External Email - Use Caution
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-mac… 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…
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 (keskinmelih07(a)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/…
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#Si… 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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Hi, freesurfer team
Is there a way to calculate the intensity of a voxel.Let say, I have a
voxel with coordinate 20, 30 and 34 and I wanna know the intensity of it.
Can it be done in freesurfer?
External Email - Use Caution
Hi Freesurfer Developers,
If Freesurfer is available as a module on a computer cluster, is it still necessary to source/configure the freesurfer module in a .bashrc script on Linux?
Sincerely,
Yilei
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#Si…
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
