Re: [Freesurfer] Problem installing FreeSurfer

2023-05-31 Thread fsbuild 
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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
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[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] source freesurfer error

2023-05-31 Thread Pedro henrique barradas 
External Email - Use Caution

Hello
Thank you for the reply.

I tried to re-install the file but I have run into 2 problems.
When I attempt to export $FREESURFER_HOME=$HOME/freesurfer it tells me:

  *   bash: export: ´#HOME/freesurfer=root/freesurfer`: not a valid identifier

When I source it, it now says it cannot find the directory
and gives back the following answers:

  *   bash: /root/freesurfer/SetUpFreeSurfer.sh: No such file or directory

I also tried doing "source SetUpFreeSurfer.sh" from the freesurfer directory 
and I got this response:

  *   bash: /root/freesurfer/FreeSurferEnv.sh: No such file or directory

Also,
When I type echo $FREESURFER_HOME I get
root/freesurfer

But when I type pwd $FREESURFER_HOME it gives me
c/mnt/Users/ASUS/Downloads/freesurfer



De: fsbuild 
Enviado: segunda-feira, 29 de maio de 2023 22:27
Para: freesurfer@nmr.mgh.harvard.edu 
Cc: phbarra...@hotmail.com 
Assunto: Re: [Freesurfer] source freesurfer error


Try using $ instead of # to tell the linux shell to expand an environment 
variable, e.g., here to the path of where freesurfer was installed.

  echo $FREESURFER_HOME


  source $FREESURFER_HOME/SetUpFreeSurfer.sh

- R.

On May 29, 2023, at 07:52, Pedro henrique barradas  
wrote:

External Email - Use Caution

Hi everyone!

I am trying to run freesurfer on a windows machine using ubuntu but I am having 
trouble with the source command

When I try to source freesurfer i get the following message:

source #FREESURFERHOME/SetUpFreeSurfer.sh
-bash: source: filename argument required
source: usage: source filename [arguments]


Thank you very much


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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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