big 
SurExternal Email - Use 
CautionHello,I have installed 
Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The installation was 
successful, but every time I need to open freeview, it quits unexpectedly.The 
environment seems to be set up correctly and I have also downloaded my license 
and copied it to the freesurfer directory.I tried downloading version 
7.2.0 and I keep having the same issue.Any ideas as to why I am unable to open 
freeview?Thanks,Sara___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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 
 .
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 quits unexpectedly on macOS Big Sur

2022-08-15 Thread Addison, Reuben

Sara, do you have a double screen by any chance ?

Reuben A.

Get Outlook for iOS

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sara Sanchez-Alonso 

Sent: Monday, August 15, 2022 5:07:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur


External Email - Use Caution

Hello,

I have installed Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The 
installation was successful, but every time I need to open freeview, it quits 
unexpectedly.

The environment seems to be set up correctly and I have also downloaded my 
license and copied it to the freesurfer directory.

I tried downloading version 7.2.0 and I keep having the same issue.

Any ideas as to why I am unable to open freeview?

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

Re: [Freesurfer] freeview crashes after new fs install

2022-08-10 Thread fsbuild

External Email - Use Caution

The wiki information may be out of date. Having multiple versions of 
freesurfer installed on your system may cause running an application bundle 
like freeview.app to crash if the system is confused about which version of 
freesurfer is installed. So I would avoid having multiple releases of 
freesurfer on your system.

If you expanded the tar archive instead of doing an actual installation with 
the .pkg installer, then I would drag your ./freesurfer subdir(s) to the trash, 
empty the trash, and then check no freesurfer distributions remain on your 
system. Then try installing the version of freesurfer you need by 
downloading its .pkg file, double clicking on it, and following the menus.

The installer .pkg puts an uninstall script as,
/Applications/freesurfer/release number/uninstall.sh
- into each freesurfer release. Running that uninstaller is the most 
reliable way to tell the system that freesurfer distribution (and Freeview.app) 
have been uninstalled.

There's no need to add a license file to each freesurfer distribution. 
You can keep your license file in one place, e.g., your home directory where 
you login to. Then in your environment set FS_LICENSE to the path of your 
license.txt file. If it's in your home directory, then you would do
$ export FS_LICENSE=$HOME/license.txt

If you add the setting for FS_LICENSE to your shell initialization file, then 
it will be defined every time you open a terminal window. Your license 
file will be found in that central location no matter what freesurfer release 
is installed.

- R.

On Aug 10, 2022, at 23:54, Miriam Taza miriam.t...@mail.mcgill.ca 
wrote:External Email - Use 
CautionHi,I recently installed 
the new FS on my mac. I renamed my old "freesurfer" folder as instructed on the 
wiki.However now freeview crashes. it opens but when i try to load volume 
it crashes. Below you will find the report. (this happens if I use either the 
old freeview or new freeview).i also got a new license and put it in freesurfer 
directory.I also moved to trash then deleted the old fs but still get the 
error.
___
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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 
 .
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 Closes Unexpectedly

2022-08-04 Thread fsbuild

External Email - Use Caution

You need to use the sudo command to modify something under /Applications, so 
you could do$ sudo cp ~/Downloads/license.txt /Applications/freesurfer
You could also just set FS_LICENSE to point to license.txt% setenv 
FS_LICENSE~/Downloads/license.txt
You could also add that setenv in your shell initializaztion file so it will be 
set the next time you open a terminal window.
- R.


On Aug 4, 2022, at 17:48, user2038...@gmail.com 
wrote:External Email - Use 
CautionThank you!When I try to 
copy the license.txt file I receive this:% cp ~/Downloads/license.txt 
/Applications/freesurfercp: /Applications/freesurfer/license.txt: Permission 
deniedHow can this be resolved?On Fri, Jul 22, 2022 at 6:37 AM Wang, Ruopeng 
rwa...@mgh.harvard.edu wrote:Here is the instruction:MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1OShD5Wc9pbKTVxIZ4IEWEKwdg0ubHAEIAp6kaB9bGAjbqY1l_wlY48GO5hDw5cVxtEW90PwDnvAkWpMzJl6fSQzOz0yZgN2hvlJOilMaUpCovPhTXhRsWD9Q9dl16HcCmU3P9Hofdm5FyiN6OUeOuS_PSqlCh7uHqFgQIfZPFYNOZqaXbBVa4K0MLGWa1nqQzMTQDMOP_qGkw3AoLFgTSJZWirap_c4ew6IV73pu1DLSk6g5t6-DkXCbclhVe-O5mSjr2lqXLL3TNP9zR6xLC_SBdk7jStVtaaZDejzjXeD3186O7yD98kO0A9gfQ0YjsdtkdkIQ-SdyJf1f7NVSYw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLicenseOn
 Jul 22, 2022, at 12:52 
AM,user2038...@gmail.comwrote:External
 Email - Use CautionHi,To make 
sure, can you send me the instructions on how to download the FS license 
file?On Fri, Jul 22, 2022 at 1:31 AM Wang, Ruopeng 
rwa...@mgh.harvard.edu wrote:Have you install the FS license file 
properly? Another thing to check is to make sure you have granted freeview 
permission to access your disk files. You can check it in the system 
preferences.RuopengOn Jul 21, 2022, at 12:31 
PM,user2038...@gmail.comwrote:External
 Email - Use CautionHi,When I 
try to open any files in Freeview on a MacBook, the application closes 
unexpectedly. I onlyreceive a message from Apple that says "Freeview quit 
unexpectedly" but gives no reason.This happens after I open the 
application and try to load a volume. After Freeview closes, I can open it 
again but the file does not open. How can this be 
resolved?___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/1dv8o7rEH_IGxjNFFEfw-XePreZ1nr2vzA4y3a63LBstwhtyqMmqA8qwhe0_c-IB1F8sPZ-Jywl4gqORS8cbKbj6MPtT53lrEhoVMRWdHDHL7cyo54XkeLlBsGGm4aDnqIyrCy_85tnisMaKmBo6QlbnE1E2r7izC2B39uFSy_E7vVrp2Iy7PgBALOrkFWGQ1r6cQggzKcaLJ824QggexwyI4tbYKblnt_i3Jxjt6-LvoxneYCS4Sp3DXvehYasslkXzkRAa1ja0fRwHd-bDL74dZEuGHGHfms8i8FrdRTPVMZ23ueR2s-sg1IUzY61ZiJtFTjjxkC5W-B9yE5sbDUw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
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Re: [Freesurfer] Freeview Closes Unexpectedly

2022-08-04 Thread _ _

External Email - Use Caution

Thank you!

When I try to copy the license.txt file I receive this:

% cp ~/Downloads/license.txt /Applications/freesurfer

cp: /Applications/freesurfer/license.txt: Permission denied


How can this be resolved?



On Fri, Jul 22, 2022 at 6:37 AM Wang, Ruopeng 
wrote:

> Here is the instruction:
> https://secure-web.cisco.com/1PJWGSKkIsBrtyu20MQQH8XR-9VXjBDZs1-aTgdpzQjEboB0QZxEzp6wnhVTwK7Jl-fpIvLaoB7V_0Id6WQDF44cv6kqld7v-yFTe20l7-Ek5mmebG3WOkGj__XC87v5CsjyXI57Kdlcmr2tchd6tYK_knRTT6sp_7rQMP4I8KmAsyLYTmfb2mBqhefghZgfGqpaznkpqHwmOn4vwWw7zbBttVBsnMASJzwtuxGXSN9hevqFvpK7fGvIymVoUgoF86PamJ3F4E1OWomNPMEcFBqxhBRNsRjMA9oaIrnPYJzabRlhJd94m5nSYVAOp81ta/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLicense
>
>
> On Jul 22, 2022, at 12:52 AM, user2038...@gmail.com wrote:
>
> External Email - Use Caution
>
> Hi,
>
> To make sure, can you send me the instructions on how to download the FS
> license file?
>
>
> On Fri, Jul 22, 2022 at 1:31 AM Wang, Ruopeng 
> wrote:
>
>> Have you install the FS license file properly? Another thing to check is
>> to make sure you have granted freeview permission to access your disk
>> files. You can check it in the system preferences.
>>
>> Ruopeng
>>
>> On Jul 21, 2022, at 12:31 PM, user2038...@gmail.com wrote:
>>
>> External Email - Use Caution
>>
>> Hi,
>>
>> When I try to open any files in Freeview on a MacBook, the application
>> closes unexpectedly. I only receive a message from Apple that says
>> "Freeview quit unexpectedly" but gives no reason. This happens after I
>> open the application and try to load a volume. After Freeview closes, I can
>> open it again but the file does not open. How can this be resolved?
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1SFQE8fwGmQIxht4LwAhBbwX9gWxsw8ls6x2L_4TZgkvGK-SkZ_LVToJxpf406RsbEBpNkANcVMzVOXb6ucqd9kMDiFMMfFbbyMeq0StE56e4qWYWK7p9fct_cK-qpWcYokZq-mCr4C7KQxF_nPFxmVhUgS0ee45cME2-eQHgMa43IqUr0FXGO87GxN3J7QFUpp53TiGPBbUegJww4sQkXnFOXDQ9lHIgeDbE8XTeWUYK0MefziBkmfS2XpVC8kio8suTwUh0QnvtslWjfUziPW7aODpVXY10Y56TM0xFbRs-L9b4KXpsrSpq3OivNyMz/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 *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
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>>

Re: [Freesurfer] Freeview Closes Unexpectedly

2022-07-21 Thread _ _

External Email - Use Caution

Hi,

To make sure, can you send me the instructions on how to download the FS
license file?


On Fri, Jul 22, 2022 at 1:31 AM Wang, Ruopeng 
wrote:

> Have you install the FS license file properly? Another thing to check is
> to make sure you have granted freeview permission to access your disk
> files. You can check it in the system preferences.
>
> Ruopeng
>
> On Jul 21, 2022, at 12:31 PM, user2038...@gmail.com wrote:
>
> External Email - Use Caution
>
> Hi,
>
> When I try to open any files in Freeview on a MacBook, the application
> closes unexpectedly. I only receive a message from Apple that says
> "Freeview quit unexpectedly" but gives no reason. This happens after I
> open the application and try to load a volume. After Freeview closes, I can
> open it again but the file does not open. How can this be resolved?
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1Pgof7oSsV6jIF0I1DwvmhijBjIMhoBhQVYMLEVVlQD-OAVrFKDwYiC9zmDpHmoW0B3IcuFuZn7KhJ71sNmPmzEWG-vwYmdA4go-7jRxET9FEE3Pnz1EEinf6-yCot6HmmRv-uCecj30SVjRgZWL7y_M83zFONcrf2eoeidkbonZY-0xXS1k9QhVeBaGlZK2BVltL9m4S3DI31i8yilFxNo5ZQ72GfsjWsFV39x0uaBC1XIc0rXY47JEG_jYzs0-XLMK9jH7472Pqxvdt0HzQoWQmMjRarPj5WGT7ykmLpDHwxer1B6i2251-BcGli_mE/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1Pgof7oSsV6jIF0I1DwvmhijBjIMhoBhQVYMLEVVlQD-OAVrFKDwYiC9zmDpHmoW0B3IcuFuZn7KhJ71sNmPmzEWG-vwYmdA4go-7jRxET9FEE3Pnz1EEinf6-yCot6HmmRv-uCecj30SVjRgZWL7y_M83zFONcrf2eoeidkbonZY-0xXS1k9QhVeBaGlZK2BVltL9m4S3DI31i8yilFxNo5ZQ72GfsjWsFV39x0uaBC1XIc0rXY47JEG_jYzs0-XLMK9jH7472Pqxvdt0HzQoWQmMjRarPj5WGT7ykmLpDHwxer1B6i2251-BcGli_mE/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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/1k9mkd-jjqU-FFKeqqoZuiKU3kKDnr-_ZLIUdkTd9VAkbAg4TE4I0seLYY_gPSOuqw5aL_IBnS1sx9NgpHb0FLGnpoYghfoIEqJBbw1ex9LNMec0E86X1akl3ZolguY0dRivZ-m7mstRSLUOJRNxYo2zkXz7vIReVEAu1ZINZz6ygBOEDCb60t73_9zyeDaCCJuwx6NXRumyFjaamBs_ATGc7ZByqyxylKl0KP_f1CiJmk5GlLIr_Ce8gM3zDd7y0JyeJEImEgiryqy6jJYES5aiRfn5I08SBsKzCu79DfW9QX0H8XQFBAQ1yqU93sMFL/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1k9mkd-jjqU-FFKeqqoZuiKU3kKDnr-_ZLIUdkTd9VAkbAg4TE4I0seLYY_gPSOuqw5aL_IBnS1sx9NgpHb0FLGnpoYghfoIEqJBbw1ex9LNMec0E86X1akl3ZolguY0dRivZ-m7mstRSLUOJRNxYo2zkXz7vIReVEAu1ZINZz6ygBOEDCb60t73_9zyeDaCCJuwx6NXRumyFjaamBs_ATGc7ZByqyxylKl0KP_f1CiJmk5GlLIr_Ce8gM3zDd7y0JyeJEImEgiryqy6jJYES5aiRfn5I08SBsKzCu79DfW9QX0H8XQFBAQ1yqU93sMFL/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.
>
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Re: [Freesurfer] Freeview Closes Unexpectedly

2022-07-21 Thread Wang, Ruopeng

Have you install the FS license file properly? Another thing to check is to 
make sure you have granted freeview permission to access your disk files. You 
can check it in the system preferences.

Ruopeng

On Jul 21, 2022, at 12:31 PM, 
user2038...@gmail.com wrote:


External Email - Use Caution

Hi,

When I try to open any files in Freeview on a MacBook, the application closes 
unexpectedly. I only receive a message from Apple that says "Freeview quit 
unexpectedly" but gives no reason. This happens after I open the application 
and try to load a volume. After Freeview closes, I can open it again but the 
file does not open. How can this be resolved?
___
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Freesurfer@nmr.mgh.harvard.edu
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 
 .
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 GUI overlay and registration

2022-06-19 Thread Douglas N. Greve




On 6/15/2022 1:26 PM, Kuo, Yi-Ling wrote:


Hello,

The below solutions sounded like data need to be analyzed with 
Freesurfer individually to get the registration file?


The anatomical  must be analyzed in FS, but not the fMRI. See eg 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview


I realized that the stats can be presented in Freeview with the 
correct locations in T1, but when it comes to inflated surface, the 
BOLD signals always present in a specific location regardless of 
dataset (please see the attached figure, looks like it’s a 
registration issue). I wonder if the data were already analyzed by FSL 
in group level, is it possible to present the analyzed group data on 
inflated surface in Freeview?



Yes, see web page above


Thank you again for helping,

Irene

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


*Date: *Wednesday, June 8, 2022 at 11:15 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Freeview GUI overlay and registration

You will need an lta file that maps from the anatomical to the fmri. 
You can get this with something

bbregister --mov template.nii.gz --s subject --t2 --reg reg.lta
where template.nii.gz is the fmri motion correction template or the 
mean fmri (I forgot what it is called in FSL)


On 6/3/2022 5:12 PM, Kuo, Yi-Ling wrote:

Hi Freesurfer experts,

I am trying to use the Freeview GUI to load fMRI BOLD activation
data (analyzed in FSL) and project on the inflated surface. I used
the feature “Overlay/Load generic” and was prompted to select
overlay file and/or apply registration. The selected overlay file
didn’t seem to project on the right spot on the inflated surface
as would be seen in T1. If registration was the issue, what
registration file should be selected in the Freeview GUI?

My Freeview was updated. Thank you very much for helping.

Irene



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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 
<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 GUI overlay and registration

2022-06-08 Thread Douglas N. Greve

You will need an lta file that maps from the anatomical to the fmri. You 
can get this with something

bbregister --mov template.nii.gz --s subject --t2 --reg reg.lta
where template.nii.gz is the fmri motion correction template or the mean 
fmri (I forgot what it is called in FSL)


On 6/3/2022 5:12 PM, Kuo, Yi-Ling wrote:


Hi Freesurfer experts,

I am trying to use the Freeview GUI to load fMRI BOLD activation data 
(analyzed in FSL) and project on the inflated surface. I used the 
feature “Overlay/Load generic” and was prompted to select overlay file 
and/or apply registration. The selected overlay file didn’t seem to 
project on the right spot on the inflated surface as would be seen in 
T1. If registration was the issue, what registration file should be 
selected in the Freeview GUI?


My Freeview was updated. Thank you very much for helping.

Irene


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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.

Re: [Freesurfer] Freeview XDG_runtime_dir not set

2022-06-06 Thread Wang, Ruopeng

This thread might be helpful:
https://stackoverflow.com/questions/59790350/qstandardpaths-xdg-runtime-dir-not-set-defaulting-to-tmp-runtime-aadithyasb

Ruopeng

On Jun 5, 2022, at 9:29 PM, Manuela Dorado Novoa 
mailto:manue...@uw.edu>> wrote:


External Email - Use Caution

Hi Freesurfer team,

I am having issues launching freeview from my linux terminal. My freesurfer 
works fine but when I call freeview it opens but I can't load images, I get an 
error message in my terminal that says: "QStandardPaths: XDG_RUNTIME_DIR not 
set, defaulting to '/tmp/runtime-manuela.dorado'"

I noticed that a user had the same issue but their 
post
 did not reflect any reply so I do not know what the solution could be to this.

Thank you for your help.

MANUELA DORADO NOVOA
Research Scientist I
Buffalo Learning & Memory Lab
Dept. of Physiology & Biophysics

[https://secure-web.cisco.com/1al1A4ftN0gkykUTrGbL263m9nbGndnjlrhhOIXkRKah4teUO4Sy_yo96MdhiKeL58G-AooeRN6j1Mye-VxiZU6iPR0ioM2q5BYa2kjkaqlOGKWIgxDTV0s2c6mzmLmlpZHquWrugoGIeH6XLzk3n100RBmvf7dXpL18WNO-lWDpdGyD8oQGeDqqolddsD3EvePAj9qNMhnfCKB4EvZUpTvefRFE6kkFaau9KITgnO7vt_eKFAxrsR_KAtCqZ5gqVDT-T2gS_iNfMCAtZtYNONkf57F5hoWGgj3EYMJCEdPN77fscFiNariXHsvQmZJES1I7NaH6Jb8DS7uKC0lhn8g/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4zQqZOgBkEvdWZ4l4w5u9PHG8ozQXqGaWrJPxusNas5iADBRQJHC-zsCeGloU0U7uq_fDUjmLY]

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 .
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Re: [Freesurfer] Freeview XDG_runtime_dir not set

2022-06-05 Thread fsbuild

External Email - Use Caution

I've seen XDG_RUNTIME not be set/recognized if you are logged in as root/admin
user or prefacing your commands with sudo when you run them logged in as a
normal or non-privileged user.

It might help for us know what operating system you are on, what version of
freesurfer you are running and how freesurfer was installed, e.g., did you use
the package installer or the tar archive.

- R.
On Jun 5, 2022, at 21:29, Manuela Dorado Novoa manue...@uw.edu
wrote:External Email - Use
CautionHi Freesurfer team,I am
having issues launching freeview from my linux terminal. My freesurfer works
fine but when I call freeview it opens but I can't load images, I get an error
message in my terminal that says: "QStandardPaths: XDG_RUNTIME_DIR not set,
defaulting to '/tmp/runtime-manuela.dorado'"I noticed that a user had the same
issue but theirpostdid not reflectany reply so I do not know
what the solution could be to this.Thank you for your help.MANUELA DORADO
NOVOAResearch Scientist IBuffalo Learning Memory LabDept. of Physiology
Biophysics___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] [Freeview] View Flatmap

2022-04-21 Thread Douglas N. Greve


in freeview, runsomethiing like
freeview -f rh.white:patch=rh.full.flat.patch.3d
The rh.white is just there to give freeview a full surfce to load. You 
will only see your patch


On 4/14/2022 4:30 AM, Morgenroth Elenor wrote:


External Email - Use Caution

Dear Freesurfer Experts,
I have been using
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch 


to create flatmaps of individual subjects. This ran without any errors and I 
have a 'rh.full.flat.patch.3d’ file now.
I can’t figure out how to visualise it to check it (in freeview).
I have also tried to use pycortex to visualise this as I’m eventually aiming to 
plot data onto my flatmap, but that isn’t working either (I get a different 
error (ExpatError) using my flatmap as I get with the example flatmap, but I 
also can’t visualise the example flatmap in freeview).
Thank you for your help!
Ellie

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Re: [Freesurfer] freeview crashes

2022-04-04 Thread fsbuild

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Hello Stephen,

I'll assume the VM is setup according to the online instructions, e.g.,
the VM is assigned 8G of RAM and 2 cores from the host machine. I'll
also assume you are opening files with freeview from within the VM's
virtual disk, e.g., from the home directory you login to on the VM.

I would try upgrading to the latest version of VirtualBox for Windows
which is currently 6.1.32. When you launch VirtualBox it should notify
you there is a new version available and ask if you want to upgrade.

Do you have some version of the Windows Subsystem for Linux (WSL) also
installed? That can sometimes be an issue, but the error you report
does not look to be from that..

- R.

"Ogier, Stephen E. (Assoc)" (stephen.og...@nist.gov)
April 4, 2022 at 13:41

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Caution

Hi,

I’m new to Freesurfer, and I’m running into a reoccurring crash issue when I
use freeview. I’m following the instructions at
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1DlH8w4XzRPlr6j2W2uoSddaowTh89VvPAV2BtYs1gUDJdNrhxHoNiJ-3FIH4dCs_NwT-Cwm5dARFHAD5_tw9OBGOiZklIFhTvRMaWCiqtzbqYOdY5V6XHGtEs_R4olJdoPfHA6f79sXT82IUzw1qmviXd5K8eCoBxZ3Ki8R7G81B6Bp_NVtopFTbJWlTTW5JTTFGhQoFlaJhA5ldbM9a6ZidLsa5ncUglZdF-2WxNeTMObqfrDkgSqulebLV9PQTy0uGAcxU2wUyxldfHBjoMeyh6i3Q3VX2Gl7_m2EbZW-yMv22SGo3SxeO01ivkLA9/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview
After I open freeview, if I use the mouse to manipulate the image,
eventually the program crashes and I receive this error message.

The instruction at 0x7ffa0d9b3460 referenced memory at 0x0010.
The memory could not be read.

Click on OK to terminate the program

I’ve received this kind of error multiple times.
The addresses for the instruction varies, and the memory address has
also been 0x.

Has anyone else come across this problem? For
reference, I’m running the FS_7_2_0_ubuntu_18_04_06 VM in VirtualBox 6.1
on a Windows 10 PC (Version 20H2, OS Build 19042.1586).

Thanks,

Stephen Ogier, PhD
Postdoctoral Associate, Magnetic Imaging Group, Applied Physics Division
National Institute of Standards and Technology

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Re: [Freesurfer] Freeview error on centos7

2022-03-14 Thread Wang, Ruopeng

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

Thanks,
Ruopeng

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


External Email - Use Caution

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

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

Thanks in advance for your help.

Best,
Wen
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Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

2022-02-20 Thread Harriet Dempsey-Jones

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Hi Ruopeng,

My apologies – I am not completely across all the details of my remote machine 
access and a bit unfamiliar with the terminology.

I have attached below details of how I connect to the remote windows machine 
from my mac. I first open a VPN and enter my university details, I then hit 
this page where I enter my university details again and it takes me through.

Looks like it is powered by FastX from StarNet, I think? Is this the detail you 
meant?

Thank you again for your help,

Harriet


[cid:image001.png@01D82719.1C7B7BF0]

The above is an image so I included the links here:

FastX link: 
https://secure-web.cisco.com/1l6q0I7n4VYN05ZCq7ruEwTR97Gp6VXIhUH27rZA5UpL9ziEMD-2qRpBeHcBov5ehLIS2JahRk9fRLZN17hAN2r7_60wwZ9TY_9qE5IKhwR3cQMklno5Iy-uhkWE37004msPSeQ5EM36fbuP3HEka403vLVZBan8JDzBz9_QtpYWgGg2o6A5TMMXjGqHjzT6e6YdtfzsBbmtz8Vjl1SuVtYsBP1k5OpDBDAvoyxU4MWVh0RA8r5CVOpWIbmXJtTazqz2X_woXGyWc4KoqB0gkwRMVSAJ7iY5MCAYmTKtOxr9UIckPDrNwj9ihGjUWS8vu/https%3A%2F%2Fwww.starnet.com%2Ffastx%2F%3Fsource%3DFastX3-3.2.34

Build 3.2.34 link: 
https://secure-web.cisco.com/1Kl5EpdIPbDRC6a61pkfp7FHRJPpw6OTCKXOKr0fy4CzohuQUDZVURnNw94BFtO0VLVQr4yMVPJMN0NReQ5Ofehr1ZlSQR_gfJDxuxFhDHtpIgnS4RygRBBGPT8egfB8u5-CoWV9-G9cKt4-sIchJmDmAj-zR78ZUYnqb4wy-Dufd2t1VkPalhumLWHzA3Jkzz2DyiJ5G4rBIftgxb9kVUbR_xRnWsD_ZCz4mUTy-vVEyu88UX_93l1I7Cf7CvBAsV9ta_yuN5xCEr_LyNKOPmvRQzlPyafl5XKSZ2oQ5gIec_kKodr9FxkNkknnwdpVk/https%3A%2F%2Fwww.starnet.com%2Fxwin32kb%2Ffastx-3-server-release-notes%2F%3Fsource%3DFastX3-3.2.34


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

Date: Saturday, 19 February 2022 at 1:28 am
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind 
volumes
That question was for Windows. How do you connect to the remote machine from 
your mac? via VNC? Nomachine?


On Feb 18, 2022, at 1:02 AM, Harriet Dempsey-Jones 
mailto:h.dempseyjo...@uq.edu.au>> wrote:

External Email - Use Caution
Hi there,

Thank you for your response!

I'm not sure 100% what the answer to this is - I am connecting to the remote 
machine from a mac (well, two different macs, my home and work macs).

I am not sure what the x-term software is. Do you mean the terminal I use 
inside the remote desktop to open freeview? (see image below)

Thank you,

Harriet




Dr Harriet Dempsey-Jones
Postdoctoral Researcher
School of Psychology
The University of Queensland
Brisbane Qld 4072 Australia

E  h.dempseyjo...@uq.edu.au<mailto:h.dempseyjo...@uq.edu.au> W 
uq.edu.au<http://secure-web.cisco.com/1g0mnyf7Mh5mlYyGV5FOnPmMxbqxAL20rRleOF-_ytgqGNG3HgzFcSZM9S-PhyvJTsDcJtkbt5UCtI1slB22dhxaoHwz6EcU_nqwJUpL9NK3ekqPIeRKJPflpVl7JSpafLxkz0HmbVpqja_n-wwaz1-WEz0qMP3WQhszo1AsJBCwj1uCcROh3VljV_jePxtEOQXO9QtPhFnUx2h1QaQAqReC1ZcstRtYySPVFL9HTgKoLutYRwl4gDrH2xk6ZIMLcseFhoI5IsUt8vnaxsIkWJZyLFFzvvgYfASQFEZuHR1nFMbQAMyQ8tmZX0zWApafsLcfGxuo7xe421XP5W7YzmA/http%3A%2F%2Fwww.uq.edu.au%2F>






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: Friday, 18 February 2022 8:25 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind 
volumes

It sounds like a remote display issue. Are you connecting from a Windows 
machine? If so what x-term software do you use?

Ruopeng


On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones 
mailto:h.dempseyjo...@uq.edu.au>> wrote:

External Email - Use Caution
 Hi there,


I am having a weird problem with freeview… When l load some volumes and some 
surfaces together, I can’t see the surfaces because they are hidden ‘behind’ 
the volumes. They normally sit on top, but now I can only see them if I toggle 
off the volumes – which is not useful as I need both at once.


They are definitely in alignment as I can see them when I toggle, and when I 
look at old data that I know I could view properly (and surfaces-volumes are in 
alignment) I have the same issue. I can't move them up, as you can only move 
position within volumes and surfaces. I tried to attach a video but my email 
got bounced for being too large - happy to send directly if it is helpful


I am using the below code to load things (though have also manually loaded 
stuff in freeview). The code has not changed since it worked in the past…


I have tried searching the freesurfer help, but can’t find anything on my 
issue… Any help would be appreciated


Thanks!


Harriet


p.s., I am using freesurfer/ freeview on a remote machine of my university. 
They inform me no updates have been performed




CODE


freeview -v mri/T1.mgz \
mri/brainmask.mgz \
mri/wm.mgz:visible=0 \
-f surf/lh.

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

2022-02-18 Thread Wang, Ruopeng

That question was for Windows. How do you connect to the remote machine from 
your mac? via VNC? Nomachine?

On Feb 18, 2022, at 1:02 AM, Harriet Dempsey-Jones 
mailto:h.dempseyjo...@uq.edu.au>> wrote:

External Email - Use Caution

Hi there,

Thank you for your response!

I'm not sure 100% what the answer to this is - I am connecting to the remote 
machine from a mac (well, two different macs, my home and work macs).

I am not sure what the x-term software is. Do you mean the terminal I use 
inside the remote desktop to open freeview? (see image below)

Thank you,

Harriet





Dr Harriet Dempsey-Jones
Postdoctoral Researcher

School of Psychology
The University of Queensland
Brisbane Qld 4072 Australia



E  h.dempseyjo...@uq.edu.au<mailto:h.dempseyjo...@uq.edu.au> W 
uq.edu.au<http://secure-web.cisco.com/1g0mnyf7Mh5mlYyGV5FOnPmMxbqxAL20rRleOF-_ytgqGNG3HgzFcSZM9S-PhyvJTsDcJtkbt5UCtI1slB22dhxaoHwz6EcU_nqwJUpL9NK3ekqPIeRKJPflpVl7JSpafLxkz0HmbVpqja_n-wwaz1-WEz0qMP3WQhszo1AsJBCwj1uCcROh3VljV_jePxtEOQXO9QtPhFnUx2h1QaQAqReC1ZcstRtYySPVFL9HTgKoLutYRwl4gDrH2xk6ZIMLcseFhoI5IsUt8vnaxsIkWJZyLFFzvvgYfASQFEZuHR1nFMbQAMyQ8tmZX0zWApafsLcfGxuo7xe421XP5W7YzmA/http%3A%2F%2Fwww.uq.edu.au%2F>







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: Friday, 18 February 2022 8:25 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind 
volumes

It sounds like a remote display issue. Are you connecting from a Windows 
machine? If so what x-term software do you use?

Ruopeng

On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones 
mailto:h.dempseyjo...@uq.edu.au>> wrote:

External Email - Use Caution

 Hi there,



I am having a weird problem with freeview… When l load some volumes and some 
surfaces together, I can’t see the surfaces because they are hidden ‘behind’ 
the volumes. They normally sit on top, but now I can only see them if I toggle 
off the volumes – which is not useful as I need both at once.



They are definitely in alignment as I can see them when I toggle, and when I 
look at old data that I know I could view properly (and surfaces-volumes are in 
alignment) I have the same issue. I can't move them up, as you can only move 
position within volumes and surfaces. I tried to attach a video but my email 
got bounced for being too large - happy to send directly if it is helpful



I am using the below code to load things (though have also manually loaded 
stuff in freeview). The code has not changed since it worked in the past…



I have tried searching the freesurfer help, but can’t find anything on my 
issue… Any help would be appreciated



Thanks!



Harriet



p.s., I am using freesurfer/ freeview on a remote machine of my university. 
They inform me no updates have been performed





CODE



freeview -v mri/T1.mgz \
mri/brainmask.mgz \
mri/wm.mgz:visible=0 \
-f surf/lh.smoothwm:edgecolor=yellow \
surf/lh.pial:edgecolor=red \
-viewport cor -layout 1



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Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

2022-02-17 Thread Wang, Ruopeng

It sounds like a remote display issue. Are you connecting from a Windows 
machine? If so what x-term software do you use?

Ruopeng

On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones 
mailto:h.dempseyjo...@uq.edu.au>> wrote:

External Email - Use Caution

 Hi there,



I am having a weird problem with freeview… When l load some volumes and some 
surfaces together, I can’t see the surfaces because they are hidden ‘behind’ 
the volumes. They normally sit on top, but now I can only see them if I toggle 
off the volumes – which is not useful as I need both at once.



They are definitely in alignment as I can see them when I toggle, and when I 
look at old data that I know I could view properly (and surfaces-volumes are in 
alignment) I have the same issue. I can't move them up, as you can only move 
position within volumes and surfaces. I tried to attach a video but my email 
got bounced for being too large - happy to send directly if it is helpful



I am using the below code to load things (though have also manually loaded 
stuff in freeview). The code has not changed since it worked in the past…



I have tried searching the freesurfer help, but can’t find anything on my 
issue… Any help would be appreciated



Thanks!



Harriet



p.s., I am using freesurfer/ freeview on a remote machine of my university. 
They inform me no updates have been performed





CODE



freeview -v mri/T1.mgz \
mri/brainmask.mgz \
mri/wm.mgz:visible=0 \
-f surf/lh.smoothwm:edgecolor=yellow \
surf/lh.pial:edgecolor=red \
-viewport cor -layout 1



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Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations

2022-01-02 Thread Douglas N. Greve


Chris/Ruopeng, you can use https://transfer.partners.org


On 12/17/2021 11:41 AM, Christopher Panks wrote:


External Email - Use Caution

Hi Ruopeng,

I can send the niftis to an individual, but I cannot post them to a 
listserv.


Version info:

freesurfer-linux-ubuntu18_x86_64-dev-20211028-42af00d

FreeView Version 3.0 Build Oct 28 2021 08:53:38

I get this warning when I start FreeView:

X server does not support XInput 2

failed to get the current screen resources

QXcbConnection: XCB error: 1 (BadRequest), sequence: 165, resource id: 
90, major code: 130 (Unknown), minor code: 47


QXcbConnection: XCB error: 170 (Unknown), sequence: 178, resource id: 
90, major code: 146 (Unknown), minor code: 20


QXcbConnection: XCB error: 170 (Unknown), sequence: 178, resource id: 
90, major code: 146 (Unknown), minor code: 20


Thank you so much for your help!

Chris Panks

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Wang, Ruopeng

*Sent:* Tuesday, December 14, 2021 6:12 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Freeview Transform Volume tool - output 
nifti keeps rotations but loses translations


What version of Freesurfer are you using? Would it be possible to send 
us the volume files before and after the rotation?


Best,

Ruopeng



On Dec 14, 2021, at 6:10 PM, Christopher Panks  wrote:

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I’m trying to get images of post-mortem brains, some from
cadavers, some excised, into standard space. I’m new to Freeview,
so I’m not sure if I’m doing something wrong, or my expectations
are wrong. I find the Transform Volume tool easy to use to get an
image that is correctly rotated, and shifted so that the image is
centered in the frame. The image looks great in the Freeview panes.

Upon saving and then opening  the output nifti, I find the
rotational changes have stuck, but the image is as off-center as
the original, with the coronal and axial off towards one side, and
the sagittal not at the midbrain.

When saving the image, I click on ‘Save Volume as…’, leave the
boxes unchecked (‘do not resample’’, and ‘crop to’ ), I modify the
file name, then click OK.  I don’t click on ‘Move Center…’, I
don’t check ‘Apply to all…’.

My expectation is that the image would not only be correctly
rotated, but that it would also be centered. Is that the expected
behavior here?

I’ve tried the ‘Move Center to Current Cursor Location’, and the
Apply to all visible volumes, and see no difference. The
off-centeredness is visible in multiple viewers, FSLEyes,
MRIcroGL, and ROIEditor. The directions seem so simple and clear,
I’m just baffled.

Thank you!

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