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It could help to see the core dump file. If you are on a Mac it
will probably display it. If you are on Linux and you have core dumps
enabled on the system, then you have to look in the logs.
- R.
On Jun 6, 2024, at 15:56, Iglesias Gonzalez, Juan E.
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Hello Rafa,
If you take a look under,
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Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use
code built with Intel processor specific instructions that cannot run on an arm
processor, i.e., there is not full backwards binary compatibility in that case
using the Rosetta
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If you still have the VM setup on your machine, you
can open a new terminal window and then you should see the Freesurfer
Environment is setup,
FREESURFER_HOME /home/developer/7.2.0/dev
FSFAST_HOME /home/developer/7.2.0/dev/fsfast
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The Intel binaries should still run on Silicon Macs using the built-in
Rosetta emulation environment. So if you want to use an official release,
then the Intel binaries from the most recent June 2023 7.4.1 release can be
found here:
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Hello Antonio,
With the 7.4.1 release, you can install R2014b or R2019b matlab runtime
environment into the freesurfer tree. Earlier freesurfer releases use
R2014b. I would setup the freesurfer environment first, and then pass in
the value of
because it is located on a
shared drive, but maybe we'll just need to install it locally if that works.On
Tue, Apr 23, 2024 at 11:23 AM fsbuild fsbu...@contbay.com
wrote:Did you try the instructions you were sent yesterday to run
the actual installer and not use the tar file (which
External Email - Use Caution
Did you try the instructions you were sent yesterday to run the actual
installer and not use the tar file (which is not an installer) ?
- R.
I would try downloading and running the actual package installer,
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You can check the post (quoted below) to verify the setup for the 7.4..1
release. Instead of running the freeview command as listed in the post,
you can run the mri_info command with no arguments to get the help info about
the command line options.
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If you setup the Freesurfer environment ... here using bash and not zsh
...
hostname ~ bashThe default interactive shell is now zsh.To update your account
to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit
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If you have not already done so, please make sure your license.txt file
has been setup in the shell for the freesurfer commands to read.
Go to the URL below, fill out the form, and wait for license.txt to be emailed
to the address you provided.
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The current nightly build dated April 12th available from
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The permissions on /scratch may not be set to allow you to write files
there. If it does not work from the terminal window to create a plain
file there via the command,
$ touch /scratch/foo
- then you will get the same permission denied error.
If the
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Use of parallelization depends upon the order of how the data needs to be
processed. The recon-all command is not single command, but a
wrapper command that runs a sequence or pipeline of many lower level freesurfer
commands in a certain order.
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You can try using the Silicon Mac development build on the M2
machine.. The download links is,
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I would try downloading an installing the latest version of Xquartz which is
2.8.5
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On Ubuntu linux the default shell may still be “dash” and not the “bash”
shell. Dash cannot parse all bash scripting, so type “bash” or try
setting “bash” to be your default shell and then run commands.
- R.
On Mar 19, 2024, at 22:17, Boscutti,
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I don’t believe the workaround will be supported or provided with future
releases intended to run on Silicon Macs. If there is still an issue with
mri_synthseg running with the current model files in the freesurfer dev build,
then please let us know
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The mri_synthseg script and python in the freesurfer disrtibution you are
running are not entirely compatible with the arm64 M1, M2, M3 processors in
silicon Macs. You could try installing and running the development build
of Freesurfer for the
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Instructions about how to setup a VM running Ubuntu 22.04 LTS Linux have
been updated on the wiki page,
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The leading ./ in the path looks like a by-product of needing to use
various/different options now in creating the tar archives and also the tar
command running may be from a different system. Not sure that can be
reverted.
- R.Hi Freesurfer,Wasn’t
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It could help to know what OS version and what Freesurfer version you are
running. From your path /usr/local/freesurfer it looks like you are
running a Freesurfer release, e.g., 7.4.1.
- R.
On Feb 25, 2024, at 21:45, Agata Wolna awo...@mit.edu
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If you don’t have a license.txt file setup to read, then freeview will not run.
If you have not already done so, I would set the environment variable
FS_LICENSE to point to the license.txt file you downloaded after registering,
e.g., if license.txt
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The recon-all log contains this entry,
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
If you go to where that log file is, which I think would be,
$ cd $SUBJECTS_DIR/mri/transforms
… then look in that log file to see what the error is. It
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The python distribution in the 7.4.1 release cannot run all the python based
tools on a Silicon Mac (M1, M2, M3 chip) because at that time we did not have a
python distribution that was completely compatible with the arm64 architecture.
We currently
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We don’t expect things to work reliably with 8G total RAM for the machine.
The host machine itself will always consume some memory when running its
OS, probably up to a few Gig, leaving even less than 8G to be used for
running the VM with
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I would look for the core file under /var/crash as close to the time to the
command failure and see what it says.
Signal 11 is a segmentation violation meaning invalid memory access. It
could be that a VM on your machine does not have enough memory
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The current 7.4.1 (Intel binary) release from June 2023 should run on
Silicon Macs and I believe was tested with MacOS (13.X) Ventura. We did
not have MacOS (14.X) Sonoma available at that time for testing. The
Freeview image viewing application
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We have seen the (Mac or Linux) OS automatically kill resource greedy
processes, e.g., commands using large model files. Increasing the limit
on physical RAM usage and/or increasing how much data is swapped out to disk
may still not allow the
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At this point, I think your best bet is to install and run the freesurfer
7..4.1 release from June 2023 which was tested with R2019b. Although The
MathWorks does not support R2019b on MacOS Sonoma, I think we tested the 7.4.1
release on BigSur,
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I don’t see what FREESURFER _HOME is set to, but if you used the .deb package
installer, it would be /usr/local/freesurfer/7.4.0, i.e.
$ wget
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It looks like you did not use the .pkg file installer to install Freesurfer on
the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to
use as FREESURFER_HOME. The installer should ensure the privileges should
be correct to
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It would help for us to know what your machine is running, e.g., linux or
MacOS (Intel or Silicon Mac) - and what the version is for the operating
system, e.g. Linux Ubuntu 22, MacOS 12, etc. If you are running Linux on
Windows thru either WSL or a
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A remote connection working to display images from the glxgears or xeyes
commands run on the linux host forwarded to your local machine does not mean
Freeview graphics will do the same. If Freeview still displays an empty
or black screen, then there
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Is SUBJECTS_DIR for Freesurfer being set to live under a temporary
scratch directory initially created by and then subsequently used by Matlab?
If so, maybe Freesurfer is deleting files and/or changing file permissions
there - causing Matlab to
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I would check with your IT support staff about the error including asking
if the machines in your cluster are setup to display X Windows sessions with
image viewing applications like Freeview. If the machines support
remote graphics, they should be
long do they take to respond? Also can I do subcortical thalamic
segmentation with it? How is the LUT calculated both for infants and adults?
Would you recommend an eleven year old's data analyzed by regular FS or infant
FS?On Mon, Jan 8, 2024, 6:19 PM fsbuild fsbu...@contbay.com
wrote:Looks
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Looks like you need to fill out the request form,
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Let me add that it will not work to use shared mount point from the
Windows filesystem as you list below,
/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri
-
for your SUBJECTS_DIR when running a recon-all command. The command
will fail because the
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tksurfer has beendeprecated and essentially replaced with
tksurferfv bashshell scriptwhich runs freeview. But whether
or not you run the front-endtksurferfv bash script or the freeview
command directly, I’m not aware of an option wherebyyou cantell
Abeoseh B. flemist...@missouri.edu
Sent: Saturday, January 6, 2024 12:24:40 PM
To: fsbuild fsbu...@contbay.com; freesurfer@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
No, I installed using tar.gz
freesu
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If you do a case insensitive search for the string “error" in the log, you
should see there are multiple listings of,
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR
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Did you install Freesurfer 7.4.1 using the Debian installer package
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For issues with Freeview displaying graphics when running via Linux on a
Windows host thru WSL, you could look at the recent thread with the subject
"Re: [Freesurfer] Freeview not showing output",
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As Ruopeng said, even if simple X-Windows programs like glxgears run, that does
not mean freeview will display graphics.
If freeview is not displaying images after X-ming (or a different)
X-Windows server runs on the Windows host and displays
xcb-shape0 \ libxcb-shm0
libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \
libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \
libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6
zlib1gOn Fri, Dec 29, 2023 at 12:14 PM fsbuild
fsbu...@contbay.com
wrot
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That message could be the result of missing system libraries which the
Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, download
and install for you. You can download the package via the
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On linux, that file is under $FREESURFER_HOME/bin and will be found in
your PATH after you setup the Freesurfer environment, e.g. for the 7.2.0
release installed via the .rpm file, you setup the environment with,
$ export
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The freesurfer 6.X and 7.x release release notes summarize some changes for
Freeview (listed below) since version 5 was released in 2013. If none of
the improvements in features/stability are relevant to what you are doing, then
I don’t see why you
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I don’t think there is any GUI or graphical interface with the runtime
environment (which does not require a Matlab license). Neither does it
contain the matlab compiler to build matlab executables, etc. So if you
still need to create Matlab
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We hope to have a binary rpm installer for CentOS9.
I have not tried it, but the existing FS 7.4.1 CentOS8 binary rpm installer
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There’s no need to have a license file in a particular location if you set the
environment variable FS_LICENSE to point to the license file.
If you are using the Ubuntu 18 VM made available with Freesurfer 7, then adding
the license.txt file you
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I believe the assumption is the freesurfer 7.3.1 distribution has already
been installed (under /usr/local/freesurfer/7.3.1 by the *.deb or *.rpm
linux installer file) and that FREESURFER_HOME is set in the
environment
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It
reads like something is not right with your setup/shell environment.
Once you have setup the freesurfer environment via, e.g.,
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source
$FREESURFER_HOME/SetupFreesurfer.sh
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Hello Sophie,
Just FYI, there is no matlab distribution included in the 7.4.1 release
and we so not support using R2023b. So I presume someone at your site
installed R2023b separately via a Mathworks matlab installer. We do
provide a script,
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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
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The install location of freesurfer under /usr/local is on purpose read
only (like the location of most Linux package installs) so you should not be
trying to process and write subject data there. We provide example
subjects under
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Hello Mahdi,
If you have not already done so, you might want to look at the Freesurfer wiki
notes about setting up an X-server on Windows so linux applications running in
WSL can display graphics using
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If you have been launching Freeview using the Finder by double clicking on the
icon, then try running it from the command line in a terminal to open a file,
e.g. in bash or zsh ...
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source
nner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 914 526
9298
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Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer
package from the download page and installed it from your Downloads folder via,
$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
The link for that file on the downloads
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I could be wrong, but it reads like those errors are from the libqt5xcb.so
running intoerrors
communicating with X windows. Since freeview runs fine displaying
those images on the machine when not exec'd thru fsxvfb, then maybe fsxvfb
cannot
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From what I can see, the freesurfer release 7 installers do not modify the
shell init file, e.g., bashrc, and neither did the VM provided in the past with
freesurfer 7.2.0 pre-installed have an entry with FS_DISABLE_LANG set in the
bashrc file.
- R.
ial rh-pial to view on freeview for some reason.
I have the same problem for all of recon'd files.
Is this another recon-all error or is this just my data problem?
Thank you in advance.
Best,
Alice
-Original Message-
From: "fsbuild"fsbu...@contbay.com
To: freesu
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It looks like permissions on the installed freesurfer files and/or what
you set FREESURFER_HOME to may not be correct.
I would delete your current freesurfer install and then use the Mac installer
package (.pkg) file to install the 7.4.1 release.
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Please try using the Matlab runtime environment which can be installed directly
into the freesurfer tree via a script we provide. The runtime environment
is free and requires no paid for Matlab license (since it does not include the
Matlab
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If you add these 2 commands to setup the freesurfer environment, e.g., for
csh/tcsh as your default shell,
$ setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1$ source
$FREESURFER_HOME/SetUpFreeSurfer.csh
- to your shell initialization file,
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Python code (including 3rd party python packages) in the Intel Mac
build cannot be guaranteed to run on Mac M1, M2 arm processors. Package
developers may still build their code using Intel processor specific
instructions which cannot be emulated by
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Try setting DYLD_LIBRARY_PATH to point to the subdirectories containing the
Matlab libraries.
You could just delete what's there,
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2
$ cd $FREESURFER_HOME
$ sudo rm MCRv97
- and re-run
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Please try the following,
… open a new terminal and run the bash shell … I am cd’d to /tmp though it
should not matter ...
$ cd /tmp$ bashThe default interactive shell is now zsh.To update your account
to use zsh, please run `chsh -s /bin/zsh`.For
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If your host machine has 32G of RAM, then it should work to give the VM
16G or perhaps even 24G of RAM.
If most all swap space is in use, then it’s likely something is under-running
or exhausting the available physical RAM. Some machines start to
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Not clear if "8G of RAM" below means 8G is assigned to the VM, or the host
machine has 8G RAM total. Assuming the VM has ~8G assigned then the
host should have 16-24G RAM total.
It reads like the VM is thrashing, e.g., swapping out to disk
n haben, informieren
Sie bitte sofort den Absender und löschen Sie diese Mail. Das
unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht
gestattet.
Universitätsmedizin Mannheim
universitär - modern – menschlich
Von: fsbuild fsbu...@contbay.com
Datum: Mittwoch, 27. Sep
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You can try using the fs_install_mcr script to install the matlab runtime
environment instead of using a generic or full install of Matlab on the
machine. Below the PATH to FREESRUFER_HOME is listed
as/Applications/freesurfer/7.4.1, but you should
...@mgh.harvard.edu
wrote:External Email - Use
CautionHi Julian,I have
managed to run recon-all on my Apple M1 macOS Ventura using the 7.3.2 version
of Freesurfer. It does not work on 7.4.2 or dev versions, however. These
instructions were posted in a previous correspondence from fsbuild
t allow me to change the format for the storage drive. So,
I was hoping to look for a workaround that allows me to continue working on
exFAT
storage.Cheers,MervinFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
on behalf of fsbuild fsbu...@contbay.comSent:25 Sept
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I don’t see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a
different name) will work, i.e., anything that makes a soft link may
subsequently test for a soft link using the
External Email - Use Caution
A native silicon Mac build (darwin_arm64) from the freesurfer
development branch is currently available for download (along with the
usual darwin_x86_64 Intel Mac build). This means freeview and most
binaries should run on current Macs with M1, M2,
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I don't think we can guarantee upgrading freeview will work with the
existing libraries in a sufficiently old freeview distribution. I’m not
sure what version of Ubuntu is running from the kernel listed below, but you
could create a backup of your
Email - Use
CautionOK, I've attached the
log file.--- Original Message ---On Friday, September 15th, 2023
at 2:59 PM, fsbuild fsbu...@contbay.com
wrote:External Email - Use
CautionIt might help if
you could send along the crash report as an attachment..-R.On Sep 15, 2023, at
14:36
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It might help if you could send along the crash report as an attachment.
-R.
On Sep 15, 2023, at 14:36, KennethSPrice kennethspr...@protonmail.com
wrote:External Email - Use
CautionUpdate: I tried running
recon-all (5.1, ubuntu 18) on a sample
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If you are getting an “illegal instruction” error running Freesurfer on
Linux, then the hardware (CPU’s) do not have those instructions available
in their instruction set to execute. As far as I know that error only
happens with Freesurfer binaries
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The private email notice you received with the VM information explicitly stated
NOT TO POST ANY PASSWORDS. We will look to suspend the VM image and
change the login credentials.
- R.
On Sep 11, 2023, at 17:23, Ynze Hokken ylhok...@gmail.com
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I’ll suggest a couple of things - (1) you are using a development build of
freesurfer which could be unstable. I would instead try the most recent
7.4.1 release for Ubuntu, and install it via the .deb file installer (system
updates may be needed),
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The captcha authentication will not work if javascript is blocked from
running in your browser. Check that you browser preferences are not set
to block/filter javascript in its preferences and/or by using some added
browser extension. I’m not aware
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If you have not already done so, I would try installing and running a
version of the Matlab runtime environment (which is not a full blown Matlab
installation) that freesurfer was tested with. For the 7.4.1 freesurfer
release, that should be R2019b.
or install
the package and I'm afraid I have forgotten the commands.Maybe someone
else can chime in here?I use VcXsrv for my X-server graphics
interface.MichaelOn Sun, Sep 3, 2023 at 7:23 AM fsbuild
fsbu...@contbay.com
wrote:External Email - Use
CautionHello Sabrena,We have
some notes posted
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Hello Sabrena,
We have some notes posted about setting up WSL on the wiki page
External Email - Use Caution
If you have not already done so, I would try installing and using the newest
version of theMatlab runtime environment that the 7.4.1 release was
tested with, i.e. R2019b. Once you have set $FREESURFER_HOME, then run
the fs_install_mcr script
External Email - Use Caution
If you search the freesurfer mail archives for WSL you should find
postings about how to setup an X-server on the windows host in order for
Linux applications to run in WSL and use X-Windows to display images. We
provide some documentation, however
External Email - Use Caution
Check if you see the following output for these commands,
% which mri_sclimbic_seg
/usr/local/freesurfer/7.4.1/bin/mri_sclimbic_seg
% which fspython
/usr/local/freesurfer/7.4.1/bin/fspython
Try running that command as listed below followed by your own
External Email - Use Caution
You should be able to use either of the paths below for FREESURFER_HOME
to run the freesurfer CentOS7 7.4.1 release. You should see the same
output using either path. If one of these commands does not work, then
it means that path is not
External Email - Use Caution
…. to do that, you can set FREESURFER_HOME to
/autofs/cluster/freesurfer/centos7_x86_64/7.4.1On Aug 20, 2023, at 17:52,
Douglas N. Greve dgr...@mgh.harvard.edu
wrote:External Email - Use
CautionCan you try the 7.4.1
version? Can you also send your
External Email - Use Caution
Please let us know what FREESURFER_HOME is set to, and what (Linux or Mac)
operating system your machine is running. If you are on a Mac please
indicate if it is one of the current silicon Macs (M1, M2, chip) or one of the
older Intel Macs.
- R.
On
/freesurfer/7.4.1 freesurfer$ls freesurferoutput
deleted)
check you have 7.4.1 ...
$ cat
freesurfer/build-stamp.txtfreesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460
- R.
On Aug 19, 2023, at 08:00, Matthew Lynch matthewl...@gmail.com
wrote:External Email - Use
CautionThank you fsbuild
ile before
installing it. However, I am still experiencing the same issue.Kindly find
attached a copy of the text from the terminal after I tried this.Kind
regards,Praise MatseketeFrom:freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fsb
External Email - Use Caution
Hello Praise,
This post,
External Email - Use Caution
Please try the following,
… open a new terminal and run the bash shell … I am cd’d to /tmp though it
should not matter ...
$ cd /tmp$ bash
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For
External Email - Use Caution
Hello Gizem,
Are you by any chance running Ubuntu Linux through WSL or a VM on a Windows
machine - AND/OR - trying to write your data from Ubuntu linux to a
mounted NTFS file system on a Windows machine? The Windows file system
does not support
External Email - Use Caution
Hello Joost,
It looks like you are using an old 2020 development build prior to fspython
being updated to version 3.8.X with a newer version of tensorflow installed.
The latest 7.4.1 release from June 2023 should have a tensorflow version 2.12
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