Re: [Freesurfer] freeview quit unexpectedly on Mac OS M1

2023-01-03 Thread fsbuild 
External Email - Use Caution

Please try the following with the latest 7.3.2 release.  The release page 
is https://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 
is https://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 $HOME/license.txt/Users//license.txt$ export 
FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou@youremail.something  
   <— email you used to register with
4) Setup the environment,
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220803-878457d Setting up 
environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME   /Applications/freesurfer/7.3.2FSFAST_HOME  
     /Applications/freesurfer/7.3.2/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR    
  /Applications/freesurfer/7.3.2/subjectsMNI_DIR     
      /Applications/freesurfer/7.3.2/mni
5) Try running freeview from the command line w/o any arguments to see if it 
opens an empty window,
$ freeview
6)  If that worked, quit freeview and then run freeview from the command 
line again to open one of the provided volumes in the 7.3.2 release,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
7) If that worked, then try running freeview from the command line on one of 
your own volume or surface files.
- R.
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[Freesurfer] freeview quit unexpectedly on Mac OS M1

2023-01-03 Thread Philipp Klar 
External Email - Use Caution

Hello FreeSurfer Developers,

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

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

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

Thank you for any advice,
Philipp



-
Translated Report (Full Report Below)
-

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

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


Time Awake Since Boot: 200 seconds

System Integrity Protection: enabled

Crashed Thread:19  ThreadIOWorker

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

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

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

Thread 0::  Dispatch queue: com.apple.main-thread
0  0x11512ea40 ???
1  0x11512f3c8 ???
2   libsystem_malloc.dylib0x7ff8004dd2d9 
nanov2_allocate_outlined + 246
3   libsystem_malloc.dylib0x7ff8004dd8e1 
nanov2_malloc_zero_on_alloc + 521
4   libc++abi.dylib   0x7ff80062c95a operator 
new(unsigned long) + 26
5   QtGui0x11eb09154 
QBrush::init(QColor const&, Qt::BrushStyle) + 276
6   QtGui0x11eb0992d 
QBrush::QBrush(Qt::GlobalColor, Qt::BrushStyle) + 45
7   QtGui0x11ea84557 0x11e934000 + 
1377623
8   QtGui0x11ea7b1ea 0x11e934000 + 
1339882
9   QtGui0x11ea7bbf9 0x11e934000 + 
1342457
10  QtGui0x11ea7b39c 0x11e934000 + 
1340316
11  QtGui0x11eaaadea 0x11e934000 + 
1535466
12  QtGui0x11eaae5db 
QTextDocumentFragment::fromHtml(QString const&, QTextDocument const*) + 
107
13  QtGui0x11eaa8411 
QTextCursor::insertHtml(QString const&) + 257
14  QtWidgets0x11dda7787 0x11dba7000 + 
2099079
15  QtWidgets0x11dd7f0a3 
QTextEdit::append(QString const&) + 83
16  freeview 0x1027533da 0x1025dc000 + 
1536986
17  freeview 0x102753bd7 0x1025dc000 + 
1539031
18  QtCore   0x11fe278cc 
QMetaObject::activate(QObject*, int, int, void**) + 3132
19  QtCore   0x11fe2f432 
QTimer::timerEvent(QTimerEvent*) + 98
20  QtCore   0x11fe1fcf6 
QObject::event(QEvent*) + 102
21  QtWidgets0x11dbb770d 
QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
22  QtWidgets0x11dbb8b12 
QApplication::notify(QObject*, QEvent*) + 594
23  QtCore   0x11fdf6564 
QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
24  QtCore   0x11fe4fb7f 
QTimerInfoList::activateTimers() + 991
25  libqcocoa.dylib  0x11f652472 0x11f61e000 + 
214130
26  CoreFoundation0x7ff80074bee1 
__CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
27  CoreFoundation0x7ff80074be90 
__CFRunLoopDoSource0 + 157
28  CoreFoundation0x7ff

Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

2023-01-03 Thread miracle ozzoude 
External Email - Use Caution

Hello Doug,

Thanks for the quick response. I did see the error. However, I specified
doss in the mri_glmfit command and my mtx looks accurate as indicated
above. Does that mean it can only work with dods? The reason I'm using 2
groups is because I want to regress out the effect of sex. However, the
recommended way to do it in fsgd is to create a class for it and I only
have 3 males.

Is there a workaround for this?

Many thanks.

On Fri, Dec 30, 2022 at 6:37 PM miracle ozzoude 
wrote:

> Hello,
>
> I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like
> to regress out the effects of groups + other variables by using doss.
> However, whenever I specify doss with the mri_glmfit command, it gives me
> an error message (see below). I saw that others have experienced similar
> issues without any solutions. How can we solve this? Any insight is
> appreciated.
>
> Best,
> Paul
>
> mri_glmfit command:
>
> mri_glmfit --y
> ../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
> --fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres
> --nii.gz
>
>
> design.mtx:
>
> 0 0 0 0 0 0 0.5
>
>
> Terminal output:
>
> gdfRead(): reading dti_RPQ_3.fsgd
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variable Means (all subjects)
>
> 0 Age 46.9333 9.86216
>
> 1 Sports 0.067 0.249444
>
> 2 Games 1.1 1.62754
>
> 3 Days_TBI 1903.2 907.81
>
> 4 RPQ_3 7 2.28035
>
> Class Size and Means of each Continuous Variable
>
> 1 PPCS_Male  3  33.   0.   2. 1337.3472   6.6667
>
> 2 PPCS_Female 12  50.   0.   0.8333 2044.6632   7.0833
>
> ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS, you
> need at least 6 members
>
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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 
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