Re: [Freesurfer] Problem installing FreeSurfer

2023-06-01 Thread Michelangelo Fabbrizzi 
External Email - Use Caution

Dear all,

thanks for your reply. I did as below and the first time I run the command 
“freeview”, it works. Then if I try to open it again, it gives the same error 
as below…can you help me please?

Thanks, appreciated,

Michelangelo

> Il giorno 31 mag 2023, alle ore 23:43, fsbuild  ha 
> scritto:
> 
> 
> Please make sure you have downloaded a freesurfer license.txt file by filling 
> out the form at,
> https://secure-web.cisco.com/1hc5Xc7px__3EjuoO1_Ni4orsJzMv2R3iM-TJ3g17W6pD1Jv2-zP7lu8luJ73VfXWqrsbHX_7eZc4dqW0qWuk88NFuUNQxZ7E35P7PaGZrx3_HXCb5RW8jZWDDtzYCB_ukWSy3Fz5lbERnNvMc0l8SgVPh66EIA3pkAdAz9x6wHNX_sxP2xYQ4KCLPgHYRndbQ5stn4tNAVOQ7iNJMa_86RhGR2kP6sEXQ_MQzPRxYuQdUq-PQnSOzmYT1KnKZFMtzRCEAgwtXdhwDvUybAWLzyl6qjmND8kf0yQveUBT1m0eM_PHPXIOqS9cs64lCoxG/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
>  
> 
> 
> Place the license.txt file you will receive in your home directory, e.g., 
> 
> $ cd $HOME
> $ head -1 license.txt
> 
> 
> Set the FS_LICENSE environment variable manually (and/or in your shell 
> initialization file, e.g., .bashrc) to point to the license file,
> … here set from a terminal window running bash shell ...
> 
> $ export FS_LICENSE=$HOME/license.txt
> 
> Setup the freesurfer environment,
> 
> $ export FREESURFER_HOME=/Applications/freesurfer/7.4.0
> $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>  freesurfer-darwin-macOS-7.4.0-20230504-55dcf98 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/7.4.0
> FSFAST_HOME   /Applications/freesurfer/7.4.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/7.4.0/subjects
> MNI_DIR   /Applications/freesurfer/7.4.0/mni
> 
> $ which freeview
> /Applications/freesurfer/7.4.0/bin/freeview
> 
> Then try running freeview with no arguments to see if it brings up an empty 
> window,
> 
> $ freeview
> 
> If that works, quit freeview and try running it again with an example volume 
> included in the distribution,
> 
> $ freeview  $SUBJECTS_DIR/bert/mri/brain.mgz
> 
> If that works, quit freeview and try your own surface/volume files.
> 
> - R.
> 
>> On May 31, 2023, at 17:05, Michelangelo Fabbrizzi  
>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Dear Sirs,
>> 
>> I am new to Freesurfer. I installed as shown on website and added the 
>> license.txt, however when I open freeview I get an error 
>> "/Applications/freesurfer/7.4.0/bin/freeview: riga 2:  2047 Segmentation 
>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“”
>> Attached the report.
>> 
>> Freesurfer version: freesurfer-darwin-macOS-7.4.0-20230510-e558e6e
>> Platform: MacOS12.6.6
>> Mac: Macbook Pro Intel Core i5 dual-core
>> XQuartz2.8.15
>> XQuartz2.8.5
>> Can you help me please?
>> 
>> Thanks!
>> 
>> Michelangelo
>> 
> 
> 

___
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] Problem installing FreeSurfer

2023-05-31 Thread fsbuild 
External Email - Use Caution

Please make sure you have downloaded a freesurfer license.txt file by filling 
out the form 
at,https://secure-web.cisco.com/1jgHYKP0gy8_587mR2rxpzl3o6QwcsGjVygS8rScUOspFTxWDtMmYhVhh6hU-aNAXMR1qSecHes0FARTm1N88hQVXJ1HyCBQqYAvKw0Qa5D_vX6JKYipGqWQZB-NtPRVEg-gY-2H60q15hHSBeS8oWRBXs22WKoo_FHa42Xsbn5STf0zYCW5SWi4lZASwEZPtYTCtvtQWFQpzhPl1R2kBpPyAGuPQ6CWFX0LyZoJtXBSccps_g8oCOWXYEx7_wPfCc8EiW8PSnm7Ko48ktM35qkcOIVYy-6M5CkLgvsM6Zoo8kB3-baWzfmvJk1y1E-s1/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
Place the license.txt file you will receive in your home directory, e.g.,
$ cd $HOME$ head -1 license.txtemail you used to register
Set the FS_LICENSE environment variable manually (and/or in your shell 
initialization file, e.g., .bashrc) to point to the license file,… here set 
from a terminal window running bash shell ...
$ export FS_LICENSE=$HOME/license.txt

Setup the freesurfer environment,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.0$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-darwin-macOS-7.4.0-20230504-55dcf98 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.4.0
FSFAST_HOME  /Applications/freesurfer/7.4.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.0/subjects
MNI_DIR
/Applications/freesurfer/7.4.0/mni

$ which freeview/Applications/freesurfer/7.4.0/bin/freeview
Then try running freeview with no arguments to see if it brings up an empty 
window,
$ freeview
If that works, quit freeview and try running it again with an example volume 
included in the distribution,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If that works, quit freeview and try your own surface/volume files.
- R.
On May 31, 2023, at 17:05, Michelangelo Fabbrizzi michef...@gmail.com 
wrote:External Email - Use 
CautionDear Sirs,I am new to 
Freesurfer. I installed as shown on website and added the license.txt, however 
when I open freeview I get an error 
"/Applications/freesurfer/7.4.0/bin/freeview: riga 2:2047 
Segmentation fault: 
11$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview 
"$@“”Attached the report.Freesurfer version: 
freesurfer-darwin-macOS-7.4.0-20230510-e558e6ePlatform: MacOS12.6.6Mac: Macbook 
ProIntel Core i5 dual-coreXQuartz2..8.15XQuartz2.8.5Can you help me 
please?Thanks!Michelangeloreport.txt
___
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.

[Freesurfer] Problem installing FreeSurfer

2023-05-31 Thread Michelangelo Fabbrizzi 
External Email - Use CautionDear Sirs,I am new to Freesurfer. I installed as shown on website and added the license.txt, however when I open freeview I get an error "/Applications/freesurfer/7.4.0/bin/freeview: riga 2:  2047 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“”Attached the report.-
Translated Report (Full Report Below)
-

Process:   freeview [2074]
Path:  
/Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview
Identifier:org.martinos.freeview
Version:   7.3.2 (100)
Code Type: X86-64 (Native)
Parent Process:bash [2073]
Responsible:   Terminal [1299]
User ID:   501

Date/Time: 2023-05-31 23:02:37.7243 +0200
OS Version:macOS 12.6.6 (21G646)
Report Version:12
Anonymous UUID:0FF1F8BB-D74E-EBFE-3D6D-3F90E594D1DE


Time Awake Since Boot: 2500 seconds

System Integrity Protection: enabled

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

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x02280021
Exception Codes:   0x0001, 0x02280021
Exception Note:EXC_CORPSE_NOTIFY

Termination Reason:Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process:   exc handler [2074]

VM Region Info: 0x2280021 is not in any region.  Bytes after previous 
region: 2366109110306  Bytes before following region: 103182294319071
  REGION TYPESTART - END [ VSIZE] PRT/MAX 
SHRMOD  REGION DETAIL
  mapped file 118c4-118e83000[ 2316K] r--/rwx 
SM=COW  ...t_id=d4d67611
--->  GAP OF 0x5ffee717d000 BYTES
  MALLOC_NANO  6000-6800 [128.0M] rw-/rwx 
SM=PRV  

Thread 0 Crashed::  Dispatch queue: com.apple.main-thread
0   freeview   0x102019b98 0x101e26000 + 2046872
1   QtWidgets  0x1136ef413 
QWidget::event(QEvent*) + 1283
2   QtWidgets  0x11382e5a4 
QMainWindow::event(QEvent*) + 276
3   QtWidgets  0x11369f0b7 
QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
4   QtWidgets  0x11369fffc 
QApplication::notify(QObject*, QEvent*) + 508
5   QtCore 0x1147d71da 
QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
6   QtWidgets  0x113706de4 0x113693000 + 474596
7   QtWidgets  0x113704d5a 0x113693000 + 466266
8   QtWidgets  0x11369f0b7 
QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
9   QtWidgets  0x11369fffc 
QApplication::notify(QObject*, QEvent*) + 508
10  QtCore 0x1147d71da 
QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
11  QtGui  0x112b6e82d 
QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*)
 + 493
12  QtGui  0x112b6f036 
QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*)
 + 470
13  QtGui  0x112bc729c 0x112ae6000 + 922268
14  libqcocoa.dylib0x113cdba50 0x113c92000 + 301648
15  libqcocoa.dylib0x113cd48c9 0x113c92000 + 272585
16  libqcocoa.dylib0x113cd437c 0x113c92000 + 271228
17  QtGui  0x112bb893e 
QWindowPrivate::create(bool, unsigned long long) + 206
18  QtWidgets  0x1136ddd9d 
QWidgetPrivate::create() + 1037
19  QtWidgets  0x1136db881 
QWidget::create(unsigned long long, bool, bool) + 321
20  QtWidgets  0x1136dd8e7 
QWidgetPrivate::createWinId() + 103
21  QtWidgets  0x1136dd8e7 
QWidgetPrivate::createWinId() + 103
22  QtWidgets  0x1136dd8e7 
QWidgetPrivate::createWinId() + 103
23  QtWidgets  0x1136dd8e7 
QWidgetPrivate::createWinId() + 103
24  QtWidgets  0x1136dd8e7 
QWidgetPrivate::createWinId() + 103
25  QtWidgets  0x1136dd8e7 
QWidgetPrivate::createWinId() + 103
26  QtWidgets  0x1136de631 QWidget::winId() 
const + 65
27  freeview   0x102121964 0x101e26000 + 3127652
28  freeview   0x10212188f 0x101e26000 + 3127439
29  freeview   0x101eb159f 0x101e26000 +

Re: [Freesurfer] Problem Installing Freesurfer

2016-03-01 Thread Z K 
My guess is that pico did not actually save the license file because by 
default all directories under /Applications is protected. Which mean the 
"sudo" command is required.

Do you definitely have a file called license.txt (or .license) in your 
FREESURFER_HOME directory? What happens when you type the following in a 
terminal window?

   $> cd /Applications/freesurfer
   $> ls -l license.txt

-Zeke





On 03/01/2016 11:14 AM, Millan, Carlos wrote:
>
>
> Dear Freesurfer Team,
>
> I am a researcher here at University of Miami and recently downloaded
> Freesurfer to do Cortical Thickness analysis. Unfortunately, I have
> followed the installation steps very carefully as indicated on your web
> page but I do not know if there is a security issue on this Mac or what
> is it? But when I am trying to test freesurfer I get a message that says
> "license not found".
>
> I have tried to install the license by copying and pasting the license
> text I received (license.txt) into the $FREESURFER_HOME directory but it
> did not work; so I tried to write the commands “cd
> /Applications/freesurfer” and then “pico license.txt”. In the next
> window I also pasted the license and then I saved the changes in pico,
> but that did not work either.
>
> Is there anything else I should do?
>
> I am attaching some screenshots from the terminal. Maybe those help you
> assessing the problem.
>
> Thank you,
>
> Carlos Millan
> Research Assistant
> Epilepsy Division – Neurology Department
> University of Miami
>
>
>
>
>
> ___
> 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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.