[Freesurfer] freesurfer results QC

[yunus soleymani]

External Email - Use Caution

Hi Freesurfer users,
I have recently used the FSQC algorithm 
(https://secure-web.cisco.com/1EzTQr-pZpN3NDVSECe0dGNYNhra0JW3OGYIpwSTpVNT4vxODxghAli6kPP9TwN8sZnTisGBBFM1GrOQ02XnTu3sRnNyMTuE-yEqScIQFgCHQFAUmdiJucGAl_RdzKVclgzJ-4S1o3hyVPj_0L2cfG_mwtsfyWmy4AxwGwyzsSSv2mYHSJX_g0xlb4zy2Cwb9QIBQN7IwlDN86tpgNPVkiU9MBI0XXxpJ5z3G4NI4iRQ4zCINu0LtkecfldLDBrNPFv0cEbJN4ejg_j90CciHy4yce6DujbvtPWLs8pMA69y4T0VIqE3tYYpv9YTecrLBOxsOUQdDZ_nbL7cw89PFkgULs7Cglyq9Pmpu-lblOJc/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc%23usage)
 to check the quality of my Freesurfer volumetric results. However, I am having 
trouble understanding the meaning of the output numbers. What is the acceptable 
threshold number of SNR? I would appreciate any help you can provide.
Thank you,
Yunus
 

 

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Re: [Freesurfer] license issue with the updated version

[fsbuild]

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Please let us know if you are runningMacOS 14 (Sonoma) on an Intel 
or silicon Mac (M1, M2 chip).  The system requirements at 
https://secure-web.cisco.com/10qwlQRot-nOOCuaXBtxsk1Ua4Tfh-PQlj0cP9-E6KzZM5idg3c7iTvMmQOzSG9PAcBrbFYMe35KnBiCn3y7IG-rVgEj0kSLvVbOHwxylEX_7qd2UpvZd0RI-joHMIjoQqJdBRMrn0pnSFHnz-SFFpzBuN9LN_tXR69BAZD8GdgOe42Qemok-1oStCPJooJ1xLsKbXOVgiFxHk0d55wZOgkW-uv9xSSB5VxhPx4QaNdwbS0mGZXww_bzMfboFOLEITeum3djwVx3EMwWM__x1IexmzFZEqSnGdgzzfIzKOYETgIxs35-X4U51g2Caz2Zn--cVCQFL8QZpew0IVrOvKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
 list MacOS 13 (Ventura) as the latest supported MacOS for the 7.4.1 release.
- R.

On Nov 18, 2023, at 18:29, Atena Akbari atenaakb...@gmail.com 
wrote:QObject::killTimer: Timers cannot be stopped from another thread

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Re: [Freesurfer] license issue with the updated version

[Atena Akbari]

External Email - Use Caution

Thanks a lot, Yujing, I updated the FS_LICENSE accordingly, but when I want
to load a surface in freeview I get the following error:

QObject::killTimer: Timers cannot be stopped from another thread
QObject::~QObject: Timers cannot be stopped from another thread

also, with tkregister2 or tkregisterfv I don't get the GUI, it gives me the
"MRIread failed" error. I appreciate your help.

All the best,
Atena

On Sat, Nov 18, 2023 at 1:00 PM Huang, Yujing 
wrote:

> Hi Atena,
>
>
>
> Can you check if you have environment variable FS_LICENSE set?
>
> >echo $FS_LICENSE
>
>
>
> Set FS_LICENSE to your license file in 7.4.1,
>
> >export FS_LICENSE=
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Atena Akbari
> *Sent:* Friday, November 17, 2023 6:06 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] license issue with the updated version
>
>
>
> *External Email - Use Caution*
>
> Dear freesurfer team
>
>
>
> I have uninstalled the previous versions of freesurfer on my mac (Sonoma
> 14.1), and have installed a new version 7.4.1 based on the step by step
> freesurfer installation info on the website. I have set the freesurfer home
> directory as follows:
>
>
>
> export FREESURFER_HOME=/Applications/freesurfer/7.4.1/
>
> export SUBJECTS_DIR=path/to/my/data
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>
>
> and the license is in the /Applications/freesurfer/*MailScanner has
> detected a possible fraud attempt from "7.4.1" claiming to be* *
> MailScanner warning: numerical links are often malicious:* 7.4.1.
>  But when I run a freesurfer command I get the following
> error:
>
>
>
> ERROR: FreeSurfer license file /Applications/freesurfer/7.2.0/license.txt
> not found.
>
> QObject::killTimer: Timers cannot be stopped from another thread
>
> QObject::~QObject: Timers cannot be stopped from another thread
>
> /Applications/freesurfer/7.4.1//bin/freeview: line 2:  2938 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>
>
>
> Could you help me with this issue?
>
>
>
> thanks so much.
>
>
>
> Best,
>
> Atena
> ___
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> 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/1FS2W3Ked5KnVBVcy1_V77W_0hRtD5Y3ayHccRVbabdim2UmWAT61-LfKKvn8a_TuA2jNG-L0m9NSiMlV_G6Am4_H26dIpKwy8hJ8Oagsl8AiJfwOvZUyGE7L2vIj5QePEq0H-AqIruY8nfbaKHpJ2bmgVlDWoZAUucBhkUD3IWf0mY9EEPbmd7eX5yrFYX80A9vatjglXwqePyuzvqQYneBqB6PgFuDO7YU3jvStNKAnCS3o9BfIuSFvDXUUUtAlPZ0QRJJFVPk-48lfpSUvpBI8BjXlMI-w2rdJaLCgTs7Rhrw8DS0XpTRPecDih5ehI9B9Bpz9RgVWdZeLmw00rg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1FS2W3Ked5KnVBVcy1_V77W_0hRtD5Y3ayHccRVbabdim2UmWAT61-LfKKvn8a_TuA2jNG-L0m9NSiMlV_G6Am4_H26dIpKwy8hJ8Oagsl8AiJfwOvZUyGE7L2vIj5QePEq0H-AqIruY8nfbaKHpJ2bmgVlDWoZAUucBhkUD3IWf0mY9EEPbmd7eX5yrFYX80A9vatjglXwqePyuzvqQYneBqB6PgFuDO7YU3jvStNKAnCS3o9BfIuSFvDXUUUtAlPZ0QRJJFVPk-48lfpSUvpBI8BjXlMI-w2rdJaLCgTs7Rhrw8DS0XpTRPecDih5ehI9B9Bpz9RgVWdZeLmw00rg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
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Re: [Freesurfer] license issue with the updated version

[Huang, Yujing]

Hi Atena,

Can you check if you have environment variable FS_LICENSE set?
>echo $FS_LICENSE

Set FS_LICENSE to your license file in 7.4.1,
>export FS_LICENSE=

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Atena Akbari
Sent: Friday, November 17, 2023 6:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] license issue with the updated version


External Email - Use Caution
Dear freesurfer team

I have uninstalled the previous versions of freesurfer on my mac (Sonoma 14.1), 
and have installed a new version 7.4.1 based on the step by step freesurfer 
installation info on the website. I have set the freesurfer home directory as 
follows:


export FREESURFER_HOME=/Applications/freesurfer/7.4.1/

export SUBJECTS_DIR=path/to/my/data

source $FREESURFER_HOME/SetUpFreeSurfer.sh



and the license is in the /Applications/freesurfer/MailScanner has detected a 
possible fraud attempt from "7.4.1" claiming to be MailScanner warning: 
numerical links are often malicious: 7.4.1. But when I run a 
freesurfer command I get the following error:



ERROR: FreeSurfer license file /Applications/freesurfer/7.2.0/license.txt not 
found.

QObject::killTimer: Timers cannot be stopped from another thread

QObject::~QObject: Timers cannot be stopped from another thread

/Applications/freesurfer/7.4.1//bin/freeview: line 2:  2938 Segmentation fault: 
11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"



Could you help me with this issue?



thanks so much.



Best,

Atena
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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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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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