from:"fsbuild"

Re: [Freesurfer] MAC compatibilty

2024-05-25 Thread fsbuild

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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:
https://secure-web.cisco.com/1PlXQxoEX-x05USM5h21mbTgkWDKGf26NwLJXc-0TKpfOiCFIPKTNfixRTstm4lwdFle1ckZQaNDG9K2uXTrL4PgECdRb1kB_7yoS7khQb0ehN9jhQdUEx760OIsW4yS15fGVX2egl-kP-gUfA8mcGgT60fYkpOBtL34Q4XfiQpnY1cyK4Qqix_1L2MqBZwQmqpy77YwZet2977GkKZQWCJJH3Efq_fu4bs31PqnDT7GH0wKw4xpynQgYZqKFDx2AkPPLgjGxEE4pw0Wi67HAZl4XlGt1_52MXZDtYFdwJ-LmwkxE_VdxXa68ba42bxgnpVTNDrEMR3T3qZGRJ5NzYw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
There is however a newer development (non-release) build compiled natively for 
the Silicon (arm64) Macs. You can find development builds under,
https://secure-web.cisco.com/1bqoWa8LCXJXDBOMIgjvymagPdUuAoVFBzhDkQcCJ8BO0z-AZtSuIBxg3dgBxnDm_R3YCWCP73q0CQsSKFyW2x74gcZTMU-skv2NKEJpxs8JrKVEBT9cduIT3bgaeRqTaKYbAPkmyixKaV3b5DspaTK1FKHuF3XoG-_UI7jDI2Wlh7nRboHjFUkY65GZX8wF1RiHq8O6Lma-thaFJNoIPCW47mSNy_k8BfzB06E6t9dnJ2ebKfeuJvhvRc2jgf4x-yYmD6Q3l6kpMd0APnM1cXP-hxyldsY86BJmBjC1agSZGZgW3NFrcB3Sh836GHFxKKixmeiyxw8GocHHyif1H3A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev
- and the current arm64 .pkg file installer is:

https://secure-web.cisco.com/1v7jUCTarAa0YZGcgQjK2FDqKV6MOl2jENY0Cmgh3LS7Tbjl3BBwYxUBU9KrYpFUz3kNsQXeNAsuR87a0V4E9JSverkt5GYgtXxTTr6_bL8FBO9kdzQ99iyRTfPKFsLSMXBpJ4maosVp3cAWGAFzfc4nWl-dxrxBTSHHomvryS8Vyq0T4byXQRjA_3hAvxNL2-uHTW4X4q4Cf89AxweyE8ewSJ9IZUQen4XPJAmNuVMZhYrQIP2iPIgateMIe6ARMmsEORI-tXGrYBL8Hq83RiW-3YwQ7kDJl0sbadpIsRabO9xxP6FCfjbSv4odPFCdyucnownn7fGoh9s7c_EGhyw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
- R.

On May 25, 2024, at 04:58, Silvia Montanari silymontanar...@yahoo..it 
wrote:External Email - Use Caution 


Good morning, my office needs to buy a new computer and it’s mandatory that it 
can run free surfer properly. I couldn’t really find definitive informations 
about the compatibility with latest Mac machines with M2-M2pro-M3 processors. 
Since I always had Intel, can you help understand which Mac it’s better to have 
in order to not have problems with freesurfer?

Thank you in advance,
Silvia Montanari

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Re: [Freesurfer] MCR install for parcellation

2024-05-09 Thread fsbuild

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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 FREESURFER_HOME on the command line as listed below. Below,
I have shown using R2019b with a linux install of Freesurfer 7.4.1 using bash
shell.
- R.
- - - - -
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
--- linux install path
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
... output deleted ... showing SUBJECTS_DIR and other environment
variables
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
I believe this sets things up (for R2019b) so the libmwm* libraries are
installed under $FREESURFER_HOME/MCRv97/bin/glnxa64. You can try adding
that path (or any path the fs_install_mcr script output recommends) to the
start of LD_LIBRARY_PATH. You should remove any other entries to a
different MATLAB distribution other than the one you actually install.
On May 9, 2024, at 12:45, Antonio Di Renzo antoniomp...@hotmail.it
wrote:External Email - Use
CautionMessers FreeSurfer
developers,I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from
MatLab website.I extracted files in new foldern named
Matlab_Component_Runtime_R2014b in Downloads.I am trying to install Matlab
Component Runtime, but the the following command:fs_install_mcr R2014b
does not work.Where can I find the right step by step MCR installation
guide?Thank
you,Antonio___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Problem running recon-all

2024-04-23 Thread fsbuild

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If you use a shared drive that is formatted in a way that is not 
compatible with the linux (ext3, ext4) file system, e.g., a shared windows 
drive, then running the linux software is not expected to work. A Windows 
file system does not support soft links, permissions etc. which means recon-all 
will fail when it tries to use soft links to point to files. So 
SUBJECTS_DIR has to point to a directory you can write to (on a linux file 
system).Similarly, the linux packaging tools (apt, dpkg, yum, 
rpm) expect to install Freesurfer on to a linux file system in order to set 
permissions, etc.
- R.

On Apr 23, 2024, at 11:50, Gregory Book gregory.a.b...@gmail.com 
wrote:External Email - Use 
CautionI did not see that 
message, which is why I posted again. Sorry about that!I will try using the 
package installer. We're using the .tar.gz method 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 is not an installer) ?- 
R.I would try downloading and running the actual package 
installer,MailScanner has detected a possible fraud attempt from 
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 to the target system.. Then change directories to where you downloaded 
the package and try,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debI 
cannot guarantee the installer will work as the Debian linux packaging tools 
may find requirements in the Ubuntu package they cannot resolve/satisfy on your 
Debian system. We don’t test on debian linux. But the installer 
should notify you if it fails and why that is.On 4/23/24 09:21, Gregory Book 
(gregory.a.b...@gmail.com) 
wrote:External Email - Use 
CautionI recently installed 
freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When 
running recon-all, I get the following error:-bash: 
/opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file 
not foundPaths are all set, and all scripts and executables have execute 
permissions.What might be 
happening?___
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Re: [Freesurfer] Problem running recon-all

2024-04-23 Thread fsbuild

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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,



https://secure-web.cisco.com/1mB3zzEt6hQJ2VvtNrO3nW8sgR7_P581WGaaGeCTSIwiN-Z-x8Mtw6Z5nF23uvW00XlyjmsjQtPTwUkHji_2-9LmsBV2L2NfcLNBFy1Gsw0HvQ045CqPAZjAVhMRFnyyvnfw4xOPMnU-gIj1bM4eLgNASRmckkz7PGd6j28HxgvfDZkF1VK3pZSwTcISKqhKHuNQatTZ9vZjaWbY5k7I5N6dvIOuntBKrq-p5rjI7Q9G73EQ-rCrhQLcAOOyFsAtGAF4BJS1Ph12Iri8OA0T7HkE4bJHEf8g0Rde3zzo82KH1VslH5icbSMuRfXtKveMgAUF6jySJNeW6klBJSbUdsw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb


on to the target system. Then change directories to where you 
downloaded the package and try,


$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb



I
 cannot guarantee the installer will work as the Debian linux packaging 
tools may find requirements in the Ubuntu package they cannot 
resolve/satisfy on your Debian system. We don’t test on debian 
linux. 
But the installer should notify you if it fails and why that is.


  
  



On 4/23/24 09:21, Gregory Book (gregory.a.b...@gmail.com) wrote:



  External Email - Use 
Caution
  I recently installed freesurfer 7.4.1 on a Debian 12 
system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the 
following error:
-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required 
file not found

Paths are all set, and all scripts and executables have execute 
permissions.What might be happening?

  

  
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Re: [Freesurfer] Freeview problems

2024-04-17 Thread fsbuild

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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. If mri_diff runs and prints out the help 
output, then the issue is likely your command line arguments.
- R..
bash-3.2$ mri_info
USAGE: mri_info fname1 fname2 options

 --conformed : print whether a volume is conformed stdout
 --conformed-to-min : print whether a volume is conformed-to-min 
stdout
 rest of output deleted

SETUP ENVIRONMENT
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If you setup the Freesurfer environment ... here using bash and not zsh ...
hostname ~ bash
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$source 
$FREESURFER_HOME/SetUpFreeSurfer.shfreesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
 Setting up environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME /Applications/freesurfer/7.4.1FSFAST_HOME 
  /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR   
/Applications/freesurfer/7.4.1/subjectsMNI_DIR
 /Applications/freesurfer/7.4.1/mni
 and point FS_LICENSE to your license.txt file, e.g., in your $HOME 
directory 
$ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export 
FS_LICENSE=license.txt$ head -1 license.txt...@somewhere.com  
email you used to register
 then try running from the command line ...
$ freeview$SUBJECTS_DIR/bert/mri/T1.mgz
Please keep in mind you will need to change SUBJECTS_DIR to some other path, 
e.g., $HOME/subjects
$ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects
 and put files there if you want to write /modify subject files and data 
since /Applications/freesurfer/7.4.1/subjects is read only by default (not 
intended to be used to write data).
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Re: [Freesurfer] FreeSurfer Download and Install Error: Segmentation Fault

2024-04-15 Thread fsbuild

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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 
https://secure-web.cisco.com/1RXVOTUqK1IY787C_o3ARLPP6BLZ_gJwBTdWVVnMp01gcO_F-J6H9b6Zq3d5SK5kRaqVP1Dy7gp_ZUzinjn0e1fJiF91lrnT1f-P3z6-4fS0DPdhVFDkHU3VunBCO6PI4W_n_Moh_kpeDUesFuUdMUKJDHyaSJQxz89stfjN4o2S63-wtgXWD69-NcnvfiXHCVemaN-MwXtjWqf_Ob0XZE_DueuAv03mLL7fBehx-acCMOgp9xydtvm8w9mx-wczMuXjDTd3hO0qUCvj5pZKKat0Ct5VKXipXjPJB17x_PK0jh8ATayA_VW0fH_wd9yQf9MLWMtHhE5vJD0-saUcUoN7EGGDqZHMa6GkDpFiw9YQ/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$source 
$FREESURFER_HOME/SetUpFreeSurfer.shfreesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
 Setting up environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME /Applications/freesurfer/7.4.1FSFAST_HOME 
  /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR   
/Applications/freesurfer/7.4.1/subjectsMNI_DIR
 /Applications/freesurfer/7.4.1/mni
 and point FS_LICENSE to your license.txt file, e.g., in your $HOME 
directory 
$ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export 
FS_LICENSE=license.txt$ head -1 license.txt...@somewhere.com  
email you used to register
 then try running from the command line ...
$ freeview$SUBJECTS_DIR/bert/mri/T1.mgz
Please keep in mind you will need to change SUBJECTS_DIR to some other path, 
e.g., $HOME/subjects
$ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects
 and put files there if you want to write /modify subject files and data 
since /Applications/freesurfer/7.4.1/subjects is read only by default (not 
intended to be used to write data).
- R.On Apr 15, 2024, at 21:55, Angenelle Rosal 
angenelle.ro...@mail.utoronto.ca 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I am currently using FreeSurfer 7.4.1 and I am attempting to 
upload the T1 image from subject “bert” using the terminal (I am using MacOS 
Ventura 13.5), as described in the demo video. However, freeview keeps quitting 
unexpectedly showing “2406 Segmentation fault: 11 
$FREESURFER_HOME/Freeview.app/Contents/MAC0S/freeview “$@” when I type in 
“freeview/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz”.When I 
manually open Freeview without the terminal and load such image using the “Load 
Volume” tab, it works fine. I’ve searched the archives list and it might be due 
to the location of my license. However, I believe my license is located in the 
correct file, as it is located in my Freesurfer file 
(/Applications/freesurfer/license.txt). And so, any advice to also solve this 
problem would be greatly 
appreciated!Thanks___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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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 
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 .
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] freesurfer doesn't work

2024-04-13 Thread fsbuild

External Email - Use Caution

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.
https://secure-web.cisco.com/1S0vdVHQI48_A4EBWTDRa1pv58cpXoGqSkuGFlQee0x1XYr-fPSsM4eHw_WEylrMZxyT6U5ViGv76nFrvLuXJzi4HBwJnBZpfhdbXoRAnkFDpfxJyh710zWgTCqYzqHYfY6myV39Eh5l8mkMgKv-IIKl-7mbrcgdNm58-LvGSR8nwkU9YJEOQuryCauBUfsNsucCK4bB6sg9tImwv0MAELBM_c3UetB20q1H6I__j3P6wWELbVCiJ_c5S334dEbZZQgOENSMQolfi_9moqK1g-FvgnafjL53gKv7w5TmqpI7V0oJ832xMYhY-EpmVnCA7NSx2ow4YDGmg9QN7RfOwEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
Download license.txt file,e.g. into your Downloads folder. Then in
bash or zsh you can do,$ cd $HOME… download license.txt from email into
Downloads folder ...$ mv Downloads/license.txt .$ export
FS_LICENSE=$HOME/license.txt$ head -1 $fs_license...@somewhere.com
—— email you used to registerYou can add the export command above into your
shell init file so FS_LICENSE will be set when you launch a new terminal window.
- R.
On Apr 13, 2024, at 13:08, 이준하 dlwnsgk1...@naver.com
wrote:External Email - Use
CautionI can't open freesurfer
and I don't know why. It says 'Freesurfer quit unexpectedly'

Re: [Freesurfer] WMH-SynthSeg - Torch module not found

2024-04-11 Thread fsbuild

External Email - Use Caution

The current nightly build dated April 12th available from 
under,https://secure-web.cisco.com/1eprQplECVjQEgFy-DNvfPnzwSjew2U260XYR6pjQfShhM9gtsn58XZ4YRUlHYleeawzdPreispMAkZ2MQM7djCWtpvLAsdUowgmUhDSJuQv8O_5fefPPEs1LslaJbLvtLiYSihrPpDMqQl8XI-wfA6fvBLvdZGEorSSHkE8HZc964yhAJAU0LYSYOy9cD9hlCMe5NUexf5FlsSHnL5tt8VUWpdEbJ4kGOxPh5yeIs8vl4_Cv8UwrnmG7lIrS6lOu9oUQLQnNBK5VKpADCMYEek0svgu1wUv1NH8cYOpg4jfy9cfhhXCpznkSR99lHGKlu4Wnj2ZdK-iefKmAPd91yQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F-
 should have all the modules as well.
- R.

On Apr 11, 2024, at 10:03, Iglesias Gonzalez, Juan E. 
jiglesiasgonza...@mgh.harvard.edu wrote:The idea would be to 
source 7.4.1 and then run:fspython 
[location_of_FS_dev]/python/packages/WMHSynthSeg/inference.py 
[arguments]Cheers,/Eugenio--Juan Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6aeFlVMFOtu6kJDKPxwTMe7ZJnmmIkRXMNWFEGYYGq8NlCAbNhKFyGulewwR4fTOUBHQBiQDI0dEdGr0ZJP2jrcZbc10tC1447QVz6_ZVvrhVUx5n-lgiJJVXzeCOZ-6vl-bx6VFTc10EYES77izWOBFVPPlHLBqzSdlysIuI93NkD8E_G4I-HwZg0EpyNtwvLbO4TvKg0137MivLsXAZkuJTY-am7YdxPIonKE3oUFJDeblwytpcKdrOrio7MJX3S3xjSQOA-7Oo4DIYbpVrrldmcLJNWe8x_Syu0HnwnbLJlaS_76DMzUyCQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Corinne Alison 
Donnay corinne.don...@linacre.ox.ac.ukDate:Wednesday, April 10, 
2024 at 8:39 AMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
WMH-SynthSeg - Torch module not 
foundExternal Email - Use 
CautionHi 
Eugenio,Thanks for getting back to me – I had the newest version 
installed and still get the same error (pasted below).mri_WMHsynthseg --i 
flair_ax.nii.gz --o flair_ax_WML.nii.gz --threads -1Arguments seem 
correct; loading Python packages...Traceback (most recent call last): 
File 
"/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py",
 line 284, in module  main() File 
"/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py",
 line 76, in main  import torchModuleNotFoundError: No module named 
'torch'I also installed FreeSurfer 7.4.1. Would you be able to expand on 
what you mean by “a way around this is installing FreeSurfer 7.4.1, and 
using its fspython to run the WMh-SynthSeg code”?I loaded FreeSurfer 
7.4.1, and then changed the location of the model in inference.py and tried 
using FreeSurfer 7.4.1 fspython but now its missing the'unet3d' 
module:[donnayca@cn4270 anat]$ module load freesurfer[-] Unloading 
freesurfer 7.4.1 on cn4270[+] Loading freesurfer 7.4.1 
on cn4270[donnayca@cn4270 anat]$ fspython ../inference_cd.py --i 
flair_ax.nii.gz --o flair_ax_WML.nii.gzArguments seem correct; loading Python 
packages...Traceback (most recent call last): File "../inference_cd.py", 
line 285, in module  main() File 
"../inference_cd.py", line 79, in main  from unet3d.model import 
UNet3DModuleNotFoundError: No module named 'unet3d'[donnayca@cn4270 anat]$ 
fspythonPython 3.8.13 (default, Apr 21 2022, 14:55:37)[GCC 8.3.1 20190311 
(Red Hat 8.3.1-3)] on linuxType "help", "copyright", "credits" or "license" for 
more information. exit()Thank 
you!CorinneFrom:freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of "Iglesias Gonzalez, Juan E." 
jiglesiasgonza...@mgh.harvard.eduReply-To:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduDate:Saturday, April 6, 2024 at 
1:04 PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
WMH-SynthSeg - Torch module not foundWrong answer: apparently this has 
been fixed in the latest dev; maybe try that?Cheers,/Eugenio--Juan 
Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6aeFlVMFOtu6kJDKPxwTMe7ZJnmmIkRXMNWFEGYYGq8NlCAbNhKFyGulewwR4fTOUBHQBiQDI0dEdGr0ZJP2jrcZbc10tC1447QVz6_ZVvrhVUx5n-lgiJJVXzeCOZ-6vl-bx6VFTc10EYES77izWOBFVPPlHLBqzSdlysIuI93NkD8E_G4I-HwZg0EpyNtwvLbO4TvKg0137MivLsXAZkuJTY-am7YdxPIonKE3oUFJDeblwytpcKdrOrio7MJX3S3xjSQOA-7Oo4DIYbpVrrldmcLJNWe8x_Syu0HnwnbLJlaS_76DMzUyCQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, 
Juan E. jiglesiasgonza...@mgh.harvard.eduDate:Friday, April 5, 
2024 at 3:58 PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
WMH-SynthSeg - Torch module not foundDear Corinne,A bunch of libraries are 
currently broken in the development version; apologies for this. A way around 
this is installing FreeSurfer 7.4.1, and using its fspython to run the 
WMh-SynthSeg code. Apologies for the inconvenience!Cheers,/EPS: I just updated 
the wiki to include this information.--Juan Eugenio

Re: [Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied")

2024-04-03 Thread fsbuild

External Email - Use Caution

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 above fails, then you should contact whoever setup the machine, your IT 
department, etc. and ask them to provide write permission there.
- R,

Begin forwarded message:From:XinRan Wu wxr1173199...@gmail.com
Subject:[Freesurfer] Question about mris_compute_lgi error: 
/scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission 
denied")
Date:April 3, 2024 at 12:14:38 EDT
To:freesurfer@nmr.mgh.harvard.edu
Reply-To:Freesurfer support list freesurfer@nmr.mgh.harvard.edu

ERROR: could not open /scratch/

___
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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 
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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] Support for GPU on Freesurfer

2024-04-03 Thread fsbuild

External Email - Use Caution

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. It’s not unexpected for recon-all of the
subject bert data to take ~8 hours on a consumer (non-server, non-cluster),
stand-alone machine, e.g. recent Intel I9 chip with 8 physical (performance) ~3
GHz cores, 8 virtual cores, 32G of DDR4 RAM and an SSD drive. If you have
access to a computing cluster, you could try running recon-all there - which
should reduce the processing time.
- R.

On Apr 3, 2024, at 14:58, Camargo, Aldo acama...@som.umaryland.edu
wrote:External Email - Use
CautionHi there,I was
wonderingif there is support for GPU on FreeSurfer. I really would like
to use it on GPU because is taking 9 hours per subject to recon-all.Thanks a
lot and have a nice day,Aldo CamargoSenior Postdoctoral Fellow at the
University of Maryland,
Baltimore___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

2024-04-01 Thread fsbuild

External Email - Use Caution

You can try using the Silicon Mac development build on the M2
machine.. The download links is,
https://secure-web.cisco.com/1sX8Y1I4GPyZJYzijtfGnav0Xe1MBg-Yv4HzZ07-_su8lv08rzyK4H8-8kXDApCOFJi1XX2mYF4_iH04jySngiX_PsKXZ8K48PCmsO5rOdoTp9xOkS_lWIvP4_shoz9L0juTGXnI-cJu2OkSgIHq0t6kpJ57R6CDFuWwj6oo8ei6KgjsNlR3paBqlrIqqcBQfav6WRebfuIDaklO-u0z1WbqE8x5ZAYkk1eEWo54Lx3BivsKo1mU8doLnUImjSzTlys0yMQMxLZGbQ6ImK6nlKCF1Oetn2F4eojop3JuQT_CvEul9WKC1RN8IawLUeyXxhXl7B8LJ_c2ZifIfLarE6A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev-20240327.pkg
Right click on the pkg installer and then select the “open with installer.app
…” option.

- R.

On Apr 1, 2024, at 20:40, Martin Juneja mj70...@gmail.com
wrote:External Email - Use
CautionHi Koen and Doug,I am
trying to do similar analysis but when I run run_samseg command, it gives me
error "Illegal Instruction: 4"I am using the FreeSurfer 7.4.1 version on Apple
M2 Max MacBook Pro 14.4.1.Is it because run_samseg is incompatible with Apple
M2? If so, could you please suggest any solution (if available) how I can run
run_samseg on my Apple M2 computer?Thanks.
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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
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Mac OS Monterrey and XQuartz 2.8.2

2024-03-21 Thread fsbuild

External Email - Use Caution

I would try downloading an installing the latest version of Xquartz which is
2.8.5
from,https://secure-web.cisco.com/1QbY1_LKpOs8rxg9YmC2vjno1Z4v2i9V4XhLfDJzwmqCqCNtKYV5iKJ97aqCHBWhugUhe9IammuJUWqdIs7TNqvfslqQ7-iNicm1kKFw4SdTFJkeKTstQV2uZgF4LkFiKVqH_sXmfx4-EyPNQaC-IQhbg6vzxSrPPX9tOITRWcrJAOMPi1YGa5Dl09v7xbqRK9OUZ9YQ44l5cfCBcqoEVYtS3E_ktAaWhBM4NFOXOZuv9n-8Q3grR9r0qor3mFFQR4iL_agscdQM2Ia1iey1d6gjN6-c2SbHRikXbWdVZIp0yC3bWj7QD_htWCal6UddDd-B1CQUGn8Fct_OewW2hRA/https%3A%2F%2Fwww.xquartz.org%2F
Works fine with Monterey (at least on an Intel Mac).
- R.

On Mar 21, 2024, at 19:05, Hugo Sandoval guayosando...@gmail.com
wrote:External Email - Use
CautionHi, i am trying to
install freesurfer usingMac OS Monterrey and XQuartz 2.8.2. I get
an error message. Is it not
compatible?___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Bug reporting - longmc: case-sensitive issue in variable

2024-03-19 Thread fsbuild

External Email - Use Caution

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, Andrea andrea.boscu...@uth.tmc.edu 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,When attempting to run "recon-all -long" in subjects with multiple 
T1 inputs, I get the following error when "longmc" is run:concatLtas: Undefined 
variable.if: Expression Syntax.Command exited with non-zero status 1For the 
entire log, see attached "longmc_error.log".The following change at line 188 of 
"freesurfer/bin/longmc" fixes it (case-sensitive issue in "$concatLtas"):set ud 
= `UpdateNeeded $origvol $CrossList $concatLtas -- set ud = 
`UpdateNeeded $origvol $CrossList 
$ConcatLtas`Best,Andrealongmc_error.log___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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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] mri_synthseg fails with current model files (was Re: Support Request NextBrain)

2024-02-28 Thread fsbuild

External Email - Use Caution

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 the details.
- R.

On Feb 28, 2024, at 20:11, Sorby-Adams, Annabel 
asorby-ad...@mgh.harvard.edu wrote:Hi Helen,I managed to run 
mri_synthseg on my M2 Mac by coping over the model file to the 7.3.2 version of 
freesurfer, and installing the tensorflow workaround previously posted on the 
forum for apple silicon machines.I have not been able to get it to work on the 
7.4 or most recent dev versions unfortunately. The work around for 7.3.2 isn’t 
ideal, but does the trick.Freesurfer gurus may have more insight 
though!AnnabelOn 28 Feb 2024, at 20:03, Friedrich, Helen 
hfriedr...@bwh.harvard.edu wrote:Hi R,Thanks for your quick 
response.We actually did that initially and it did not work 
unfortunately.Could you provide me with segmentations for a certain scan? Or do 
you see any other possibility to make it 
work?Best,Helen__Helen Friedrich, B.Sc.Doctoral 
StudentNetstim LaboratoryCenter for Brain Circuit 
TherapeuticsDepartment of NeurologyHarvard Medical SchoolBrigham and 
Women’s Hospital75 Francis St, Boston MA 
02115brighamandwomens.orgOutlook-rrf3zs4o.pngVon:fsbuild
 fsbu...@contbay.comGesendet:Mittwoch, 28. Februar 2024 
17:20An:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.eduCc:Friedrich, Helen 
hfriedr...@bwh.harvard.eduBetreff:Re: [Freesurfer] Support 
Request NextBrainExternal 
Email - Use CautionThe 
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 silicon Mac via the link below. (After download, right 
click on the .pkg installer, and select open with default, then follow the 
prompts).https://secure-web.cisco.com/1lFsgk7vtXlatyZGhw2wfTf_WTyioo4BmLzbKYJKS0chTLAdh3oNub0eu9G9qOzY1R1TPfh7O0cjIMQFuYhTlqUAiRdSgB91d0F3QHYByNFAVNjpsEEv4j8KUjqvzZLZqXEgP3pCVveZdU3qRAuGidK7qzpvBYz_YCjvjuBw1oBU1uPE747lnnMIYvx8VMwRVlcOMe3jWSxtNYLK8z_NDUA_K1a4C_SuFXhsDf1Div6UKtS7i7jpzOLjru_-tpPY3gKSfhG_l5s6JEbjagAkRoXdEm1sYZTLvjnL5yV99Wpxmx2NKrzlsvr_ucGSkEhwaNz9EMh0iPkmf8X102ExqfA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkgWe
 would be interested to know if you run into such issues with the above 
development build. Please keep in mind a development build can be 
unstable and has not been tested like an actual release. Your numerical 
result may differ with the development build compared to the previous 
build/release.- R.On Feb 28, 2024, at 14:25, Friedrich, Helen 
hfriedr...@bwh.harvard.edu wrote:Dear Support Team,I'm reaching out for 
assistance with setting up NextBrain - mri_synthseg.Unfortunately, I 
could not make it work. There seems to be an issue with the 
np.float128-section. This error keeps showing up:image.pngI have 
also tried to delete np.float128 from the script (as per suggestion from my 
colleague). However, the same error showed up.I'm working on a macOS 
M1.I would be very grateful for your 
assistance.Best,Helen__Helen 
Friedrich, B.Sc.Doctoral StudentNetstim LaboratoryCenter for Brain 
Circuit TherapeuticsDepartment of NeurologyHarvard Medical SchoolBrigham 
and Women’s Hospital75 Francis St, Boston MA 02115MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
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Re: [Freesurfer] Support Request NextBrain

2024-02-28 Thread fsbuild

External Email - Use Caution

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 silicon Mac via the link below. (After download,
right click on the .pkg installer, and select open with default, then follow
the prompts).
https://secure-web.cisco.com/1lATTVPHpR_oCFmftTB7zqKpLVwajHCxZOKmxSn1tiCG2YsAguxO-onjfRFFoIAelBuq4VwcqflHZjVdKsNn_DE-IM537PyttVIVTZWBlmPHAOh6E6aox44M20RF1jIcKx-xJ1eCPhC9LpLjlB6V67UnFHLwxveDI7e1JBdPwIAbo---1k4E5Vd2QlLAc5xoVz7FNJa-WbB08QJI5kmBVhydQXQClQzGSK4_II7tzn_4XlAiNzRSotGH9cQ_HqzqOo_WfwfMmjdFzYPlYrggTgEyf2t9-LW9-TjBC_y1WWsJo0hegy1WIhcQ7jhakR2SkdHVF-pCrQesnLvB5CVGIfg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
We would be interested to know if you run into such issues with the above
development build. Please keep in mind a development build can be
unstable and has not been tested like an actual release. Your numerical
result may differ with the development build compared to the previous
build/release.
- R.

On Feb 28, 2024, at 14:25, Friedrich, Helen hfriedr...@bwh.harvard.edu
wrote:Dear Support Team,I'm reaching out for assistance with setting up
NextBrain - mri_synthseg.Unfortunately, I could not make it work. There
seems to be an issue with the np.float128-section. This error keeps showing
up:image.pngI have also tried to delete np.float128 from the
script (as per suggestion from my colleague). However, the same error showed
up.I'm working on a macOS M1.I would be very grateful for your
assistance.Best,Helen__Helen
Friedrich, B.Sc.Doctoral StudentNetstim LaboratoryCenter for Brain
Circuit TherapeuticsDepartment of NeurologyHarvard Medical SchoolBrigham
and Women’s Hospital75 Francis St, Boston MA
02115brighamandwomens.orgOutlook-jaw0jfh4.png___Freesurfer
mailing
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[Freesurfer] Updated instructions for running Freesurfer in a Linux VM (virtual machine)

2024-02-26 Thread fsbuild

External Email - Use Caution

Instructions about how to setup a VM running Ubuntu 22.04 LTS Linux have 
been updated on the wiki page,
  
https://secure-web.cisco.com/1-hfMzPT3UMB77kyvVjV7UDTVoojwvFmLCgo5iFkfwXwZ25LXFS9Roz8W9yuwq3ZMgs5tjQSEKQlcqIQbRxJ1rps2AabjEIivAzU8ekg5AsJLT6mntG2Nc4NnzZYDPJZG2wf_aLnz6uKLNaustProbSHYKiMbskeae7cLki3u_nSnw4xu4chaYhm-Z5kLiuCwcqECsDkdCMoITT-JKqqCHPkmz-brMCz3F9oCcmaqFMirOwqvqcbah9n7ycsFnHd3RDgkGDoMo6zuiX8aecB8B0MO5X6QvJKUslOgGjkBUQ4W4ItrfjjElVnPeg2YV9CgmgVdxPZUx-arGQMnQ7ZyPg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67The
 instructions include how to install and run the current Freesurfer release 
(7.4.1 from June 2023).
Please keep in mind that while the VirtualBox virtualization application runs 
on hosts with Intel processors, it does not run on arm64 machines (including 
silicon Macs with M1, M2, M3 chips).
- R.
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[Freesurfer] 7.4.1 release archive has extra directory prepended

2024-02-25 Thread fsbuild

External Email - Use Caution

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 sure where to post this as the github is more 
for source code issues.The 7.4.1 archives all have ‘./’ prepended to them 
(i.e., ‘./freesurfer/’ vs ‘freesurfer/’). This is causing an issue with 
neurodocker as the definition file it creates strips the first directory 
when building images. Thus, containers built on the 7.4.1 archives need to have 
their paths changed compared to prior versions or they need to strip the first 
2 levels of the path.It’s not a big deal and easy to fix in the def files 
once it's figured out, but given that it’s a departure from prior releases and 
is breaking some of the downstream tools, perhaps the next releases can go back 
to just 1 level deep (i.e. ‘freesurfer’)?Cheers,Dylan 
WagnerAttached Message Part.txt
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Re: [Freesurfer] recon-all-clinical synthseg error

2024-02-25 Thread fsbuild

External Email - Use Caution

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 
wrote:External Email - Use 
CautionHi!I'm trying to run 
recon-all-clinical but I'm running into an error with the SynthSeg at the very 
beginning. Do you have any hints what the problem might be here? Here's the 
full error message:the following problem occured with 
image[mypath]/mri/native.mgz :Traceback (most recent call last): 
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in 
predict  image, aff, h, im_res, shape, pad_idx, crop_idx = 
preprocess(path_image=path_images[i], File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in 
preprocess  im, _, aff, n_dims, n_channels, h, im_res = 
get_volume_info(path_image, True) File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in 
get_volume_info  im, aff, header = load_volume(path_volume, 
im_only=False) File "/usr/local/freesurfer/python/scripts/mri_synthseg", 
line 1377, in load_volume  x = nib.load(path_volume) File 
"/usr/local/freesurfer/python/lib/python3..8/site-packages/nibabel/loadsave.py",
 line 110, in load  img = image_klass.from_filename(filename, 
**kwargs) File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
 line 503, in from_filename  return klass.from_file_map(file_map, 
mmap=mmap, keep_file_open=keep_file_open) File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 526, in from_file_map  header = 
klass.header_class.from_fileobj(mghf) File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 171, in from_fileobj  + 
int(klass._data_type_codes.bytespervox[tp]) * 
np.prod(hdr_str_to_np['dims'])KeyError: 10resuming program executionERROR: some 
problems occured for the following inputs (see corresponding errors 
above):[mypath]/mri/native.mgzError in 
SynthSegBest,Agata___Freesurfer 
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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 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Mac OS M2 M3 computers

2024-02-17 Thread fsbuild

External Email - Use Caution

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 is in your home directory and your user name is “cstevens” 
then
$ export FS_LICENSE=/Users/cstevens/license.txt$ head -1 
$fs_license...@somewhere.com —— email you used to register
You can put that define in your shell initialization file so you do not have to 
set it again when you login.
If you are doing long term work, we recommend you download and install the 
7.4.1 release from June 2023. Those are Intel binaries, but they should 
run. You should use the standard Mac .pkg file. Right click on the 
.pkg file icon, select open with installer.app (default) which should provide 
some security exemptions.
June 2023 7.4.1 
releasehttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.pkg
There is a native Silicon Mac development build, but it is unstable and has not 
been tested as a full release has been. But if you are only running 
freeview, then you could try that instead.. Install the same way as 
listed above by right clicking.
Development 
buildhttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev.pkg
- R.

On Feb 17, 2024, at 22:09, Charles Leger 
charlie.stevens.le...@gmail.com 
wrote:External Email - Use Caution 
Really. I have a Mac Mini M2 (16GB), 
8 cores. I downloaded FreeSurferMac OS 7.4.1. Then tried freeview and loaded a 
T1 image. Freeviewimmediately closed. I tried this 3 times with the same 
result. PerhapsI should try a different version, ideally a version that allows 
CPUrather than a GPU install.Best,COn Sun, Feb 4, 2024 at 12:50 AM Fatima Karim 
fatimakareem...@gmail.com 
wrote:External Email - Use CautionI 
have been using free surfer for a year nowon Mac m2 max and it's working 
fine.On Sat, Feb 3, 2024, 23:42 Charles Leger 
charlie.stevens.le...@gmail.com 
wrote:External Email - Use 
CautionThere seems to be some contention if FreeSurfer will support Mac 
OSsilicon (M2, M3) computers. In the technical requirements section, itis 
clearly specified that a " 3D graphics card with its own graphicsmemory  
accelerated OpenGL drivers" is required. But in the emailarchive (caution 
suggested) it is noted that "binaries should run oncurrent Macs with M1, M2, M3 
arm64".Currently. Apple has not indicated plans to support eGPUs, which, 
onpaper, makes all newer non-intel Mac computers not compatible 
withFreeSurfer.Any suggestions would be greatly 
appreciated.--*Dr. Charles Stevens 
LegerPhD Psychology, Neuroscience diplomaDepartment of PsychologyConcordia 
University7141 Sherbrooke Street W.Montreal, Quebec, CanadaH4B 
1R6___Freesurfer mailing 
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Re: [Freesurfer] mpr2mni305 failed

2024-02-09 Thread fsbuild

External Email - Use Caution

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 is usually at 
the end of the log file.
- R.

On Feb 9, 2024, at 07:16, Francesco Lomi francesco.l...@unifi.it 
wrote:External Email - Use 
CautionUnfortunately I've tried 
to change the directory but I've encountered the same error, as shown in the 
log file.Best,FrancescoIl giorno gio 8 feb 2024 alle ore 17:59 Huang, 
Yujing yhuan...@mgh.harvard.edu ha scritto:This is from your 
recon-all.log:“setenv SUBJECTS_DIR 
/home/ubuntu/freesurfer/subjectsFREESURFER_HOME /home/ubuntu/freesurferActual 
FREESURFER_HOME /home/ubuntu/Freesurfer“Your SUBJECTS_DIR points to your 
Freesurfer install directory - /home/ubuntu/freesurfer/subjects. I’m not sure 
if this is the reason for the failure. But it is a good idea to set 
SUBJECTS_DIR to some other directory where you have write permissions.Can 
you re-set SUBJECTS_DIR and try 
again?Best,YujingFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfFrancesco LomiSent:Thursday, February 8, 2024 11:44 
AMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] mpr2mni305 
failedExternal Email - 
Use CautionYes, sure. This is 
the fileThanks.Il giorno gio 8 feb 2024 alle ore 17:03 Huang, 
Yujing yhuan...@mgh.harvard.edu ha scritto:Can you re-send 
recon-all.log as 
attachment?From:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfFrancesco LomiSent:Thursday, February 8, 2024 10:58 
AMTo:freesur...@nmr.mgh.harvard.eduSubject:[Freesurfer] mpr2mni305 
failedExternal Email - 
Use CautionHello 
everybody,I'm new on Freesurfer and I've installed the softwareon 
my Ubuntu 20.04 machine. The installation should be fine. just tried to run 
recon-all on my subject data but i got stuck on the following error you can see 
on the screenshot:image001.pngAny idea on how to fix 
this?Thank you in 
advanceBest,Francesco___Freesurfer
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Re: [Freesurfer] Synthsr command !

2024-02-08 Thread fsbuild

External Email - Use Caution

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 have a development build for the Silicon Mac, and you can 
download/try the installer package from:
https://secure-web.cisco.com/1iKFStD8SwFv0R2HIbwHmO8r1CRu1iDcQPEOYPG7jJvIjrAZDc0sJfHDQhWwcyZciKr78g2onoB2sSzz0vQI9hVrgYAlB6is6icLuMg76sWtQfUyNgcNnd1Q1wRYOF1dtT7BTdoIZesFyDrdB8pc3sSifAM_h9enQbvhLW4Fpsq9yGMR8UFc_k8RJbm43sAox64SI8W4Kj6foRBXU_6oeiy43-jspvGAXGRjGJEUNvS2ySV30aGfFwbfZpwL4oaHGelrKhzER-r6Eb1-Ikus3WmL6dTNPOYDZFhvhpZQoiknNDp1rGQyDXPL5soFZag0R2QFjbjrBsXSdTFdZ5ECtAA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
But we cannot recommend this build for ongoing work as it is currently unstable 
and not a tested release.
- R.

On Feb 7, 2024, at 17:05, Martin Juneja mj70...@gmail.com 
wrote:External Email - Use 
CautionDear Juan and FreeSurfer 
developers,I am trying to run themri_synthsrcommand on a MacPro M2 
Max chip (OS 13.6.4) - but somehow, I am getting the followingerror when 
I try to run this command. I am using FreeSurfer's7.4.1 version.Illegal 
instruction: 4I would greatly appreciate any help in getting this 
resolved.Thanks.___Freesurfer 
mailing 
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Help Download FreeSurfer Windows VM

2024-02-06 Thread fsbuild

External Email - Use Caution

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 freesurfer.
The Virtualbox VM is no longer available because the security/login credentials 
were compromised on this list.
Since you are on Windows, you could try using the windows OS built in Windows 
Subsystem for Linux (WSL). We have some notes about setting that up at,
https://secure-web.cisco.com/15CztkRxVJ7Ddir4MS_9Arksy0DkD_t2mgoGcHYmhJKK5Lsyhn9OQQF2n11zmSLeqbeGjffl8JiKJspStS5BIEqDeW4hwjubpORcz_WfM_QelzOOGCbo0-yxIrw5CRp9OTe6G_opwaoTix1AU6qWdzQ84fN4r922b3CXNohHY0nfJE_R1L5EMyO6V8j9OBROkgqBF4F3YCyusFxnCekqZ6zfNabw_pTnvaJDgwZR0JLlJ5nw84ZNy4DAJEMie-rQ8TdAxUT8Hafmh1q3BlprlvLyJxQ9QWTHDvp0ztYKxEOP5KBlgWyaJl3eak96w5YgK1ETj64k1_2sTQtEOkUs3sQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
But you would still likely run into the same issues consistent with having less 
than 8G of RAM to run Ubuntu Linux in WSL (instead of VirtualBox) + running 
freesurfer.
- R.
On Feb 6, 2024, at 08:54, lioudadraca...@gmail.com 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. 
But I have few problems.First, I do not have the access to the compressed VM 
Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible to 
have an access to that ?Second, I've seen that it also requires a login 
password for the "Developer" account. Is it possible to also have the password 
?Finally, I have a 8Go RAM, even if a 16Go is recommended, will it be able to 
run Freesurfer ?Thank you for your help.Best 
regards,Liouda___Freesurfer mailing 
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Re: [Freesurfer] Command terminated by signal 11 when execute mris_place_surface

2024-02-05 Thread fsbuild

External Email - Use Caution

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 to run
recon-all. Or I assume the 32G RAM listed below is the total
physical RAM on the machine and the VM has some portion of that assigned to it.
If you did not assign the VM say 16G-24G of RAM out of that 32G total,
then it might be having a memory issue. You could try not running
anything else on the machine, giving the VM 24G and that would leave 8G for the
host machine. You could also try giving the VM 4 out of the 16 CPUs as
well.
- R.
On Feb 6, 2024, at 00:39, Yp Ben benyoup...@gmail.com
wrote:External Email - Use
CautionHello FreeSurfer
Developers,I'm want to run HCP T1W data of recon-all , but it always failed on
step "WhitePreAparc lh", below is my run information:OS: Ubuntu 22.04.2
LTSMEM: 32GCPU: 16….Command terminated by signal 11...Check the core dump file
under /var/crash...I use 3 different VMs to run the same sample with different
freesurfer versions , 2 are 7.4.1 and another one is 7.2 , but always failed on
this step , I don't know what's the reason cause this failed , can you please
help to have a look ? Thanks a lot
.___Freesurfer mailing
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Re: [Freesurfer] Mac OS M2 M3 computers

2024-02-04 Thread fsbuild

External Email - Use Caution

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 requires graphics/X-Windows and for that you 
need X-Quartz installed on your Mac. We have a native Silicon Mac 
development build available but it is currently unstable.
The graphics card spec assumed the graphics card has its own dedicated memory. 
That spec is somewhat obsolete now w.r.t Silicon Macs since their unified 
memory design means the CPU’s and GPU’s share the same memory. The spec 
to look for on Silicon Macs is how large is “unified memory”.

Commands that are python scripts (and not Intel or arm64 binaries) using 
modules like tensorflow may not work on Silicon Macs when trying to utilize the 
GPU’s.
If you have not already done so, download and install Xquartz,
https://secure-web.cisco.com/1m9nMZoww5EBHuzCVnK1bRHfdp34oRBsReQGIi-7nF_TereiKLeFE0wV4a4heu4IG4aeHTF9KbcxR24tjHn5fIxKqu4LxSEgeQ8wmm8Q4xbnMFHYwYTY0UHlIENTkDMLYo3DlkhFLMAJZlTu1ccE2K1eh3bvTZ-BkbC_tkl75_agj_kbF0KP5y5mHFYc7xQ90ySlgwcCg6IxgC2KaW4OLOMa901CPYe7bgKc-5NLbXuiMNAnf1vaEneXx-ScWAKTyGvJMmrMqc3PZ63Q0MH6U7ctsM465JxdY4JDmrLuiw_fYKbwEs5j8SKmg_4OFKIOugXUUbkp4dpWCQFQXYurT1Q/https%3A%2F%2Fwww.xquartz.org
The 7.4.1 installer package can be downloaded from,
https://secure-web.cisco.com/1sijobmA3UkgB0Ha5oTzDO0KSCYb2unjOllCiEFgnLqS_Tx2LDrErGMRSS2lvZUAYzU2QZ1ZTncLzfdGcfuepyVFU3QiOnQAOTCWeUaRJ1_tKS4Rte9Ip5fLBZKhbmlE0tznV3WiY2-QKfEKo2T9KPiLpeHSMHVTvZzLeYaEJVWbOk9ABy_rNH35nm3v86C9_eSRlboHzCS_Fjnz9veMWwRi5vCt0T8FtGn94DuzeQQdrq7nDOO96TLwCG2HCkk3TnYzKii68VhahsXqUmxMeF0b9KTHkPngM5SNUX1lC9jHaETzq6i8oLShzbV-OGdZMCjWlRSxqCQgURNIy1wpDFw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
RIGHT CLICK on the installer package and under “install with” select the 
default installer.app. This should bypass having to open system 
preferences to make a security exemption.
- R.

On Feb 4, 2024, at 00:49, Fatima Karim fatimakareem...@gmail.com 
wrote:External Email - Use 
CautionI have been using free 
surfer for a year nowon Mac m2 max and it's working fine.On Sat, Feb 3, 
2024, 23:42 Charles Leger charlie.stevens.le...@gmail.com wrote: 
   External Email - Use Caution   
There seems to be some contention if FreeSurfer will support Mac 
OSsilicon (M2, M3) computers. In the technical requirements section, itis 
clearly specified that a " 3D graphics card with its own graphicsmemory  
accelerated OpenGL drivers" is required. But in the emailarchive (caution 
suggested) it is noted that "binaries should run oncurrent Macs with M1, M2, M3 
arm64".Currently. Apple has not indicated plans to support eGPUs, which, 
onpaper, makes all newer non-intel Mac computers not compatible 
withFreeSurfer.Any suggestions would be greatly 
appreciated.--*Dr. Charles 
Stevens LegerPhD Psychology, Neuroscience diplomaDepartment of 
PsychologyConcordia University7141 Sherbrooke Street W.Montreal, Quebec, 
CanadaH4B 1R6___Freesurfer mailing 
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Re: [Freesurfer] Killed procees during running WMH-SynthSeg

2024-01-30 Thread fsbuild

External Email - Use Caution

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 process to run. There have been some reports of 
memory leaks in tensorflow/keras python modules, with comments suggesting some 
issues go away when the GPU’s on the machine are no longer used for data 
processing. I don’t know of a reliable workaround right now.
- R.

On Jan 30, 2024, at 16:44, Bender, Andrew bende...@ccf.org 
wrote:External Email - Use 
CautionDear Freesurfer 
Experts,I’m evaluating WMH-SynthSeg for white matter lesion segmentation 
using the most recent development version, and ran into similar issues reported 
last month:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://http://secure-web.cisco.com/1VwtYiRJfeLutN8gPbBz-bZmM0fMIW8vgmy6EkaYe2JAKQ2grPaLmCGo3UpxOnqYUUlcACTvWzy4YIWFwFgTi03QWN8oF6ljo-B1SrjF_YMYXZ8Sa8adrtmKmZC24rjNx1UvnMEKdf7Dr7aNc5Po0duEhAz6rP31ABsIBPEaSU4c8ARZ4bmFR51w452iri2Mpmvl4ZoF6xtPYHmX713youl-9Mdtl3viB5W51pE7xk-HmBcrVYhx8dYvUQPNQSTjEZX9RTAQQrHUJe-RFhDAQHRBvDK9DM9IEqwD3CK3iQRZAb0IOjD2br_bgWkX4uEqz7swGr5atJapDoPcuhXKXMw/http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76177.html%26nbsp;I
 was running this as CPU only on a Mac Studio (M2 Ultra) with 192GB RAM. I 
tried is multiple times with 1-8 threads, and the process was killed in each 
instance. Viewing memory usage through the Mac OS Activity Monitor while 
running WMH-Synthseg, it appears that memory usage ramps up to 200GB (at 
which time the process is killed). With system resources consuming ~10GB RAM, 
it seems there should still be sufficient memory if it only requires ~32GB RAM. 
Are there any other (i.e., non-documented) options for running the process on 
CPU only? Any other suggestions are greatly appreciated..Regardless of 
specific suggestions you may have, I wanted to bring this to your attention as 
a potential bug that could produce memory leaks or similar 
issues.Thanks,DrewAndrew R. Bender, Ph.D. 
| Staff Neuroimaging ResearchCleveland Clinic Lou Ruvo Center for 
Brain HealthPlease consider the environment before printing this 
e-mailCleveland Clinic is a nonprofit, multispecialty academic medical center 
that's recognized in the U.S. and throughout the world for its expertise and 
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This message is intended for use only by the individual or entity to which it 
is addressed and may contain information that is privileged, confidential, and 
exempt from disclosure under applicable law. If the reader of this message is 
not the intended recipient or the employee or agent responsible for delivering 
the message to the intended recipient, you are hereby notified that any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please contact 
the sender immediately and destroy the material in its entirety, whether 
electronic or hard copy. Thank 
you..___Freesurfer mailing 
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Re: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0

2024-01-29 Thread fsbuild

External Email - Use Caution

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, Monterey and Ventura. So it may work on Sonoma. 
The 7.2.0 release from 2021 is too old to have been tested on newer 
versions of MacOS.
You can install the 7.4.1 release with the pkg 
installer,https://secure-web.cisco.com/1rsGw8GzmRUK9yxME6fi8OiEwksVSolguqiea92G44m3nZ8vkR_pUdXoEEyyZGxT5kLITfqkOgn9K5Yi6uB4BWVSsfdeQgcNv2po-t8b5umyOs0BOD2M0pUfv1H0RRvI_KeZ3icjBIVvwrzWk7U_0QdriOPTDw8UtNebc9olqbl0vWKqGg0u37yGtGA5Gb7vy2EgH6Mys3HaeqSXocPinchKl5s4zKYgHxK_nchQ9XBHFmgQuUtdO-UnZ3Nmq-ou5cKbJ2c14SCGnIR8WJtJKI9XZAPGysNTrsd1RpoBNpaki-KGHp8CRNiOK1iDt4nFlLSwUXejfepae4z2VhG_54A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
After installing 7.4.1, you should run the fs_install_mcr_script provided in 
the freesurfer distribution to install and setup R2019b using the instructions 
below.
- R.

$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
… answer y to any installer questions ...
The script should output how to set the environment variable LD_LIBRARY_PATH to 
pick up the The MathWorks libraries. That might include a setting 
something like,$ export 
LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64:$LD_LIBRARY_PATH
Please make sure you have otherwise removed any references to your previous 
matlab R2016 environment from PATH, LD_LIBRARY_PATH, etc.

On Jan 29, 2024, at 21:02, Iglesias Gonzalez, Juan E. 
jiglesiasgonza...@mgh.harvard.edu wrote:Dear Joao,I’ll defer to our 
software specialists, but another option may be trying the Python 
version:https://secure-web.cisco.com/1gPJbJkeAwLxRG5ISVgM2USwM6OoyR8xf1PZE6EvMJf-SRaA9EGrMIWMtoTGH7aMT86QE3DlUA-XL1cyKUT3DHiXT0ma5mZHgd8ElXQmslT_wo-B2jePlem_KHUlWQToIJfu88U9chsrSFPXs215vnwwuXBvNTLJVE_lh4T6cIBV8QanuQVm3e3BjQ2EaXcYC6lhhkrsO-307Mn1YWFWI0xkVANXmWcY12KiGHnlfDB4oQwY-GjBYbyVDhcDlyZNNNweBWf11saa25eKp5Psjr8CU3zE-iQlD181J1MMo6K2lE_R2hvTnJn_7VjLF8-XpGoq_UscsjzCYr00bk4ySXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSubregionSegmentationCheers,/E--Juan
 Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1xkFYctwFMfhxok7RYaJbrw5crH_Wnw2ywE2VZjqP-qYTzxO45GiX_q_jHOGkqPmOQY12cjT47WY_TNufoQOmeAFinHtebu_tDtkJJVMmB96rzEQOlCZI1k2mTTmKDvUzHaDMbEkw4eLcStBv9BFy5ovxP_UcPTbUqlRjlE6blbq8D5Fv7VSm30vX9EUttKo8iDtVUGfS2XjFHB6gAGXA1URsH0JKHt7Q7dflcHZH_NjOHpx0Yn-QKiwXl_S6b6qeUhvyqWOImXysYCX2OZ2FK_hd1KwrVcATlaLNfRrLWT-3UAWR26hK9Kd627pXbyVKblH7o-d5_SZJqNciPeKwBQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.edu on behalf of João Ramos 
jnpra...@outlook.comDate:Monday, January 29, 2024 at 4:26 
PMTo:Freesurfer@nmr.mgh.harvard.edu 
Freesurfer@nmr.mgh.harvard.eduSubject:[Freesurfer] longitudinal 
hippocampal segmentation error in Mac OS Sonoma + Freesurfer 
7.2.0External Email - Use 
CautionDear all,I would 
appreciate your help in an issue I am having and one that I have not found a 
reference to regarding Freesurfer. Basically, I have run all of the 
longitudinal Freesurfer pipeline and I am now interested in running the 
longitudinal hippocampal / amygdala segmentation code (segmentHA_T1_long.sh), 
though I am faced with an error (log below). I have searched and this happens 
on various settings with no pattern that I could recognize (apart from iOS app 
development), and it was also pointed out on a mathworks forum post regarding 
matlab 2016 on a Mac OS Sonoma (which is my operating system, and this version 
of freesurfer uses matlab r2014b). Would this be possible to run within Mac OS 
Sonoma (v14.2.1, with current freesurfer version 7.2.0)or should I 
run a linux instance with freesurfer install and everything?Thank 
you!USER joaoHOST Joaos-MBP.lanPROCESSID 
17239PROCESSOR x86_64OS DarwinDarwin Joaos-MBP.lan 23.2.0 Darwin Kernel Version 
23.2.0: Wed Nov 15 21:54:10 PST 2023; root:xnu-10002.61.3~2/RELEASE_X86_64 
x86_64--##@#
 Longitudinal Hippocampal Subfields processing (T1) left Mon Jan 29 20:55:28 
WET 2024--Setting up environment 
variables---DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/7.2.0//MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0//MCRv84//bin/maci64:/Applications/freesurfer/7.2.0//MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0//lib/gcc/lib:***
 Terminating app due to uncaught exception 'NSInvalidArgumentException', 
reason: '-[__NSCFString stringByStandardizingPath]: unrecognized selector sent 
to instance 0x62e281b0'*** First throw call stack:(0 
CoreFoundation

Re: [Freesurfer] recon-all cannot execute: required file not found

2024-01-19 Thread fsbuild

External Email - Use Caution

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 
https://secure-web.cisco.com/1vzo5wK6ItFFFMnllsCMKRTIzcqYXDSETeXibiyz78VEk_TVHkbVLtjlltPd0g0Uvd8x0WK89GE8gU1KWFMzKnfwwgiI7LxjmgavQJ6CRuDKNdbu69lRngmJXHI_jT7Apzbthify1jBVr0Rl4tHRLO59uiYFLhP5xVv4FxnW-1brLM5t_f80dYxYqxS-tDJmUcSQBJ26bUuIwdNXHT49QU9R4-QLIUjxabN7pBG7dNNvYjk6etULRIlRTmLlKSxZ11x1M0Be8QDGN-sL353J66YtQqcu9Ew-9KlI2nYNXikCfbW-0PZolvzHu35pUzJw_8zpHpyEpfdmLOKtTKWv0Iw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.0%2Ffreesurfer_ubuntu22-7.4.0_amd64.deb%24
 sudo apt-get install ./freesurfer_ubuntu22-7.4.0_amd64.deb… answer yes to all 
queries ….,.. output deleted ...
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.0$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted …
$ which recon-all
/usr/local/freesurfer/7.4.0/bin/recon-all
$ recon-all -version
freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e
If you used the tar file instead, then some permissions might not be correct 
depending upon how/where it was unarchived (and some dependencies might be 
missing).
- R.

On Jan 19, 2024, at 15:20, Peled, Noam,PhD npe...@mgh.harvard.edu 
wrote:I'm just trying now to runthe "recon-all -version", also without 
any arguments.Both produce the same 
error.Thanks!NoamFrom:freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing 
yhuan...@mgh.harvard.eduSent:Friday, January 19, 2024 3:10 
PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] recon-all 
cannot execute: required file not foundI’m wondering how you ran 
recon-all. Do you see the error even running it w/o any 
arguments?From:freesurfer-boun...@nmr..mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfPeled, 
Noam,PhDSent:Friday, January 19, 2024 2:59 PMTo:Freesurfer support 
list freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
recon-all cannot execute: required file not foundThanksYujing,Yes, 
I looked for the file permissions using ls -l. It does have execute 
permissions.I also tried running chmod which didn't 
help..Thanks,NoamFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Huang, Yujing yhuan...@mgh.harvard.eduSent:Friday, 
January 19, 2024 2:54 PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] recon-all 
cannot execute: required file not foundAfter sourcing Freesurfer, 
$FREESURFER_HOME is added to the front of your $PATH.1. ‘ls -l 
$FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the execute 
permissions?2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the 
permissionBest,YujingFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfPeled, Noam,PhDSent:Friday, January 19, 2024 2:42 
PMTo:freesur...@nmr.mgh.harvard.eduSubject:[Freesurfer] recon-all 
cannot execute: required file not foundDear group,I'm trying to run 
Freesurfer on digitalOcean server running Ubuntu 22.10(GNU/Linux 
5.19.0-46-generic x86_64)I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)After sourcing 
Freesurfer, recon-all gives following error:.../freesurfer/bin/recon-all: 
cannot execute: required file not foundOther functions, e.g. freeview, 
mri_info, all seem to work as expectedWould love some 
help.Thanks,Noam___Freesurfer
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Re: [Freesurfer] recon-all errors (cannot execute binary file +

2024-01-16 Thread fsbuild

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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 run commands.  There are several 7.X freesurfer releases, 
but the latest release is 7.4.1 and you can download it via the link, e.g.,
https://secure-web.cisco.com/1bTTDiznaFEJgJPDoi2yskrFqRdt_lNsr8LZ0PFjdBlc19JuHE6WaWHssFDdzwRLVMRUHA3qj7h4ea64BhZk97t2IniNpnSEBUfevruwnZRT-WXrHBzlmbnxwfB-eUVqRKZYuKEwgZupdFOKnrwiz0xxPKw5DTxfL31t8mtljoZBWCtHjo8uXtSylGlGyZRzw2b6Kjz5JBf1zzrJTR_GSBoP7UPjKW3-cqENylh36UvAaYHpdFnPoZ4CrWPzQwkw7vmD7cmQcG6jBsy_w7nUkvkrhCZTYVfLg5BUluX8L0H85LGn_CikykHFVbAsE-L8Zih6Q9g6D25IvisceU2Rl_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
I would first remove what you have on your system from the terminal window with,
$ sudo rm -rf /Applications/freesurfer
Then in a Finder Window navigate to the Downloads folder (or to wherever you 
downloaded freesurfer-macOS-darwin_x86_64-7.4.1..pkg). You should be able 
to RIGHT CLICK on that file, select open with the default pkg installer, and 
then enter your password etc. to install it. Right clicking should bypass 
having to do some of the security exemptions in system preferences.
Once the install is complete, setup the Freesurfer environment in the terminal 
window,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.4.1
FSFAST_HOME  /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects
MNI_DIR
/Applications/freesurfer/7.4.1/mni
You also need a license file, license.txt. Once you complete the license 
request form 
athttps://secure-web.cisco.com/1Svw39fuKLV2rL8mAOfpPDMZrLLodE_ScR0sKC5od9QRlt9jwKuDUSQ6WtLlT9V17W1wUaBdznmlv7nMRbyPA6LYSYXyCAnP8F-Tuz_VE6STeVAxkh40QhJ8_Hz3w6xgC49SELup9uGscJnea_a5_YfPe4v_s5sGckdUErRUBLgOMN41ow4CikTKbC-IfUIre0ikhv0rLYF0iFjK9EZGFCuzHN7-z5cvA1mPBIjRTyGJsmV-behjR7Zpaho6a5uOuq1I4CB61WxtecgERQIEuY6PCEpMSMO1vfX-v7GEXY61w_SZ_5yg0kRQoolU2kwNaTPReDO7q7kH9B3AAFtRMPQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html%26nbsp;you
 will receive a file “licesne..txt” via the email address used in the form. 
 Download/copy the license.txt file to your machine from the email.
If your home directory is for example /Users/hyejung then you will see the 
following in the terminal window,
$ cd$ pwd/Users/hyejung$ echo $HOME/Users/hyejung
… if you downloaded license.txt into your Download folder ...
$ cd Downloads$ ls license.txtlicense.txt$ cp -p -f license.txt 
$HOME/.$ cd $HOME$ ls license.txtlicense.txt
You could also use the Finder to navigate and drag/drop the license.txt into 
your home directory. Once it it there, set the environment variable 
FS_LICENSE so freesurfer commands will find the license when they run,
$ export FS_LICENSE=$HOME/license.txt
Then it should work to run freesurfer commands from the terminal window 
including freeview.
- R.

On Jan 16, 2024, at 20:47, 윤혜정 hyejung7...@amc.seoul.kr 
wrote:External Email - Use 
CautionGood day.When I run 
recon-all for my nii files I get either one of the following error 
messages:1.ERROR: could not configure recon-all parameters 
Killed2.ERROR: could not configure recon-all 
parameters/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary 
file/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0Or3. a Pop 
Up message"_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified.mac OS cannot verify that this app is free 
from malware.I googled the third error message and tried"Allow 
anyways"from the privacy setting.Then the next message pops up, 
then the next and the next.Could you please help me to understand the 
cause of the above 3 error messages?I tried to redownload freesurfer as 
well as python but none worked.Thank you in 
advance.Best,Alice___Freesurfer
 mailing 
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continue to

Re: [Freesurfer] Freeview crashes when trying to load volumes

2024-01-15 Thread fsbuild

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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 VM then please mention that and if the Windows
host is running Win 10 or 11.
- R.
On Jan 12, 2024, at 11:52, Ford, Jamie K j.f...@imperial.ac.uk
wrote:External Email - Use
CautionHello,Please could I get
some advice on my installation? I've downloaded version 7.4.0 using the same
steps described in the installation videoMailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFiledo=gettarget=installFS_demo.mp4Everything
seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like
on the video). Freeview then crashes. This is the same for any
volume.Could someone please advice? Any guidance would be greatly
appreciated.Many
Thanks,Jamie___Freesurfer mailing
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Trouble with ssh tunneling & Freeview

2024-01-11 Thread fsbuild

External Email - Use Caution

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 could be issues with OpenGL graphics running on or 
being sent from the linux host.  The system requirements for Freesurfer 
include the following for running Freeview,
Graphics card: 3D graphics card with its own graphics memory 
accelerated OpenGL drivers
Updating the OpenGL drivers on the linux host will sometimes enable Freeview to 
display images remotely. My understanding is Linux servers need Mesa 
packages installed to support newer versions of OpenGL. If the Freesurfer 
Debian or RPM package installer was used to install the Freesurfer distribution 
on the Linux host, then at least some of those packages should now be 
installed, i.e., we do not recommend using the tar archive to “install” 
Freesurfer. We don’t know how EXPANSE installs/maintains Freesurfer or 
what their servers support for graphics hardware.
GLX is the X-windows extension for OpenGL graphics that can be tunneled thru a 
remote SSH connection. But GLX may not work with the newer versions of 
OpenGL over ssh. A workaround for this is to install and use VirtualGL on 
the Linux host. If VirtualGL is supported/installed on EXPANSE, try 
prefacing the freeview command with “vglrun” - 
seehttps://secure-web.cisco.com/10kzDiIcCSK5wSi3KZ4WHry8djBXAuam589oKZqs5TvrpZwtx_bg2pMLPYhP8Jy_MCc-EzDmY-dqikD_6634fXGIuWxPmIpVKc_7FvQJ1WLhxdWKQNREcPKVjjXtooJBwDbQMYGNkRFTt8kV6opy3zDRKCw2VFxn2ADZvwE-CJh_5FiVuijgz3-BKzUFkbC6C6v0BjwjdzAd3rvsTA-OMSKycamq6dtAADv6xzHGy1pd8-jWOBWz55-o6eUCbotpP3Xjkaj44Yj6JNn9W87mEonAk4nFRD7f8ZUJdi0BwhynYiOrU-XXN9NEleN4SBmflmdoT6sWwWvQHcooLyMlnww/https%3A%2F%2Fwww.starnet.com%2Fhelp%2Fvirtualgl
 We use VirtualGL and graphics acceleration on a few Linux workstations 
to accommodate Freeview running on Linux and viewing its 3D graphics thru a 
remote VPN connection.
XQuartz on the Mac is the equivalent of X-Windows on Linux.  The Mac 
should be usingXquartz 2.8.2 or newer for use with the Freesurtfer 7.4.X 
releases. I think X-Quartz will open automatically to view X-Windows 
based graphics on the Mac.
If the EXPANSE linux machines are setup to support remote connections to view 
3D X-windows graphics then the IT support staff will know about the options 
above. File/open a ticket with them, ask them what they support, and how 
to setup your environment. If they do not support it, an alternative is 
to install Freesurfer on your Mac and download/copy over the data to view with 
Freeview.
- R.
On Jan 11, 2024, at 14:18, Dong, Yilei yid...@health.ucsd.edu 
wrote:External Email - Use 
CautionHi Freesurfer 
team,I have Freesurfer installed on UCSD's Expanse HPC, which uses the 
Rocky Linux 8 operating system. Whenever we try to do ssh tunneling and more 
specifically, logging into our HPC via ssh -X to open up Freeview's GUI, it 
always aborts. Prior to logging into my HPC from my Mac laptop's terminal, I 
always open up XQuartz. Another colleague of mine has also encountered similar 
issues, where they have managed to get X11 and Xeyes to run, but also 
Freeview's window keeps aborting.We have also tried to follow 
instructions from the following links when it comes to getting ssh tunneling to 
work correctly in hopes of making Freeview's GUI pop up:MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://http://secure-web.cisco.com/12UaY28IjOvcCuzqwhVkemgeWWYzbyjV_gOl5bvSd-xgSy77ILuGBhPY6qPumJh0zLPo9B1IddZ-5F3ldYWW9jnrPdNM07lirk88wNgJrzWex0cuUCHsmM03NfVHfywusHDbKGei7iUd2RNw0Wj4tZBh8IZM0hK3N-EeXuQktbpl22fBLF8A6ZK6nbgwtaTd-UgPuGxht7pJQ5dZnPQa9ZgYj5vFk-oQNlJQJVrUQDdAu1IsSKk7-3J0xIpZGIQ3p--LPjQXvLyuurp_vQb8U7xdYkC62sEVtr7LY4ux8fTPog7UyA5usa_m75oyYIGwT54qTXS-AXEh5GS-632IA9w/http%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Fmartinos%2FuserInfo%2Fcomputer%2FremoteAccess.php%23graphicsMailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/13jhlKniK4ot1jAvrTEdLmUxfeVBEFlM0Xf3YMvRlE0gq6-vGRZz3p6eV2ZQx5RS0jNCj_reYJBdnIcOVavR5zgBEVioq5stB9hydwZvyzokRjSpJYL0wreyNtjPUlutWSbgoC8i5cbU7qN-8grDPZs-myayIL4VnGNebEO41TgXHT6EYseYu18uBPPkpaZlk4J85BkLvHnhjyuL5B2D2K9uuUkzNMNwKO-hl3br0t2sF_PstW8EW_V08RHiHyv1qmjj7Ju5Pr1ZAXQwmHG04EKPzZJZ2Fnr41B5GEGTg0ukJqIK41n_9n45WEU_JwntnaTEprGkgVxI90r9lG8fVsA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRemoteAccess.%26nbsp;If
 we operate from a Mac computer, is it better to use a VNC or XQuartz for ssh 
tunneling? In addition, can we find an error log in Freesurfer's directory to 
find out exactly why Freeview keeps aborting in our circumstance?Thank 
you.Sincerely,YileiScreen Shot 2024-01-11 at 11.01.27 
AM.png___Freesurfer mailing

Re: [Freesurfer] Scratch Directory Permissions Denied

2024-01-09 Thread fsbuild

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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 subsequently complain. I would not expect 
multiple programs writing to the same directory tree to work together if they 
use different file permissions, privileges, and/or perform independent 
clean/delete functions in shared directories.
- R.

On Jan 9, 2024, at 14:47, Michael Ruvalcaba 
michaelruvalc...@berkeley.edu 
wrote:External Email - Use 
CautionHello,I am trying to run 
the recon -all function in my MATLAB pipelineusing Freesurfer 6.0.0 and I 
haveno issues with it. However, when I run the recon -all step using 
Freesurfer 7.2.0 and run the following command (the recon -all step finishes 
without error by the way):ft_read_mri([subdir 
'3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);I get the following 
error:/bin/bash: 
/scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission 
deniedThe issue is there is no scratch file and it looks like between version 
6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory 
(which 6.0.0 doesn't)Does anyone have any inputon this? I hope this made 
sense!Best,Michael 
Ruvalcaba___Freesurfer mailing 
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Re: [Freesurfer] Freeview keeps aborting.

2024-01-09 Thread fsbuild

External Email - Use Caution

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 able to tell you what you need to set in your
terminal session for it to work. But it could be they expect
programs like freeview to run on your local client machine and read the image
files/data over the network via NFS, etc.
- R.

On Jan 9, 2024, at 18:52, Dong, Yilei yid...@health.ucsd.edu
wrote:External Email - Use
CautionDear freesurfer
help,I have freesurfer installed on UCSD's Expanse HPC, which is on the
Rocky Linux 8 operating system. Every time I try to open freeview, it always
keeps aborting. How should I fix this so that freeview's GUI can be shown? I
have included the screenshot for reference on the error.Thank
you.Sincerely,YileiScreen Shot 2024-01-09 at 3.47.14
PM.png___Freesurfer mailing
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Re: [Freesurfer] Infant fs

2024-01-08 Thread fsbuild

External Email - Use Caution

Sorry I cannot address those questions for you, but I have sent your
email along to one of the developers.
- R.

On Jan 8, 2024, at 19:17, Amrita Pal palamritaor...@gmail.com
wrote:External Email - Use
CautionThanks. I had filled out
the form. How 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 like you need to fill out the request form,MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/infantFS- R.On Jan 8, 2024, at
18:12, Amrita Pal palamritaor...@gmail.com
wrote:External Email - Use
CautionHelloI am trying to use
the infant fs for processing my pediatric data. Where can I download the
package?Thanks and
RegardsAmrita___Freesurfer
mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
mailing
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Re: [Freesurfer] Infant fs

2024-01-08 Thread fsbuild

External Email - Use Caution

Looks like you need to fill out the request form,
https://secure-web.cisco.com/1Zztv_hv2CHwkWkqDcQ75P0iZ5m3guJnkq6OOGA_AuaX-IiyZb0WPr8KCpekneZq3xdVmuMPM23fTG3Ht7xu0ZxxuE7lX3v7MtXKhOYdch26VavRXmE4TYyFgzUtcfZ8Mh10uPUrEamBqumy-FNcsmw7X_b2F1UYP4c2d7gcvt63cz8GX-LgMtaXaMwavAIFqEGWOWCd96T8ZnjtbulPm0DPyZmtcSrfnpR6765ew-pjl__K7VbzCX08ymTl8j_cLhGOLEch-DlM3gKLQeqKQZIr8dYWNag83n8Gk-CILxUMV-m5nRv5XliC_fxFPkjVewauJwD8Y04ZXBm_jIlWxOw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FinfantFS
- R.

On Jan 8, 2024, at 18:12, Amrita Pal palamritaor...@gmail.com 
wrote:External Email - Use 
CautionHelloI am trying to use 
the infant fs for processing my pediatric data. Where can I download the 
package?Thanks and 
RegardsAmrita___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Subject does not have a bstampfile

2024-01-08 Thread fsbuild

External Email - Use Caution

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 Windows file system does not support soft-links. 
 Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS 
image running freesurfer. You could however copy the files from that 
mount point to create another SUBJECTS_DIR somewhere inside your Linux 
image, e.g., under your home directory in linux.
 in your linux terminal window ...
$ cd$ mkdir subjects$ export SUBJECTS_DIR=$HOME/subjects$ cd $SUBJECTS_DIR$ cp 
-p -f -R/mnt/c/Users/GCM/Desktop/subjects/NowakG .
- R.

On Jan 8, 2024, at 16:10, Huang, Yujing yhuan...@mgh.harvard.edu 
wrote:You need to specify the input files to process. Here is the wiki page for 
recon-all - 
https://secure-web.cisco.com/1hqVY7QioPnD85rxOcGMUcCuynnW47DWZwkPX0Z-CZpPZhsuOE3Dqq56yZOR48pnqlARbSGSU1uJNTssTzOLeJZDej-4B4APtXHQmIDTAeNiz6injsGyGghBE4szgzC-CIvlktYVKAeIFD9vBNBZGTgRtRAfcxOZTJJXzk0kPtE9fSY8vo9o05Q8Lf5La4t7Av6IvB6hkO3ZqlfaDGIxlZfRhNJC0f5oWDNXpfp8nYykG-egLh8zOuhOsHSbWCac7UKV67GamZPc5FS5KwH3vo_4_Omj5v0dIRxZ5O4d9WtJGN0f3IkrLaqnXHmnqhmI4YmYtNQmp-0UBF38a-xfw4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-allBest,Yujing-Original
 Message-From: freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Joanna KidonSent: 
Monday, January 8, 2024 3:33 PMTo: freesur...@nmr.mgh.harvard.eduSubject: 
[Freesurfer] Subject does not have a 
bstampfileExternal Email - Use 
Caution Hello FreeSurfer 
Developers,I'm attempting to compute Segmentation of hippocampal subfields and 
nuclei of the amygdala (cross-sectional and longitudinal), as described on the 
https://secure-web.cisco.com/1JRIAQtmLphlXIykU3RsSWy2GeEv_y0Em3hHjyX02njKQRMzktRXyIr6AsUKD8-6mfnHs3e3VqgraV5HY65g0kcdnn-c5SO11uj3GmVopw6uBvHuq9nL41NZthselkwcmF1_pfF7tqA1mMsAKXVbGF7kWv-nHwevhhA8F6Ut_G89GsS36wOdw4Qdt0y3NAVk7FFD73D5O1AlLLXsiM0_emjpApIZBLEppGP5jjmBYXvnW-lkYFHOz1Mpazf7b7a-Tkol4Hrp9s-ygaeijb4CyTVrQYXiaqfwLwo5L2QmewMDyINYXoiDYTFnRY1ZnSd75iVr_Rv6sEbBi2merzCpAuQ/https%3A%2F%2Fsecure-web..cisco.com%2F1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAwtvXgTVrtcAutSPTrtciZPyxNbynvc15Hs2QuWbY_5s83lqlEQoYQJki7l_TF3oztafbzs30sHpSw0h-eZSPjzJ5uVCT29lxgi-ynPEhcVbMEKprxj8oqXGxzhvsFrvGlrQlowS673v0V1k05awg3ja96pJZpAes0ADbo-3Cdp-F5Ia5oD5q7fabDh5N202LPH9PNC1ruPvKvy_5987OSpV7RTftXJev5hauvVESrxnACVsA0f5bGY-t55yLWz2a-Tkq1eIulXgNxAa228gMMBHaDYc4X4fiJjG0re3rdg%2Fhttps%253A%252F%252Fsurfer..nmr.mgh.harvard.edu%252Ffswiki%252FHippocampalSubfieldsAndNucleiOfAmygdala,but
 I get the following error when I run the recon-all -all -s command:Subject 
does not have a bstampfile, copying 
/usr/local/freesurfer/7.3.2/build-stamp.txtSubject FS 
Version:freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275No 
constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% 
fs-check-version match = 1 fs-check-version DoneINFO: SUBJECTS_DIR is 
/mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME 
/usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 
SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 
GNU/Linux##@# MotionCor Sun Jan 
7 20:48:46 CET 2024ERROR: no run data found 
in/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume 
called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.If you have 
a second run of data call it 002.mgz, etc.See also: 
http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwuliarvPShgKfL_ItgaKWWnaYhDjK5FMWmDuPGEEEjW91LA3z7KDEeMiaIfV2jyXtfoUeeAjtPetkV6AuryGQBEKfk8d73IpHcgRIPrySwzLQaUtJT-A3dciz-Ma0n5qP4wsp5g9Tjvw5bGZUJlDFhJwWQrn04-RanD9XSLv0hlRr6ygjNO1BDIi4FgyjW3UWknkdWZwG9r4rG9cdS5Q0g6fBJ_QfVYe1DlgOs71lVji4Q7vMKZoWhEAgKq_5yhthldQEcJLHUmFLDrBcBX1TXcVwnrmkcLYG8z3GWHohA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversionLinux
 LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 
x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s NowakG exited with ERRORS at Sun Jan 
7 20:48:46 CET 2024I've searched the list and no similar errors have been 
reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, 
Ive attached the scripts/recon-all.log in case it's of any use.Best 
regards,Joannadr
 n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji 
Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii 
Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet 
Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. 
Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej 
Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w

Re: [Freesurfer] Tksurfer and freeview

2024-01-06 Thread fsbuild

External Email - Use Caution

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 
freeview torun tcl/tk scripts. My understandingis running 
tck/tk scripts as the -tcl switch allowed in tksurfer - is not supported in 
freeview.
- R.
- - - - -

$ tksurferfv --help

This is a script that runs freeview with arguments like tksurfer.
Not all tksurfer functionality is replicated.

tksurferfv subject hemi surface 

-tksurfer : use tksurfer instead of freeview
Can have multiple annotations

-all : load white, pial, inflated
-vgl : runs freeview with /usr/pubsw/bin/vglrun
-no-vgl : does not run freeview with /usr/pubsw/bin/vglrun
-no-outline : do not show annots as outline
-neuro : use neurological orientation instead of radiological
-rotate-around-cursor (-rca) : in 3d view, rotate around cursor (use -no- to 
turn off)
-linear, -linearopaque, -piecewise, -min_to_max (default) : overlay heat scale

tksurferfv dev


On Jan 6, 2024, at 20:59, JAEHYUN KIM jachos...@gmail..com 
wrote:External Email - Use 
CautionHello,I attempted to 
switch tksurfer to freeview in the script, but it seems like I need to change 
arguments "tcl" to something that can be applied to freeview.Option 'tcl' not 
recognized.What argument could possibly be used to replacetclin the 
scriptsuch astmp.tclandlh pial 
-tcl??Best,Ed___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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] recon-all -s SiroSTC006_pre exited with ERRORS

2024-01-06 Thread fsbuild

External Email - Use Caution



Your Linux image could be missing system files and/or graphics card driver 
updates needed for the version of Qt included with Freeview to display graphics
 via X-Windows. So I would first remove whatever currently exists under
 /usr/local/freesurfer and then follow the instructions on the Wiki page
 to do an install from scratch using the actual installer (instead of 
the tar file). The instructions are here,



https://secure-web.cisco.com/1aVasdKo9Pwif5UQ2Uch0IDTvauLowJGIckrOUQbXQ2UgjMTijxM2AHRnYW5Sikm1PLFsVxTugqk7jS8q66aPC2Wt61zvugIk0ou082bvW2Vi2HpkhPUVK5RuQZz2bLaagNV35aRFc1BnYpdMMEOV_I7Kv2taVGg0rdW4UYbH_GJbhgkvI-Qa_RFQ4NdxHnAc16p7Z3HD0wL3Y4ADaC0Bqe1RvUwRo4c9f42ae38IHeHekPpYi9ZUSGHQmOdCa1fI-XUD5NHGSIodtj96CXK30LHfH3-4qIZuhpUMifnii45pKrnP74W9KNsZeK4DZQ5G5nnKr6Vfy1E4qFgc-u2-qw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu


After you install Freesurfer and setup the X-server on the Windows host -
 stop and verify basic graphics are working by running glxgears. If 
communication from Linux running under WSL is working with the X-server 
on the Windows host, then you will see an X-Window open and display the 
spinning gears via the following Linux commands, 



$ sudo apt-get install mesa-utils

 answer Y to all prompts ... output deleted ...

$ which glxgears

/bin/glxgears

$ glxgears



The instructions on the wiki page end with running the "freeview" 
command with no arguments in order to test freeview can at least open 
and display an empty window.



If that works try displaying one of the volume files included in freesurfer,



$ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz



If that works, then try displaying one of your surfaces/volumes with your own 
freeview command.



If however glxgears worked, but the freeview command failed to open a 
window and/or display the volume as listed above, then the next step is to
 check for an upgrade to the OpenGL drivers on your Windows host. 
Freeview needs newer revisions of OpenGL in order to display graphics. 
Once you update the drivers, try running the freeview commands listed 
above again.



BTW - please remember to change SUBJECTS_DIR from 
$FREESURFER_HOME/subjects in your shell environment to a path your 
normal userid can write to w/o sudo/admin privs. That could be in your 
home directory e.g.,



$ cd

$ mkdir subjects

$ export SUBJECTS_DIR=$HOME/subjects



You could put that export command in your shell init, e.g., $HOME/.bashrc file



- R.





On 1/6/24 13:25, Flemister, Abeoseh B. (flemist...@missouri.edu) wrote:






  
I’m using Ubuntu.




Abeoseh Flemister

  

  
  From: Flemister, 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





freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz










Abeoseh Flemister







From: fsbuild fsbu...@contbay.com

Sent: Friday, January 5, 2024 9:35 PM

To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu

Cc: Flemister, Abeoseh B. flemist...@missouri.edu

Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS



Did you install Freesurfer 7.4.1 using the Debian installer package ?

https://secure-web.cisco.com/1IOiqTlEkTSd5OYr_A3naRtVr5L_K5zRpteC0_uUt7M0gRolNr7VK3lsQcU_qofF0IDf9if55xJELV6MPMHK0trMuv6brwoSd7MfQJKQ0u8rG6GpC55LrWIvHRVZ5RLVajCat58QdOxjxETxHox8d-pjPklYqzufhatlnoff9JNXFQBE2YZu1fSh7A_UI7FYF5ow5QHCaq4mgE4HIWjw_RKbxKvWi44qi3wAXyIcVfJoZw9W_iaRleXKYVjeCJHON3xsxb9jOhTdZWl0OJXUj8PIarGpr4vFjOdYhQu0_VBCO9368S1QeeP4BRzeKe2J-ZEzfrbiiNKrP3ru0vjOGZA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
- R.



On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. flemist...@missouri.edu 
wrote:



External Email - Use 
Caution



Thanks, but the issue isn't that graphics aren't displaying, it's that freeview 
won't load because qt can't be initialized.



Abeoseh Flemister



From:fsbuild fsbu...@contbay.com
Sent:Friday, January 5, 2024 8:27 PM
To:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Cc:Flemister, Abeoseh B. flemist...@missouri.edu
Subject:Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS



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",



https://secure-web.cisco.com/1KBH0OQxJdEKdxK38EEhCdBUjp55VUN1FBiZ5YthIc5pA61hlHgbL-cEwJvdn2CsRwulZb2ChiY34JUUJgqUkxjXpBjvLgaWKGc6bkkQI-gCV05RaqJb-LVMNDg3I6_MxTZjCeI91uxm1EuPx9n7v5D9B71pSaVfKcT6WwVL-gVzZdfTW4FxedwvqmFmPM3lsBtb3qeCFfgJpROJ5k8qXkYLKlc8A7Ut08BdQA1gBlcNWxRp_mVboSNqlOiAj6uP8LzJt4mix2WyTnxQ0rQVIq4byEe_gcatLHNw6KrimTL6zflLzhfSgk6CZSh22FlMw8wItE0eb

Re: [Freesurfer] mri_error_no_clear_message

2024-01-06 Thread fsbuild

External Email - Use Caution

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 GRADIENT ARE 
INCORRECT OR INCORRECT TOLERANCES out of QuasiNewtonEMA: 008: -log(p) =  
-0..0 tol 0.10
This thread indicates it could be the skull stripping is not right, and should 
be 
checked,https://secure-web.cisco.com/1diiACwYbRU5h086AYSNGiqllYdOKITn3ySdC0K_QfnQR43A65qvLhyBqoue0bb2EIdQri_zKECQVz7Dg4n1y-KrqVKkY42kR7NxqLvFqeNGpT_LHmzYmFbyZcQarr8vTSInFpkA8dw2kifIJW092CogIViPRD29ux9nSFCHAFM-MjYDP7OR8RXAbFeqv5t3P9Y-GN-S8ou2NsWtfrhciLxc_rGRla71oL66AX4Rz8RTgJfYAKgsKItsVgU7_Ze_slOiVIeiN7awFuPLq1-2OpvYI9KsK-zyirB09oD4IW93nqNnKkerwb2Pkf2KVDYAm7eHdn_m0AZbg71elbxK9Cf3csOj7VWnmzRjt2G8KtiE/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg16992.html-
 R.

On Jan 6, 2024, at 01:10, yunus soleymani soleymani.yu...@yahoo.com 
wrote:External Email - Use 
CautionHi Fargol,I recently 
heard about some problems from my coworkers who were using Ubuntu 18 and 
version 7.2.0 of the software. However, I am currently using version 7.2.0 on 
Ubuntu 22.04.2 LTS, and it works well for me. You could try it out and see if 
it works for you as 
well.bests,YunusYunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 
914 526 
9298On
 Friday, January 5, 2024 at 10:05:54 PM GMT+3:30, Fargol Rezayaraghi 
far...@uw.edu 
wrote:External Email - Use 
CautionHi FreeSurfer Team,I 
hope this email finds you well.I'm trying to use a T1 image to get the 
aparc+aseg and wmparc niftifiles.I was using this command: 
recon-all -s Subject1 -i T1.nii - all -notal -check ( I used recon-all -s 
Subject1 -i T1.nii - all first, and after getting Talairach error, I added 
-nota -check at the end).I'm getting the following messages without a clear 
error number:recon-all -s Subject1 exited with ERRORS at Thu Dec 14 
21:18:02 EST 2023For more details, see the log file 
/home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.logTo
 report a problem, seeMailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 
behttp://secure-web.cisco.com/1n6sdsWRV3TG8Jv2QrC7lr2OJkNo-vKWiVDfRMiE5lmXlfr-lokdvEt9eU6rLlP-aYqMbpq7K8EuAFgyM-6sO89wlS6SQyFVjfDrM7snkFk50KWtPcMrrMAb3-iDx3BvJzlzmHyj0ZOND6no-rksYRz4xSsFBN_9UnfKugJxeNypP2Hj8p3ohnddEIIXWWJiwXHUvl-q6ed-l--DVxtJuq-0q9GLNGkXfHafyVqJT-wYiKqyqa3_LTDndGHBRYVVjR3aNR8Yk5kzhAcfQ0V0xCnJghGvzLYBDnRmqqZBH_M2E4IbsaoFhxLjF6uz4KQphy-hq0G_fy4qWkLWvQOq0djR1FPNjJvPOTe0nl7LLpnQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReportingThe
 version of the 
freesurfer:freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bMy 
platform is ubuntu18_04_06 on Oracle VM VirtualBoxI've attached the log 
file.--Kind Regards,Fargol R. Araghi (Rezayaraghi)Ph.D. Candidate, 
University of WashingtonDepartment of Mechanical EngineeringMailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttp://secure-web.cisco.com/1MEbXNSnnv7NT1-4EzMYIfzctR98Iydj5J9JFwfH6Kv4xQ8RFYfNZ1-FLbFY0LR3b3gAbNVf39J834yCGuuDieCRxVv1PmsclTDaUtIvP9xcuHXFNd3SI-5JWP3t7QoQkPVjBDfSl5aO2ssQJ5uTSQybV2BUdc8ImY7AORL9Uz2P62vMPbegb42qe9ykB-sRrI0L5Hvjhaz6KWK9d3ewR-i9h-qytWo2MEFrrNCV3gMkYtzs5vPDIbtVNkBf9JFTVQSqFvD9o_KKDometmdLv2vgp7eHtjAswPZt6Q3W2L65Ckz2jrmXX5dknJ2nl0Dj59QdWnEGE7b-W4jR72W2lAXrMCnGVGRbuGml8G5qazXk/http%3A%2F%2Fwww.Kurtlab.com___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
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Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

2024-01-05 Thread fsbuild

External Email - Use Caution

Did you install Freesurfer 7.4.1 using the Debian installer package 
?https://secure-web.cisco.com/1Q45DaXEMcahL0g3wyejOntK1tGwx5UNQU25fdIi6ImofQsUOBUFGOhQ21vBk8sDRQfWWELU7ghl6F8QsJA6G2LpBun8SBG8VuebFtJaMobqrOERog6kz0hiKLV9ajDE2AKC1cpczWaDYkcSc4gMj3M6RFSGVTMvswdtfRVwJb-Ck23miRyGdEEMqm_Vf-b-J9o0O3vxunBYSB4cBN28DNJm4do5FWUZ4zSzRajltNg7RZ46COiMaso4uOBO2RYGe0GsZu0-WtJ9Aceq0QL43ZSK1SlxBsNnkMA4gJsKlawl_Tl3esT3lDUmN4303CUV1bHuzWMUv-G-vhN66uSWjhA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb-
 R.
On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. flemist...@missouri.edu 
wrote:External Email - Use 
CautionThanks, but the issue 
isn't that graphics aren't displaying, it's that freeview won't load because qt 
can't be initialized.Abeoseh FlemisterFrom:fsbuild 
fsbu...@contbay.comSent:Friday, January 5, 2024 8:27 
PMTo:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.eduCc:Flemister, Abeoseh B. 
flemist...@missouri.eduSubject:Re: [Freesurfer] recon-all -s 
SiroSTC006_pre exited with ERRORSFor 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",https://secure-web.cisco.com/1oaJ0JSPhxlRjzZbZiQ7yaftYm3TvYL5vsUqSvRIwn1mxTLB9TJXbethBhfapiwejmtZvkPk-Rzn2z_ad008-CzQlNve-NK6CceUt0VtPPFJdwtHKP55BXcuQhcU1YMz4-FPp9GzSTpiJ3JHu0iWTdbP786ULqlSTxSVgPgP7VkSxFmOR08R6XsMAhtGAScfuIli7yeGgO6_pGTXQjtPhYf_rpwzgCC2fxaK-4G43kajshNd4Ud6bVNH54fIM-6dcft-18wReIbRAerhMZzSx7hql2Jiwn18OCmUKqAcP8rn9FrqtaYOtu1LGeBs5QWaxiqN9ZGDiVySHjpAlv-EeZg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.htmlIn
 case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link 
is,https://secure-web.cisco.com/1EiWtVy6tBY8avsFO7RwETRF3_M-X-xF2Kpa7qQsUO9MBq9hJVTqFCn_eb9DM39rNtk3pbFG-ug4ZpEKk6X5eQ2KDMDYdDUh5TpmffuF5wXtAdJ4hB-SoNLiV1Eby6E2JQ7J-CCBMpK3-i117c1ChJq3VJ47f5OEtaSJW1rpGX1NRsG3fz4fL7KgiZcAesTpPNIIbOF0oVPc7kQgLZgqih4rx94xTA9NBpzpd1HjHFBdtCE_iQGSw6wkenZH9UDB92x5b8fE-xVb2Lshe0GJ8hZ4FWXijzgb14x-T7Jq75dJgbZtGXjWNynrOPhOFqkTqD0jXb80ORfn3PZQGWxIN5g/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu-
 R.On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. 
flemist...@missouri.edu 
wrote:External Email - Use 
CautionHiYujing,Thanks 
that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error:This application failed to start 
because no Qt platform plugin could be initialized.I sawan emailon 
this topic but I don't think it was ever answered.. Apologies if I'm reading 
the thread wrong. Any help would be greatly appreciated!Abeoseh 
FlemisterFrom:freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing 
yhuan...@mgh.harvard.eduSent:Friday, January 5, 2024 3:05 
PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with ERRORSWARNING:This message has 
originated from an External Source. This may be a phishing expedition that can 
result in unauthorized access to our IT System.. Please use proper judgment and 
caution when opening attachments, clicking links, or responding to this 
email.This is from your recon-all.log“mri_convert 
/home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgzmri_convert:
 extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“There 
is a space in your path to nii.gz. Can you remove the space by renaming the 
directory?Also, your SUBJECTS_DIR points to your Freesurfer install 
directory - /usr/local/freesurfer/subjects. You might run into permission or 
symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some 
other directory where you have write 
permissions.Best,YujingFrom:freesurfer-boun...@nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.eduOn Behalf 
OfFlemister, Abeoseh B.Sent:Friday, January 5, 2024 3:31 
PMTo:freesur...@nmr.mgh.harvard.eduSubject:[Freesurfer] recon-all 
-s SiroSTC006_pre exited with 
ERRORSExternal Email - 
Use CautionHi FreeSurfer 
Team,I am attempting to run recon-all on a 3T MRI image dataset. I used 
recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and 
recon-all failed before completeing even the first step. I tried other files 
from our dataset and using .nii files and got the same result. I sawa 
recent threadwhere someone's issue was improperly labeled WM lesions but 
my dataset is composed of healthy brains.I attached my 
recon-all.logs.. I am using a Linux virtual machine (FreeSurfer version 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if 
you have any questions!Thanks,Abeoseh

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

2024-01-05 Thread fsbuild

External Email - Use Caution

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",
https://secure-web.cisco.com/1_xzs3l0H18glGmrIaq7DLLWEnbalu4hRqRVJfIOVshijKYxcPt7YgAHaWtbElTSVhOHSVpXfVbYtsSat-VSB2AcASMfIu3iGWkg1Pr8PAWGiO-QNx_InTSbPx1SlEgEfWwHcu8Kvv6mpvP1DVjjMjrQm_tjS5mLYrxRY4oBZ9ZDYVcOJOgqZ1aNMNRZciur7DWeYIOQvMB3gIzoQ9Ezl_HmMYDUiQFPkcPHCm-jCkc9CwpFyswcD9oucICvpa2CcnjmJ_uKvLTTH3CMRECLNaxrDHkc_YoVNzJt4G1azbIURdLSwwIWcNW_J2fArM_PkVmgAJrH_G5HaO6Udtvukdw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.html
In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link is,
https://secure-web.cisco.com/1NIeWPFmWL9ULg_YLAREetdCKnwA4CAjtUSmmia-2fJLaumxUt7nyh4UJA8ETOUN9ZoOiTX5WwcajQ_sDAOOVJakF-Aqee8hi58icmc6NHSfROyRiZ5TQY-ecyB2kKnjaz0f3e5_Qg6RK-x6-rP_zvRBzKHU2gEyZgr8ivRTUzaCtcYqTpgdC7euLsajGvu0lgP3hQGs-pjDgQFqARk41W-gp9vVlFfkqZ7jqrzUHbXKJSgVrIz7OvWhnctAqDmu7vpLk74tAGnyrzsoRpHRX9TuybAZMwjHHOKh7_IVpBAwPkmQXb9UMnyrtgutVQ871ASnKlGXL3HfgSgCUITnwMA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu
- R.
On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. flemist...@missouri.edu 
wrote:External Email - Use 
CautionHiYujing,Thanks 
that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error:This application failed to start 
because no Qt platform plugin could be initialized.I sawan emailon 
this topic but I don't think it was ever answered. Apologies if I'm reading the 
thread wrong. Any help would be greatly appreciated!Abeoseh 
FlemisterFrom:freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing 
yhuan...@mgh.harvard.eduSent:Friday, January 5, 2024 3:05 
PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with ERRORSWARNING:This message has 
originated from an External Source. This may be a phishing expedition that can 
result in unauthorized access to our IT System. Please use proper judgment and 
caution when opening attachments, clicking links, or responding to this 
email.This is from your recon-all.log“mri_convert 
/home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgzmri_convert:
 extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“There 
is a space in your path to nii.gz. Can you remove the space by renaming the 
directory?Also, your SUBJECTS_DIR points to your Freesurfer install 
directory - /usr/local/freesurfer/subjects. You might run into permission or 
symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some 
other directory where you have write 
permissions.Best,YujingFrom:freesurfer-boun...@nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.eduOn Behalf 
OfFlemister, Abeoseh B.Sent:Friday, January 5, 2024 3:31 
PMTo:freesur...@nmr.mgh.harvard.eduSubject:[Freesurfer] recon-all 
-s SiroSTC006_pre exited with 
ERRORSExternal Email - 
Use CautionHi FreeSurfer 
Team,I am attempting to run recon-all on a 3T MRI image dataset. I used 
recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and 
recon-all failed before completeing even the first step. I tried other files 
from our dataset and using .nii files and got the same result. I sawa 
recent threadwhere someone's issue was improperly labeled WM lesions but 
my dataset is composed of healthy brains.I attached my 
recon-all..logs. I am using a Linux virtual machine (FreeSurfer version 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if 
you have any questions!Thanks,Abeoseh 
Flemister___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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
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] Freeview not showing output

2024-01-04 Thread fsbuild

External Email - Use Caution

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 graphics from 
glxgears, then there is likely something not right with the OpenGL drivers 
working with the graphics hardware on the Windows host. Usually the fix 
is to update to the latest OpenGL drivers on the Windows host.
If you have not read through or tried the steps on this Wiki page, then it 
might help, 
https://secure-web.cisco.com/12p37USRW5-RyLF2YXnbTAoizwyX5lHFSny043woIbJwaVA1Q6_A8YJxMdsz083PotIEQxfNhBetezn8unJ3bpT7arlesM-opVIvQ-jxqHg6UZaTwwFvbkIbzmvXhlHlC02MgLrOwtH-BShA0LaKafUr8T7AWZt5Dy1bKLSpvXObbJNND8nFFzU6ikjAOYv8JvCwMSODydsxNuBgPbsqak7GwjQ3Ap4BqUrQHcZN4UX_4jgm1-o9L_odJwgkN4z7eGgHh9wg2zsdJrbBiJSkETQeqnnIC58Lc8iamkihm7PokgUoRcCHqiEG0hpPWCb2tqimgLM9hYepeAUqcX8FTtA/https%3A%2F%2Ffreesurfer..net%2Ffswiki%2FFS7_wsl_ubuntu
If you are seeing graphics from glxgears then I would presume DISPLAY and 
XDG_RUNTIME_DIR are likely set OK in Linux.
- R.

On Jan 4, 2024, at 10:08, Wang, Ruopeng rwa...@mgh.harvard.edu wrote:It 
appears your system has some problem displaying OpenGL content properly. I’m 
not familiar with Xming. Can you try some other x display for Windows such as 
mobaxterm?https://secure-web.cisco.com/1KYKTifNL0XRk6k_SapoZX6CTHF_pDgzD6UKF0dkksoSBoqImuAD98rrLboBd_aYWt93uiZcob83wd88Crd8E4w6HbvVkhUVwS-CFa__hpvt-RsRpD40l9EbM2nCjm3OlP-ailtdAw2JpkXjxXQiLyTFabILi3agYXU2Jlj8KQ8U1mG56Pnrzu9EGa4BgFUvqu5fXNHC8JzXAm3Ktv-7W5FqCSV4yvg0ORKm7Jgt5fCYUzzQCBTvCdkJPxlX0KCk8gXd6N4W0BXKiNpFFX1N-2zy1vKf80kre0reP_cD6emR7ZsP_67hH_apBmofRuDaMT7PpM1pYGe2F2WunI4xJgw/https%3A%2F%2Fmobaxterm.mobatek.net%2FOn
 Jan 4, 2024, at 6:11 AM, Shawa, Zeena zeena.shawa...@ucl.ac.uk 
wrote:External Email - Use 
CautionHi Ruopeng,Thank 
you for your quick reply!When running glxgears I just see a blank 
window.Sincerely,Zeena 
ShawaFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfWang, RuopengSent:Wednesday, January 3, 2024 4:29 
PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] Freeview 
not showing output⚠Caution: External senderWhat if you run 
glxgears command? Do you see 3D spinning gears or just a blank 
window?RuopengFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Shawa, Zeena 
zeena.shawa...@ucl.ac.ukSent:Wednesday, January 3, 2024 9:17:00 
AMTo:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduSubject:[Freesurfer]
 Freeview not showing 
outputExternal Email - 
Use CautionHello FreeSurfer 
Developers and Community,Hope your day has been going well and happy new 
year!I'm attempting to visualise FreeSurfer outputs using freeview, as 
described on the “Introduction to Freesurfer Output” tutorial, under the 
“Viewing Volumes with Freeview” section (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1wzX4cge9MlMx5r_8jnAVeO8ue9DOKEESG6wS-RZbEzhXP-7pQaQgxBK8QyBF7hm-bqYBz_sBcNzsM9MxEQ-owoVqQmRLE8GKpOudIwJavI3EU6YF_Bs_uAcZfSLu7O8gR4W_mzt643W0rot3Z4yPSTE3IePMTVkJV27B2yH3OF6BwcPOoP1ZfXocrxR56_ANZV8XjyeQaOQ5D9BY7BRh1gcp_P57Orpb9r_0CgjBkFDZL9nBqKcNgdmgbNshaYmrvP5yk_fMjqkC87ych1b9nPkqMBOnxpXESn_d39nq6tSxFAIGSpeutQYRT9L5CNGoL4z5e5xLi2rNrI0cDiXNCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview%26nbsp;).
 The viewer launches fine and seems to load everything, but instead of showing 
any output it simply shows a black screen in the middle (screenshot attached). 
There is no error outputted in the command line either. The viewer seems to 
work fine otherwise, and I have completed the Xming X-server setup as described 
here:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/18qHMAU0T79b7NwnKw9Zpf5tUXLvkF9EnPH2_5X4-JibgPev_yLgH9bOmnOl9ki6tsL6KJAPJ89TBivch0oRDHLcHX9p2zemlApVOavfNMc-oVeLvXDLYMfg46MM5nK0UOFATMr9pJhI1-RGWNYv073vMPVhYUMtVYo0_C8Rdgsw4Fz5Pd9NcVLJBUFY7uHP2NMrO9f7Hj201yg7U7OmezaP47vYHFgVw_Um1LN2zKYmYZZtbOoGyxl--WMOdEZ6YE9BbwFADgcB6KRW3UVvjR55-8xnv8jsDNhhNH1cBrcEZPSpsUs6gxuHuJtDcu7LTvHS_ZIUJ7xLZjI51NjzLnQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming%26nbsp;.I've
 searched the archives and GitHub issues and cannot find a similar error. I 
would appreciate any feedback on how to troubleshoot this issue.Thank you very 
much for your understanding and help!FreeSurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460Freeview 
version:Version 3.0, June 14 2023 buildXming versions: Xming fonts 
7.7.0.10, Xming 6.9.0.31Platform: WSL2 Ubuntu 22.04.3 LTSuname -a: Linux 
LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxspecific command:

Re: [Freesurfer] Help (Freeview fails to launch)

2023-12-29 Thread fsbuild

External Email - Use Caution

Depending upon the state of a machine, there is no guarantee a list of 
"required" packages will encompass everything that needs to be 
installed/updated, or that a manual install will work.So we neither 
recommend or support manual/piecemal installs, e.g., via the list below, 
instead of using the built-in linux package management tools.

- R.

On Dec 29, 2023, at 22:32, Kiyotaka Nemoto kiyot...@nemotos.net 
wrote:External Email - Use 
CautionDear Akira,I agree with 
R that installing FreeSurfer using the deb is preferred, but ifyou want 
to stick to tar.gz,below is the list of the packages to be installed when you 
install FreeSurfer using the deb package.So if you install these packages, you 
would be able to run freeview.Hope this helps,Kiyotakasudo apt install -y 
language-pack-en binutils libx11-dev gettext x11-apps \ perl make csh 
tcsh bash file bc gzip tar \ xorg xorg-dev xserver-xorg-video-intel 
libncurses5 libbsd0 libc6 libc6 \ libcom-err2 libcrypt1 libdrm2 libegl1 
libexpat1 libffi7 libfontconfig1 \ libfreetype6 libgcc-s1 libgl1 
libglib2.0-0 libglu1-mesa libglvnd0 libglx0 \ libgomp1 libgssapi-krb5-2 
libice6 libjpeg62 libk5crypto3 libkeyutils1 \ libkrb5-3 libkrb5support0 
libpcre3 libpng16-16 libquadmath0 libsm6 \ libstdc++6 libuuid1 
libwayland-client0 libwayland-cursor0 libx11-6 \ libx11-xcb1 libxau6 
libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \ libxcb-randr0 
libxcb-render-util0 libxcb-render0 libxcb-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 
wrote:External Email - Use 
CautionThat 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 linkMailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deband
 the install can be done with,… cd to your Downloads to wherever the .deb file 
is …$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debIf the 
install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 which is 
the path to use for the environment variable FREESURFER_HOME,$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1If they are not already set in your 
environment, you should also set,$export XDG_RUNTIME_DIR=$HOME/.xdg$ 
export DISPLAY=:0- R.On Dec 27, 2023, at 23:17, Akira Kita 
jorrydep9...@gmail.com 
wrote:External Email - Use 
CautionI have installed 
FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tararchive 
freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the 
following error message:This application failed to start because no Qt platform 
plugin could beinitialized. Reinstalling the application may fix this 
problem.Available platform plugins are: eglfs, linuxfb, minimal, 
minimalegl,offscreen, vnc, wayland-egl, wayland, webgl,How can I solve 
this?　　　Akira___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web..cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Kiyotaka 
Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of 
Clinical Medicine, Institute of MedicineUniversity of Tsukuba1-1-1 Tennodai 
Tsukuba, Ibaraki 305-8575, 
JapanE-mail:kiyotaka@nemotos.net___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Help (Freeview fails to launch)

2023-12-28 Thread fsbuild

External Email - Use Caution

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 
linkhttps://secure-web.cisco.com/1t9e2mCgXLQVxO1_HRQVcGKF8xT7sodKwA6zzWD3PnvYpEYhzi545ja6T6zaKK2EKrLVHMv6-PenWRMiweIekDa0iPsOeO98ft16CafenUS7q9BCgUBIUTZ4DVfUj_bzh0uPOyWvS4HQa596zdcqA4rd_Q-K_M2WisVZhilBIGDxBi6g1no1JAF0xGe8QRbw1_MNpA42GJvTyE3Ps_fzXnMymgErLwVj6rpub0SX6CnI2T2f2hJ-5kA2_45a9Cuj-xUsFMqWPuXjSNYYpq3gSvNU9KSI_nj_yxnrBbLWqZOIW4xjT17yKPejFlXKp808Nd2U_ZOe-9oEV5ZotlsGDQw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb%26nbsp;and
 the install can be done with,
… cd to your Downloads to wherever the .deb file is …
$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
If the install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 
which is the path to use for the environment variable FREESURFER_HOME,
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
If they are not already set in your environment, you should also set,
$export XDG_RUNTIME_DIR=$HOME/.xdg
$ export DISPLAY=:0

- R.

On Dec 27, 2023, at 23:17, Akira Kita jorrydep9...@gmail.com 
wrote:External Email - Use 
CautionI have installed 
FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tararchive 
freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the 
following error message:This application failed to start because no Qt platform 
plugin could beinitialized. Reinstalling the application may fix this 
problem.Available platform plugins are: eglfs, linuxfb, minimal, 
minimalegl,offscreen, vnc, wayland-egl, wayland, webgl,How can I solve 
this?　　　Akira___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Re: [Freesurfer] segmentBS.sh not found

2023-12-26 Thread fsbuild

External Email - Use Caution

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 FREESURFER_HOME=/usr/local/freesurfer/7.2.0-1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/usr/local/freesurfer/7.2.0-1
FSFAST_HOME  /usr/local/freesurfer/7.2.0-1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.2.0-1/subjects
MNI_DIR
/usr/local/freesurfer/7.2.0-1/mni
$ which segmentBS.sh
/usr/local/freesurfer/7.2.0-1/bin/segmentBS.sh
$ segmentBS.sh -h
  ERROR: cannot find Matlab 2014b runtime in location:
  /usr/local/freesurfer/7.2.0-1/MCRv84… rest of output 
deleted ..
So if you have not already installed the MATLAB runtime environment for 
thesegmentBS.sh script, then you need to run the Matlab install script we 
provide. For the Freesurfer install under /usr/local on linux, the Matlab 
install needs to be done with root/admin privileges which you can try via the 
sudo option,
$ cd $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME 
./fs_install_mcr R2014b
… you will see output from downloading and installing the matlab runtime under 
/usr/local/freesurfer/7.2.0-1/MCRv84 …You should follow the instructions from 
the script output about how to set LD_LIBRARY_PATH, e.g.,
On the target computer, append the following to your LD_LIBRARY_PATH 
environment variable:
/tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64:
Your paths may be different, but you would modify the LD_LIBRARY_PATH setting 
as follows; I just cut and pasted the /tmp/* paths anover after "export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:”,
$ export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64
You could follow the same instructions as listed above for the 7.4.0 release, 
i.e.. change 7.2.0 to 7.4.0 in all the commands (and corresponding output 
should list 7.4.0 instead). The segmentBS.sh in 7.4.0 might ask for a 
newer Matlab version like MCRv97.  In that case, the sudo command to run 
the fs_install_mcr script would be,$ sudo 
FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
Once Matlab runtime is installed, try running segmentBS.sh again,
$ segmentBS.sh -h
Directory of subject to process:
 /usr/local/freesurfer/7.2.0-1/subjects/-h
does not exist
So change SUBJECTS_DIR to the path containing the subject data you want to 
process,
$ export SUBJECTS_DIR=/path/to/my/subjects
… then try running again ...

- R.

On Dec 26, 2023, at 19:32, Ganjizadeh, Ali, M.D. 
ganjizadeh@mayo.edu wrote:segmentBS.sh

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Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

2023-12-20 Thread fsbuild

External Email - Use Caution

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 could not revert to the older 5.X software. But if
you run into issues with a now ~10 year old version of Freeview, we may tell
you to use the latest 7.4.1 release from June of 2023.
- R.
- - - - -

•New: interface for x virtual frame buffer (fsxvfb). When you run
freeview from fsxvfb, no X server is needed. This is good for taking a bunch of
pictures when you don't want freeview popping up allthe time. Eg, fsxvfb
freeview orig.mgz -ss mypic.png —quit
•The filled.mgz can now be edited instead of the wm.mgz. The
advantage to this is that filled.mgz is slightly further in the process and it
is more intuitive. The filled.mgz is actually a segmentation ofthe
subcortical mass. In Freeview, you can view it in outline mode, meaning that
the edges of the segmentations are actually the surface that you are editing.
After that, run recon-all with the -autorecon2-wm -autorecon3 options, just as
you would if you had edited the wm.mgz..Landmark-based repositioning of
surfaces. Did you ever want to just make the surface move through a certain
point? You can do that now by creating point sets in freeview. Create a
separate point set for each surface (lh, rh, white, and pial), then save it in
subject/surf with a file name repos.$hemi.$surf.json where $hemi is either lh
or rh and $surf is either white or pial. Then run recon-all with the
-autorecon2-surfonly -autorecon3 options. Note that you can do this
interactively inside ofFreeViewas well; look under
Tools-Resposition Surface. If you do it interactively, the surface may be
overwritten next time recon-all is re-run, but it gives you a chance to play
with the repositioning.freeview - can now load and visualize diffusion
orientation distribution function (ODF) data.FreeViewchanges: surfce path
and label editing, surface annotation editing, automatic segmentation assisted
by Geodesic Matting algorithm, displaying two time courses at the same time,
better support for Mac (petsc error fixed on Mac)

On Dec 20, 2023, at 14:07, Edwards, Vincent
vincent.edwa...@utdallas.edu
wrote:External Email - Use
CautionHi,I'm following
up on my quick question from this time last week.I have several brains
that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview
on Freesurfer version 5 to do pial/wm/and control point edits, would I be able
to do recon-all through Freesurfer 7? Years ago, someone asked if they
could do recon-all in an older version of Freesurfer and edit in a newer GUI.
Doug said that was fine. My question is basically the inverse of their
problem.I assumed that since Freeview is a GUI, the version used
shouldn't have any actual impact on things as long as we returned to version 7
to recon-all.I just want to confirm that my assumption is correct?The
pipeline would be: F7 (recon-all), F5 (edit with freeview),F7 (recon-all
for pial/wm/cp's)Thanks,Vincent
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Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled

2023-12-11 Thread fsbuild

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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 executables either with the GUI or from the command 
line, you would need to have your own site or personal installation of Matlab 
with a license. The Matlab runtime environment in freesurfer subsequently 
allows you to run what has already been built with Matlab.
- R.

On Dec 10, 2023, at 21:31, Sophie Matis sophie.ma...@sydney.edu.au 
wrote:External Email - Use 
CautionHi there,Thanks 
for the advice, I have followed these suggestions and used the fs_install_mcr 
command and can see the the libmwm* libraries are installed under 
$FREESURFER_HOME/MCRv97/bin/glnxa64. I also added the path the script suggested 
once finished to LD_LIBRARY_PATH. I’m now not sure how to open matlab now 
though as I can’t find any executable matlab file? There were no error with the 
command but it doesn’t look like matlab was installed…Thanks again for 
the help,Sophie Matis| Data Management  Research OfficerSchool 
of Health Sciences  Brain and Mind CentreFaculty of Medicine and 
HealthThe University of SydneyBrain and Mind Centre, 
94-100 Mallett Street, Camperdown (M02G)| The University of Sydney | NSW 
| 2006sophie.ma...@sydney.edu.au |sydney.edu.auCRICOS 
00026AThis email plus any attachments to it are confidential. Any unauthorised 
use is strictly prohibited. If you receive this email in error, please delete 
it and any attachments.Please think of our environment and only print 
this email if 
necessary.From:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OffsbuildSent:Saturday, November 25, 2023 6:43 
AMTo:freesur...@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
Longitudinal LME matlab error - Matrix singular or badly 
scaledExternal Email - 
Use CautionHello 
Sophie,Just FYI, there is no matlab distribution included in the 7.4.1 release 
and we so not support using R2023b. So I presume someone at your site 
installed R2023b separately via a Mathworks matlab installer. We do 
provide a script, fs_install_mcr, to install either the R2014b or R2019b matlab 
runtime environment into the freesurfer tree for use. I don't know if 
running R2019b would affect what you report below, but you could try it via the 
commands below.- R.$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1
 --- linux install path$ source $FREESURFER_HOME/SetUpFreeSurfer.sh... 
output showing SUBJECTS_DIR and other environment variables$ cd 
$FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME 
./fs_install_mcr R2019bI believe this sets things up so the libmwm* 
libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64. You 
can try adding that path (or any path the script output recommends) to the 
start of LD_LIBRARY_PATH. You should remove any other entries to a 
different MATLAB distribution.On 11/23/23 20:42, Sophie Matis 
(sophie.ma...@sydney.edu.au) 
wrote:External Email - Use 
CautionHello FreeSurfer 
experts!I have carried out some analysis of changes in cortical thickness 
over time using the LME Matlab (R23b) Toolbox distributed within Freesurfer 
(7.4.1) in line with the instructions on this page: MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModelsAt 
this stage I just want to look at changes over time within each of three 
groups. For two groups I have been able to proceed through the steps fine and 
have my significance files which look normal. For the last group I am running 
into an error on the “[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 
2],Y,ni,lhcortex,3); “ step. MATLAB returns “Warning: Matrix is singular, close 
to singular or badly scaled” and lhTh0 and lhRe are created as matrices with 
only NaN values.Has anyone run into this error before or have any 
tips for troubleshooting it?I haven’t had any errors on the longitudinal 
processing steps and visual QC on my files looks normal. No errors on 
mris_preproc or mri_surf2surf. An aparcstats2table for thickness doesn’t 
reveal any NaNs.My design matrix is created with X = 
[ones(length(M),1) M] after following the suggested sortData code from the 
wikiContrast is [0 1]This is my qdec file:fsid 
fsid-base 
yearsfromBL108_MR1 108 
0.00199_MR1 199 
0.00199_MR2 199 
1.10199_MR3 199 
2.25202_MR1 202 
0.00204_MR1 204 
0.00204_MR2 204 
1.16204_MR3 204 
2.30223_MR1 223 
0.000821_MR1 0821 
0.000931_MR1 0931 
0.001010_MR1 1010 
0.001010_MR2 1010 
1.841031_MR1 1031 
0..001031_MR2 1031 
1.001031_MR3 1031 
2.131064_MR1 1064 
0.001064_MR2 1064 
2.011125_MR1 1125 
0.001134_MR1 1134 
0.001134_MR2 1134 
1.171134_MR3 1134 
2.281233_MR1 1233 
0.001233_MR2 1233 
1.051373_MR1 1373 
0.001439_MR1 1439 
0.001439_MR2 1439 
1.141439_MR3 1439 
2.281475_MR1 1475

Re: [Freesurfer] FreeSurfer release for Redhat Linux 9.x and its clones

2023-12-11 Thread fsbuild

External Email - Use Caution

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 
(https://secure-web.cisco.com/1mIKM9a0zhqsi_mcRwphvOt3o7Sjq5psvoHs9PCYVk-9pm31XnoNmc3uba-p0gcATG3DclmaBNOQlLGbQfbntyqmIFwtlf_Gu14HSDaAKMr0K2yeT5F8huY5-algIEf1xrr93MTyZcmApf_zFVYBqtDhy2IBQw1YyyGTijcU0hXXpzH_zypUF9sttXAJSRLW-PPd8vMTssdt4mBfHyH-gANEwifN4bAMHMc9sLUXZ8h5fyOKChUBtPaU3VMOODOFGToEX5X1ZpCrFkMxCptfhhGT6Mcaxt8ZJSl9FKmpBdFo6vWQsYSsXQe8yfgqxL8FUC7D8jkaZzMktzoyRaefM-Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-CentOS8-7.4.1-1.x86_64.rpm)
 might already install on RedHat/CentOS 9.
- R.

On Dec 11, 2023, at 11:16, Li, Mingyi lim...@ccf.org 
wrote:External Email - Use 
CautionWill there be a binary 
release of FreeSurfer for Redhat Linux 9.x clones such like Rocky Linux 9.x or 
Oracle Linux 
9.x?Thanks,Mingyiimage001.pngMingyi Li, 
Ph.D.| Director of Scientific Computing | Imaging 
Institute9500 Euclid Ave. | Cleveland, OH 44195| 
216-444-8112, 216-401-8585Please consider the environment 
before printing this e-mailCleveland Clinic is a nonprofit, multispecialty 
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Re: [Freesurfer] Issue with FreeSurfer on VirtualMachine

2023-12-11 Thread fsbuild

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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 received to developer’s home directory should have 
caused FS_LICENSE as set in the environment to read it,
$ cd $HOME$ pwd/home/developer$ ls -l license.txt… and you should see something 
like ...-rw-rw-r— 1 developer developer nn month day 
hours:minutes license.txt$ echo 
$FS_LICENSE/home/developer/license.txt$ head -1 
$fs_license...@somewhere.com   —— email you used to 
register
If the above is not working in your copy of the VM, then set FS_LICENSE 
manually,
$ export FS_LICENSE=/path_to_file/license.txt
- R.
On Dec 11, 2023, at 18:37, Fargol Rezayaraghi far...@uw.edu 
wrote:External Email - Use 
CautionDear FreeSurfer Team,I 
hope this email finds you well. I'm Fargol, a PhD candidate at the University 
of Washington. I followed your guidance to use FreeSurfer on the virtual 
machine successfully. I obtained the license as instructed.However, I faced two 
problems while trying to use FreeSurfer on VirtualMachine:I'm unable to move 
the license file to a different directory within VirtualMachine.Even when I 
attempt to add the license in a different directory, I receive an error message 
stating that I don't have permission to do so.Could you please assist me in 
resolving these issues so that I can utilize FreeSurfer effectively on 
VirtualBox?Thank you for your help in advance.Kind regards,Fargol--Kind 
Regards,Fargol R. Araghi (Rezayaraghi)Ph.D. Candidate, University of 
WashingtonDepartment of Mechanical EngineeringMailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
behttp://secure-web.cisco.com/1V9po0H9Hi_A721VJEJ_KCqT4Fl61Q3_VavajV-5Zlepm5ANo9pPC4U4LFKQ6UdR3k1UwBzZIv3Crte2Sanl5o-mm5zz0Q8VjK9Npv3zikvdEIR5-F8oLjX7e5Yr2tMDNKgz0WkoKIYgIo9GNnRJGQDPfBiBVZCU25eNnHI3hnT_PiumxN3biIJtygAAyaxp3emSC7kkExPTRxCvE7DEpOcSJceK1rGcaPxLORUbcizzsmDN7Ob4GEAOFZb5rCBEVVTBGSNPQs4Sj9ffSTtFrl2xZJC_7XaP1FVRCuxTb6lPa03DZtSriIQ-15-qwvQQKX_T1VN8buX2L6H9UQi64SA/http%3A%2F%2Fwww.Kurtlab.com___Freesurfer
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Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

2023-12-06 Thread fsbuild

External Email - Use Caution



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 (/usr/local/freesurfer/7.3.1). You should be able to 
download and run the 7.3.1 freesurfer installer using one of the 7.3.1 
links from 
https://secure-web.cisco.com/1JcyAuFpIReuF1zXqp8tlLsd3XWfOZVJNAxAaV1v1-OILtBqSGQrYB9hxeZJmR16KxuOpIYEX4SyiD60s5b0YkTlJJpaEUBj6KXV2fiheUQ1TB1u0pxsL60cXvfV8Ys62qmwfMf-f-o7q-JM-YahLFX0T7553tGWCgbLRHT2qSqpKN0Al7eFTpKNFb0_h-wxPsYa4YldQ7j16UgeL1JxO0SVH3K8PRBjEg2nGBYcnp0e9ntYcTxsFwhkOODhvnlsk48-GxpBr5A4BSeBorxZ4b0cVUvqY3sUu9LqUFYn4G99x31v9evnPWeXcyOZrDQBp/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads



After running the freesurfer installer, the steps - which it looks like 
you are already using - are listed below from a bash terminal window,



$ export FREESURFER_HOME=/usr/local/freesurfer/7.3.1



$ cd $FREESURFER_HOME/bin



 you can try using either R2019b or R2014b ...



$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b



I'm not sure the paths generated by the Maltab installer for use in 
LD_LIBRARY_PATH are always the same. They may not be if it uses 
some 
temporary path naming mechanism. So you may need to capture
 the output from the matlab installer, parse out the LD_LIBRARY_PATH 
setting each time it is run, and set it in the environment.



- R.



On 12/6/23 13:58, Na, Xiaoxu (x...@uams.edu) wrote:







  External Email - Use 
Caution

  
Dear Freesurfer Experts,

I’m building a docker file with freesurfer and 
matlab run time. May I know if freesurfer 7.3.1 should be compatible 
with matlab run time 2019b?
If so, what else can I make the environment setting correct in order to run 
localGI?

I tried to run “cd $FREESURFER_HOME/bin  
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b” and it 
finished successfully and I also appended the 
“/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so”
 to "$LD_LIBRARY_PATH". 

On the target computer, append the following to your LD_LIBRARY_PATH 
environment variable:

/tmp/tmp.T0m3Pxj9fW/install-target/v97/runtime/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/bin/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/sys/os/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/extern/bin/glnxa64

If MATLAB Runtime is to be used with MATLAB Production Server, you do not need 
to modify the above environment variable.

(Dec 06, 2023 17:26:10) Exiting with status 0
(Dec 06, 2023 17:26:10) End - Successful.
Finished
R2019b installed successfully in /opt/freesurfer-7.3.1/MCRv97
Removing intermediate container afe25e3801f1
--- ae8788b3fa89
Step 13/14 : ENV 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so
--- Running in e3601f8c33c4
Removing intermediate container e3601f8c33c4
--- 404199efd51a
Step 14/14 : RUN echo "$LD_LIBRARY_PATH"
--- Running in ac3754cb24bb
:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so
Removing intermediate container ac3754cb24bb
--- 9e9c3e2e0051
Successfully built 9e9c3e2e0051


However, when I run “recon-all -s BL-101 -localGI” 
on the subject BL-101 that was successfully finished was recon-all 
previously, it yelled Malab was not available. Could you please help 
where I did wrong? Thank you so much!

start
/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64/libmwlaunchermain.so:/.singularity.d/libs
recon-all -s BL-101 -localGI
fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn
Wed Dec 6 18:51:08 UTC 2023

setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str
cd /home/xna/fmri/data_BF_str
/opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn
-rwxrwxr-x 1 root root 18565 Dec 6 17:50 
/opt/freesurfer-7.3.1/bin/fs-check-version

freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
$Id$
Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 
x86_64 x86_64 GNU/Linux
pid 106796
Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
bstampfile exists /home/xna/fmri/data_BF_str/BL-101/scripts/build-stamp.txt
Subject FS

Re: [Freesurfer] Help

2023-11-24 Thread fsbuild

External Email - Use Caution

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 
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/usr/local/freesurfer/7.4.1
FSFAST_HOME  /usr/local/freesurfer/7..4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.4.1/subjects
MNI_DIR
/usr/local/freesurfer/7.4.1/mni
FSL_DIR
/usr/pubsw/packages/fsl/current

- then the head or start of your PATH has on purpose been modified to contain 
paths pointing to binaries in the freesurfer tree,
$echo $PATH | tr -s ':' '\n'/usr/local/freesurfer/7.4..1/bin
/usr/local/freesurfer/7.4.1/fsfast/bin
/usr/local/freesurfer/7..4.1/tktools
/usr/local/freesurfer/7.4.1/mni/bin…. rest of output deleted …
All
 python scripts in the freesurfer distribution are automatically run 
with fspython - which in turn runs the python distribution included in 
freesurfer. Any, e.g., system, python3 otherwise found in your path 
should not be used. We do not recommend activating a conda environment,
 or other python (virtual) environment that will change PATH or set 
PYTHONPATH after setting up the freesurfer environment.
$ which fspython/usr/local/freesurfer/7.4.1/bin/fspython$ which python3
/usr/bin/python3--- not used by freesurfer$ 
echo $PYTHONPATH… no output ...

- R.
Subject:[Freesurfer] HelpDate:Wed, 22 Nov 2023 08:44:18 
-0500From:Xincen Wuxlw...@groton.orgReply-To:Freesurfer 
support 
listfreesurfer@nmr.mgh.harvard.eduTo:Freesurfer@nmr.mgh.harvard.eduExternal
 Email - Use CautionHi,I
 am using freesurfer. I have gone through with the installation and 
diagnostics and everything works fine. FOr example, using the command 
recon-all --help in terminal yields a bunch of directions. Yet, when I 
enter something like:recon-all -s bert -autorecon1an
 error pops up saying my python3 is problematic. However, I regularly 
use python3 and redownloaded it after. Please advise on the issue at 
hand.Thanks,LucasAttached Message Part.txt

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Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled

2023-11-24 Thread fsbuild

External Email - Use Caution



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, fs_install_mcr, to install either the R2014b or R2019b matlab 
runtime environment 
into the freesurfer tree for use. I don't know if running R2019b would 
affect what you report below, but you could try it via the commands below..

  

- R.



$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1
 --- linux install path

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

... output showing SUBJECTS_DIR and other environment variables

$ cd $FREESURFER_HOME/bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

I
 believe this sets things up so the libmwm* libraries are installed 
under $FREESURFER_HOME/MCRv97/bin/glnxa64. You can try adding that path
 (or any path the script output recommends) to the start of 
LD_LIBRARY_PATH. You should remove any other entries to a different 
MATLAB distribution.


  



On 11/23/23 20:42, Sophie Matis (sophie.ma...@sydney.edu.au) wrote:







  External Email - Use 
Caution

  
Hello FreeSurfer experts!

I have carried out some analysis of changes in 
cortical thickness over time using the LME Matlab (R23b) Toolbox 
distributed within Freesurfer (7.4.1) in line with the instructions on 
this page: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/16TbMFKCSxY9QLMDkUoKiHpONPO8cJ5IumheTtc9oNl4e80txUMsYAc8b6sh-dB8ND2T4yKyevZcj6SoIdgd8nquWquSUgjhFRIy8HQb-wYTzCFA28w5OfBt23DxyHPwDJY7R47cWnpFBmVBjkXV7BioXniFwM9DD9P2q6dgLixlc2X1Bwx_pnJ1r2mSpL3B-A8qBrjDdcL0TzDCYzadMLqUs5uWdR2YlAZ5lA42tny6EQ_Y7PKMkw5-fjrpwzVl7CVw0oiX_WDt-wQSwceqWA3aUHgMrgjrf0P3xUxpt5_oIFpJyly4R7r3gnitkJPGNMCHgGwPhTB0UVdO1w0kNgw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels

At this stage I just want to look at changes over 
time within each of three groups. For two groups I have been able to 
proceed through the steps fine and have my significance files which look
 normal. For the last group I am running into
 an error on the “[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 
2],Y,ni,lhcortex,3); “ step. MATLAB returns “Warning: Matrix is 
singular, close to singular or badly scaled” and lhTh0 and lhRe are 
created as matrices with only NaN values.


Has anyone run into this error before or have any tips for troubleshooting it?


I haven’t had any errors on the longitudinal 
processing steps and visual QC on my files looks normal. No errors on 
mris_preproc or mri_surf2surf. An aparcstats2table for thickness 
doesn’t reveal any NaNs.


My design matrix is created with X = [ones(length(M),1) M] after following the 
suggested sortData code from the wiki
Contrast is [0 1]
This is my qdec file:

fsid fsid-base yearsfromBL
108_MR1 108 0.00
199_MR1 199 0.00
199_MR2 199 1.10
199_MR3 199 2.25
202_MR1 202 0.00
204_MR1 204 0.00
204_MR2 204 1.16
204_MR3 204 2.30
223_MR1 223 0.00
0821_MR1 0821 0.00
0931_MR1 0931 0.00
1010_MR1 1010 0.00
1010_MR2 1010 1.84
1031_MR1 1031 0.00
1031_MR2 1031 1.00
1031_MR3 1031 2.13
1064_MR1 1064 0.00
1064_MR2 1064 2.01
1125_MR1 1125 0.00
1134_MR1 1134 0.00
1134_MR2 1134 1.17
1134_MR3 1134 2.28
1233_MR1 1233 0.00
1233_MR2 1233 1.05
1373_MR1 1373 0.00
1439_MR1 1439 0.00
1439_MR2 1439 1.14
1439_MR3 1439 2.28
1475_MR1 1475 0.00
1475_MR2 1475 1.04
1475_MR3 1475 2.03
1522_MR1 1522 0.00
1522_MR2 1522 2.07
1541_MR1 1541 0.00
1541_MR2 1541 1.47
1551_MR1 1551 0.00
1551_MR2 1551 0.98
1551_MR3 1551 2.05
1572_MR1 1572 0.00
1572_MR2 1572 1.03
1625_MR1 1625 0.00
1625_MR2 1625 1.06
1637_MR1 1637 0.00
1641_MR1 1641 0.00
1656_MR1 1656 0.00
1656_MR2 1656 0.94
1656_MR3 1656 2.26
1755_MR1 1755 0.00
1755_MR2 1755 1.04
1755_MR3 1755 2.01
1829_MR1 1829 0.00
09154_MR1 09154 0.00
09154_MR2 09154 1.01
09154_MR3 09154 2.01
12110_MR1 12110 0.00
12110_MR2 12110 1.04


Any help appreciated!

Thank you,

Sophie Matis|
 Data Management  Research Officer
School of Health Sciences  Brain and Mind Centre
Faculty of Medicine and Health



The University of Sydney

Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G)|
 The University of Sydney | NSW | 06

sophie.ma...@sydney.edu.au
 |sydney.edu.au

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
 use is strictly prohibited. If you receive this email in error, please delete 
it and any attachments.

Please think of our environment and only print this email if necessary.

  




  

  
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Re: [Freesurfer] license issue with the updated version

2023-11-18 Thread fsbuild

External Email - Use Caution

Please let us know if you are runningMacOS 14 (Sonoma) on an Intel 
or silicon Mac (M1, M2 chip).  The system requirements at 
https://secure-web.cisco.com/10qwlQRot-nOOCuaXBtxsk1Ua4Tfh-PQlj0cP9-E6KzZM5idg3c7iTvMmQOzSG9PAcBrbFYMe35KnBiCn3y7IG-rVgEj0kSLvVbOHwxylEX_7qd2UpvZd0RI-joHMIjoQqJdBRMrn0pnSFHnz-SFFpzBuN9LN_tXR69BAZD8GdgOe42Qemok-1oStCPJooJ1xLsKbXOVgiFxHk0d55wZOgkW-uv9xSSB5VxhPx4QaNdwbS0mGZXww_bzMfboFOLEITeum3djwVx3EMwWM__x1IexmzFZEqSnGdgzzfIzKOYETgIxs35-X4U51g2Caz2Zn--cVCQFL8QZpew0IVrOvKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
 list MacOS 13 (Ventura) as the latest supported MacOS for the 7.4.1 release.
- R.

On Nov 18, 2023, at 18:29, Atena Akbari atenaakb...@gmail.com 
wrote:QObject::killTimer: Timers cannot be stopped from another thread

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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Unable to run recon-all

2023-11-17 Thread fsbuild

External Email - Use Caution

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 /usr/local/freesurfer/7.4.0/subjects for read only purposes.
Neither can you set SUBJECTS_DIR or write files in the process of running 
recon-all to your mounted or shared C drive. This is because the the 
Windows file system does not support creating soft links.
So please try the following. In your Ubuntu linux terminal window, 
go to your HOME directory and create a subjects directory there, i.e., 
you can always read/write to your HOME directory.  Then copy in your 
subject data to be processed there via recon-all and set SUBJECTS_DIR 
appropriately or pass the path on the recon-all command line.
… in WSL linux terminal window …$ cd $HOME$ mkdir subjects$ cd subjects$ 
pwd/home/naily/subjects$ export SUBJECTS_DIR=/home/naily/subjects… copy in your 
data to process for recon-all to live under SUBJECTS_DIR …
It also looks like your license file is not being found. You can set the 
environment variable FS_LICENSE to point to that so it will be found and read,
$ export FS_LICENSE=/home/naiy/license.txt$ head -1 
$fs_license...@somewhere.com    email address 
you used to register
… then try running some Freesurfer commands again …
- R.
On Nov 17, 2023, at 17:49, Nai, Ying Hwey n...@wustl..edu 
wrote:FSissues.txt

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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Question about Freesurfer

2023-11-06 Thread fsbuild

External Email - Use Caution

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 
X-windows,https://secure-web.cisco.com/1IeFJcAKROeUNyLVra8oNytGyzB-WvQhRkz3GN5_1Txy8oLFJDQUo-f8ZHzfjyZbyVGPM2mROYYBy22fnlN-kl_e23yBKEtB2DuEOJAe7sMTh64Q9HrFUmTU9XkuGeXTsrOc8KHmXQAru1qVCQpeLRlHb_UlVrEln22ennkW4QVIlF3A1Z0_9LOFKxQc6gPA5a7Hes1Yiks3GPrZM2SAnxS746Sqe4v42HiUmSvhXBYz5x_rY2DsC-geI6mWT9kQPjE7fLUoEWBzflVj9ELIaJv7w_mi0ozeErVsyB9F1FKKK74RMrvBaLWfE18vMaWao/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
 The setup listed there is for Xming, and you may want to look at both 
https://secure-web.cisco.com/1yLpWBJBzFQsVnx0Ncp8u61K6nbDOQ5sj4Uh-OSMos9GTrEDmiKo-ITzLOwI8tAWHPIzbOfOAECxeDE0ldl04hOCd1VkriFGjCqauUCZLbdmqbqUCV7ZayjK_Mc2TdhwhkmNs0k0YvCS4OScvNeTPTTOeOjiAaXXNPtFyCxd5w6wS2AsCdMKjy_J3qpeGWDsjRBRo8Fbqk20r3GbcGF3dkytO-RfOQddZnYExK2eFjL7gQztEIxlKKLJpJP6AIKPL6iR-9hw2xmWVNqYA4_wpBNR4s9k4kWhTYlK6VV4ggvzHmZlkjVDQqFNZLQX1eFsq/https%3A%2F%2Fsurfer.nmr.mgh..harvard.edu%2Ffswiki%2FFSL_wsl_xming
 
andhttps://secure-web.cisco.com/1STa8uko59yOcskM83ifwl-XKlLZOFpLQkufkYvxaMiNrWGCUMSwNctfrOfWtxpDsMvgHMnnx2h962-7-iLdFPsHVZDwgftFM52ZJqTOD5UeR4F8NFlt42lsbArYyaGmYV8WviUXXcc7xfeDfoNDNpfQYifN1mwrnRpMMcSkNJQCP9BLO23bex9_5A-rTHQ8uuiqNz9a2c5NRcGCMAWA4MZY8iTyQ4IlNhWb7BV_QQw-x_1DZULmDt9Pg2N6mICwfVoNe88iP9-TDc-Uu5KlgvfrnAUmv_XPdWdmocW0fz3kt6F-6eZd7jzvrJ9gdM7m6/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
Some people have found Moba 
X-term,https://secure-web.cisco.com/1ZVDzOuRds29V2esWHXhtFh_3s3wsJpkWd0i5e_OhneoPEY-dRlrXFon9sw9CxIOt6JtTwbqDcDKyeZYcfzbcHgvrp0yvwPFO-RNdG8UaZ8Q74wFaRwDMXrjYr9LFAkLp4Xak6tyOjbwZZUG5nIKgJmrNXimNrEnLbPpJDVkb1_Kg2I_bKnJgP50HXwHd52t2CSISPv94DQVYc36hP4AOD6ZyITwrGDmW9E6uW-b-2cXENpciP_ca60m9tMYC5-8F9aJV7BXDyFuh45TY1O56nqRfWJFI3p7IYBY98jcZdMPgCzTZihcLHNoIYj-VvDo4/https%3A%2F%2Fmobaxterm.mobatek.net,
 easier to setup and test with glxgears compared to using Xming.
It’s a good idea to get glxgears to display the spinning gears in an X-Window 
before trying to run freeview. Or the display of glxgears can work, but 
freeview may still display a black/empty screen. That can be from the 
graphics card drivers on the Windows host not being up to date or not 
supporting more recent versions of OpenGL.
There are also quite a few postings about WSL on the freesurfer list.
- R.

On Nov 6, 2023, at 13:48, Mahdi Babaei mahdibabai...@gmail.com 
wrote:External Email - Use 
CautionThanks for the 
reply.Yes, glxgears command shows a blank window. I thought about it but 
couldn'tfind any solution. I'm working on WSL2.Best,MahdiOn Mon, 6 Nov 
2023 at 13:16, Wang, Ruopeng rwa...@mgh.harvard.edu wrote:It sounds 
like an openGL rendering issue. If you run glxgears command, do you see a blank 
window or spinning 3D gears?RuopengOn Nov 6, 2023, at 12:37 PM, Mahdi Babaei 
mahdibabai...@gmail.com 
wrote:External Email - Use 
CautionHi Paul,Thank you for 
your response. There was an issue with my description. I meant to refer to 
volume data. Freeview is displaying a black view, even though it loads the 
images. Unfortunately, nothing is visible.Best,MahdiOn Mon, 6 Nov 2023 at 
11:30, Wighton, Paul pwigh...@mgh.harvard.edu wrote:Hi Mahdi,I'm afraid 
I don't know what you mean by "Freeview opens fine but when I load a column in 
it just shows a black view." What is a column in this context?As for 
registration between PET and MR, have you seen this page?MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1b4i3XSSINjUpxeaKg1CHfqqMtsa2ceG8AjVCHbWEJFS_lJ1b-QMOCffk_k0_xcQLsD-qCcYCkoyHek35mgBwuIOGexxlOuDvLm5xVvYNo2JiaWRbGhas9yUvDTZzuZ4x8eo_HNtPss2f1KBg1Bj_m_vrSBDH2Emrjz_c3Q8JhFAsYV3fiwnUEUCM1k7o6deyZs8tmtC36Vv5MK7Jj9HRzZ6TyfJWxDy2zALLdkYSqKyAIbDRC-C-XrKIWL644j_VMEQHeqUPwwsGlc08i28HJL6MZ3zqjQ7SAcChI8K1XNPhKGHAsRN1vYTlLrnsB6qE/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurferIt
 suggests using 
mri_coreg.-PaulFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Mahdi Babaei mahdibabai...@gmail.comSent: Sunday, 
November 5, 2023 2:25 PMTo:freesur...@nmr.mgh.harvard.eduSubject: 
[Freesurfer] Question about FreesurferExternal 
Email - Use CautionDear FreeSurfer Team,I'm currently a PhD student at Stevens 
Institute of Technology in New Jersey, USA, where my research focuses on MRI to 
PET translation. I have a number of problems. Freeview opens fine but when I 
load a column in it just shows a black view. Have you ever encountered this 
problem?I'm so confused about using the tool for registration. Can I do 
registration between MRI and PET modalities of the same subject using 
"bbregister"?Best,Mahdi___Freesurfer
 mailing

Re: [Freesurfer] Freesurfer crash when loading "volume" surf

2023-10-27 Thread fsbuild

External Email - Use Caution

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
$FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted ...
… set the environment variable FS_LICENSE to point to your license file, e.g.,
put license.txt file you received via email after you registered into your home
directory under /Users/your userid ...
$ export FS_LICENSE=$HOME/license.txt$ head -1 $fs_license...@somedomain.com.
— email address you used to register with
$ which freeview/Applications/7.4.1/bin/freeview
… test displaying a known to be good volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If the above works, then try opening your file(s) from the command line instead
of the volume file listed above.
- R.

On Oct 26, 2023, at 20:42, Mirsol Choi mir...@ualberta.ca
wrote:External Email - Use
CautionHi there,I have
processed a t1 image using recon-all function, and when I try to open the
surface file "lh.volume" or "rh.volume", freesurfer crashes everytime. This
crash also occurs for other surface files as well, such as
"lh.area.pial".Attached is the error message, do you know how I can go
about this?For your reference I am using a macOS, running freesurfer
7.4.1.Thank you, I look forward to hearing from you.Screen Shot
2023-10-26 at 6.41.05 PM.pngScreen Shot 2023-10-26 at 6.41.55
PM.png___Freesurfer mailing
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Re: [Freesurfer] Freeview issue

2023-10-22 Thread fsbuild

External Email - Use Caution



The Qt graphics libraries may need virtualGl over a 
remote X connection. So try prefacing your freeview command with 
"vglrun". See the introductory text about vglrun and the install commands 
on this page, 
https://secure-web.cisco.com/1_jeLuB9K3YFX-_vkUZquNAqePEbWUSsW-inupVmdbjXlex4rhufV8pNS0NPj6_HwmfTXNTHj-f1VpwO5L1FxVZxjTuZd_jIKlPJYkhBZ0iXvHGrpj7gUiuE2Lt9vAZeu4ieazTNok61_W9Fp6jv7ukbRi4jmQb63yTPmjlf8IpULZuGieE0qGkioK4gcDBDplqwVm2PqqQMutUxdvd0z6GI-TTBv2AO2A7sAqo_dHWkHoPVMDaUl6alNIUg8L8JeYe3Rn_pHVqDrgHUhSpcXzqgCp6DA-cdBz0bQoVnRi_CXCU8BaXBwqbrOUYck_W1vMDl_8y3cgoynupChWihsJAmC-LOIkKi9YdqpiuqCh5U/https%3A%2F%2Fwww.starnet.com%2Fhelp%2Fvirtualgl%2F
Then once the remote display of images is working, you might run into an issue 
trying to map the display size to your
 remote screen resolution.

  

- R.



On 10/22/23 03:57, yunus soleymani (soleymani.yu...@yahoo.com) wrote:



  External Email - Use 
Caution
  I did the following codes 
respectively:cdwgetMailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/11GVLnIDWxo_vR8D2Oa9AP0rLkOmLrhl51L-g0K4pY8mWNpc25hCXYg5qw8EPIDzfeeqnv5cyYNzMcPC4QuvC50tzwwJorW1AfzALLGmEBRBXCgyXxcZc_hE7PwJ4tlnTT6sGRSjGObyGuLSiWR2CqZwl8RzH1BkEi9Ym8xXnYWGsmvBrglSgH16t-SgIKgF6aa5ME4NabctEizZwF8Z-I-2GkQcbaTmEQswaBOEXeplL7RIF-NDXzFrqplw2TJ5IOZ20pTaB80VCXGMqxLxT39ijfH-d0u5-loTVFRtTYIfeFpKjtCAO_Q304dRytXSKFjZ5De30yK8NnZkJ9fATbgdcDc9KYYSfx1p0yFs8GJQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
ls freesurfer_ubuntu22-7.4.1_amd64.deb
sudo apt-get update -y
sudo apt-get -y install ./freesurfer_ubuntu22-7.4.1_amd64.deb
export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1"  
$HOME/.bashrc
ls $FREESURFER_HOME
ls license.txt
echo "export FS_LICENSE=$HOME/license.txt"  $HOME/.bashrc
echo "export XDG_RUNTIME_DIR=$HOME/.xdg"  $HOME/.bashrc
echo "export DISPLAY=:0"  $HOME/.bashrc
echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh"  
$HOME/.bashrc
.
 The
 above codes all worked correctly and the software was installed 
successfully. Also, the software analyzes the subjects correctly by 
using parallel recon-all code. The only issue is that the Freeview 
interface doesn't work and the error mentioned above appears. Is it 
because of that I am using a remote desktop connection tool to connect 
to my institute servers?


Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 914 526 
9298






  


    
On Sunday, October 22, 2023 at 11:12:08 AM GMT+3:30, 
fsbuild fsbu...@contbay.com wrote:





External Email 
- Use CautionWondering
 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.debThe link for that file on the 
downloads pageMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1P6sJsKdfjhSOlm7uHbTXJ8nsEFCHNYGKzdj0djukhVoPCyG91EdBhVxbHi53kwpdQYCT-ByuHLRTukUzTBvHVUXJo03E4wEptjCsZFOVgHNqY15mUXlHsG7f_vvg0sAtr1BNs0Zq8iy1MDkYvqy_XHV1uXFLEzVBxejhxdjQTN5CXaz8hynqEdriY2-0tNSKP0TeFutwa5N8m6gYsk9nXS75QwEy1K3knJhXby-Pm_ZYQ_1LXXTArPv-7n0rrxguvS0zsbj-5MiODIlxB2KbSgy267kxc-qAcb_bj1_9j9MlCZjv_0PHnxJn8SSicHG5S2qZxz31VQe-xgh-gooxtMr4pSp0hF9d3j2pX8pAUVI/https%3A%2F%2Fsurfer.nmr.mgh.harvard..edu%2Ffswiki%2Frel7downloads%26nbsp;ishttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb-
 R.On Oct 22, 2023, at 02:19, yunus soleymani soleymani.yu...@yahoo.com 
wrote:External Email - Use 
CautionI have the same 
problem.I would greatly appreciate your help with 
this.Yunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be MailScanne

Re: [Freesurfer] Freeview issue

2023-10-22 Thread fsbuild

External Email - Use Caution

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 
pagehttps://secure-web.cisco.com/1_35_maf1qeyDwN-YbnCQ8jOb6jvY5lINnAzztz0hRLD0JseUsdcHLQQn-9oN4Xf-0aaTL-xA7oSZSleQrdE_yI-urkuo_8dbOO2aiY13AYtsJTRILkzHGZi1TGwCD8Ywi8woTfAO3wh_9v1Xgux9lnFhVCVb_XtZeAmupzyWe44oapIbnV7FxQ-SHiFFd6No6MeMtAV2bj4l_Tb0oyF4xPb51zNX2UW4sCtlr3XDT3E_jZWpa7Wfg9OutA3mWKZX-EwQZS83QmQEdq_lPlHr69Ck5qqSVMhCUnNw8b5MrCyOZpcPbS4WKnC6_OQaSXxyUhRdO_phUm9N6pB0UhdiYAatDutIdTKQI-qx-8lpM-g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%26nbsp;ishttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb
- R.

On Oct 22, 2023, at 02:19, yunus soleymani soleymani.yu...@yahoo.com 
wrote:External Email - Use 
CautionI have the same 
problem.I would greatly appreciate your help with 
this.Yunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 
914 526 
9298On
 Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu 
mgrameshbabu2...@gmail.com 
wrote:External Email - Use 
CautionDear Expert,Recently I 
installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is 
installed successfully, but freeview gives some errors which I pasted below. 
Please provide your suggestions.Thank YouRameshfreeviewThis 
application failed to start because no Qt platform plugin could be initialized. 
Reinstalling the application may fix this problem.Available platform plugins 
are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, 
webgl, xcb.Aborted (core 
dumped)___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1BZ4_HvToI5a6OuM5gIFWs2VyFinjkWLi8C5L5ny7WeSkoUPm5JKinKYGrfFLsEEF6vXjSSB20skB1EH-5lApynTVgrUWDRK6SYlzq7r_QITnqNOo7cdyNRDmeFg2IBypvUo11FF3iBvcCmldzGq4fUTBIXuuSU6A6hFQcj0jB-aOU055LyuED92RNGc3XyiZ5YqQI0p57CfVu0qZZlh-KwwTsUcpaxB0tdN7hR3-W5uhj2D2OK1GW5QBa4Dg9hc3fxMFboPH8PBvkJstq_3knPEMjnYxzfa0osNnEkqDYsyi_mQ01W0AvSIB65LMi-IKrNLcMNXAUF1tW-I5QZLaPvx6PAtiBikmWKoFykv5bRg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] fsxvfb error: Falling back to using screens root_visual

2023-10-20 Thread fsbuild

External Email - Use Caution

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
capture because it is not expecting freeview to (still) run using Qt
graphics and X-windows . I believe the release notes say fsxvfb
does not need an X-server and so perhaps it is trying to capture images
directly from the graphics hardware. Could be something is not up to
date on your system with the graphics hardware drivers/system libraries.

Another thing to consider is the freesurfer 7.4.1 release was not built
for nor tested on Ubuntu 16 - the minimum version tested was Ubuntu
18. Given you are running it from the path
/usr/global/freesurfer/7.4.1 then I suspect you did not download and run
the 7.4.1 debian package installer for Ubuntu 18 as recommended on the
freesurfer download page,
https://secure-web.cisco.com/1pa_Juw1rvYdwKxiYGrhHioNA_vUa-3QRuSL2A9WRhRTgvRuNTlbqumOYdkFLoeMjU_rWgh1UP8tarqEvB5UE6aoIgGhJvYzzrbdKfm3dpEYTLfVNPmASjXkZ5aqziSPs85bAm9uH5jJwateGLOqKDRl5GoCIe7ehl-qH_X8_8P63d8JsR4oALTRtN1Wo_Q8vkZRIap_xWTZZbWuNQPxDafEOVwKLfvbUUBstFI3f5vpPbNFdrpaxaiy8nTlmnsZN8RL33Ley7Izxbed5ctd5K7Re0lBjXiMqHamlrTOd_MKaUcBQjowAxDqNgre2l05H/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7download
(which would
install under /usr/local/freesurfer). It would not be surprising for
the Ubuntu 18 binary installer to fail trying to update an Ubuntu 16 system,
but you could try running it. You can
decline/abort the installation if you don't approve of the system
updates it reports are needed before installing freesurfer. Even if
the installer succeeds, we can't guarantee 7.4.1 will work correctly on
Ubuntu 16.

- R.
On 10/19/23 17:50, Dani Del Rubin (rubin...@ohsu.edu) wrote:

QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133,
major code:

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread fsbuild

External Email - Use Caution

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.

On Oct 17, 2023, at 06:04, Marina Fernández 
marina.fdez.alva...@gmail.com 
wrote:External Email - Use 
CautionHi Andrei and Freesurfer 
experts,We had the same problem in the past and we noticed there was an extra 
line in the .bashrc file of Ubuntu:export FS_DISABLE_LANG="true"Deleting 
this line solves the problem.The .bashrc file should contain only the 
following FS lines:#Freesurfer:export 
FREESURFER_HOME=/usr/local/freesurfersource 
$FREESURFER_HOME/SetUpFreeSurfer.shMake sure you do this for home and root 
.bashrc files.Hope this helps.Best 
wishes,Marina___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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
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] ERROR: could not configure recon-all parameters

2023-10-15 Thread fsbuild

External Email - Use Caution



Just FYI, it is not intended that you process your 
own subjects using SUBJECTS_DIR set to a path under where freesurfer is 
installed, i.e., SUBJECTS_DIR in the log is set to,

  

  setenv SUBJECTS_DIR /Applications/freesurfer/subjects/recon-all

cd /Applications/freesurfer/subjects/recon-all/MR7312_501/surf

  
  

Writing files there normally fail without the sudo command, 

% touch /Applications/freesurfer/foo

touch: /Applications/freesurfer/foo: Permission denied
That will prevent recon-all from being able to create soft links. Neither 
should recon-all be run with the sudo command or that 
path 
down-protected to allow writing files there w/o the sudo 
command.




After the setup of the freesurfer environment with,




  
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1
  

  
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
  

  
 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
  

  
Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME/Applications/freesurfer/7.4.1

FSFAST_HOME  /Applications/freesurfer/7.4.1/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects

MNI_DIR
/Applications/freesurfer/7.4.1/mni
  



- then change SUBJECTS_DIR to point to a directory where you already 
have write permission like somewhere under your home directory,



$ cd $HOME

$ pwd

/Users/your userid

$ mkdir -p $HOME/subjects



 and reset SUBJECTS_DIR to point to the path you just made ...



$ export SUBJECTS_DIR=$HOME/subjects

$ echo $SUBJECTS_DIR

/Users/your userid/subjects



Then try running your commands.



- R.



On 10/15/23 20:19, 윤혜정 (hyejung7...@amc.seoul.kr) wrote:



  External Email - Use 
Caution
  Hi Yujing,
Thank you for your help. I see it works now.I have attached my recon-all 
log for you to see.Can you please go through it and confirm that it has 
no errors?
Thank you.
Best,Alice-Original Message-
From: "Huang, Yujing"yhuan...@mgh.harvard.edu 
To: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; 
Cc: 
Sent: 2023. 10. 13. (금) 20:54 (GMT+09:00)
Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters








lh.pial and rh.pial are created as symbol links to lh.pial.T1 and rh.pial.T1.
rh.pial - rh.pial.T1
lh.pial - lh.pial.T1

Do you have lh.pial.T1 and rh.pial.T1 in your surf/ directory? 
Symbol links may be disallowed for your machine. Can you attach 
recon-all.log?

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh..harvard.edu
On Behalf Of ???

Sent: Thursday, October 12, 2023 9:32 PM

To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters



External Email - Use 
Caution


Thank you for your swift reply. I will try that soon.





I
 have other pack of data that finished recon-all process and I don't 
have lh-pial  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: freesurfer@nmr.mgh.harvard.edu; 

Cc: hyejung7...@amc.seoul.kr; 

Sent: 2023. 10. 13. (금) 10:04 (GMT+09:00)

Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters


External Email - Use 
Caution


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. That should
 ensure all the file privileges
 are correct so the files can be executed. You will need sudo 
privileges for these commands.





… open a terminal window and delete the current freesurfer installation …





$ cd /Applications


$ sudo rm -rf freesurfer


… you will be asked to enter your password ...


$ cd





Download the 7.4.1 package installer in your browser using the 
link,MailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/16QsjI_IFOK8Xo0B1gMl3uWmO7oo4wVgTL1WN7x8nR916ZXpeDKxxuAWopZIjbfqH72qVw4Ms5TqQNmSvrAeAYV_mOKhiwg0yIYNx8fsLKI-nL7x3tgxF3-2bl0EIwA2SBk-At_d1hnfHcIEMYX8crxT7XRLsiknyl8FOQGRAGE4ToF4KANVZoZe6cLpfQ-CrV_EnA1KG9AIAJm9_wfyCQ7DF_YvNwdxGTGTgWPThn7eL2JLYtrb8A7rCmFbhjnPn1gA5y1_SzPvM2BfefpFMSwZrY8lMB68UFHpUvkWy-YdmWhYqq7jjo01KKnfXS1weRikAyDcnqCNx5nwpw3r5tQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg





In a 
Finder window, open your downloads folder (or go to wherever you 
downloaded the .pkg file). Then RIGHT CLICK with the mouse on the icon 
for the filefreesurfer-macOS-darwin_x86_64-7.4.1.pkg
 and select “Open With” installer.app (defa

Re: [Freesurfer] ERROR: could not configure recon-all parameters

2023-10-12 Thread fsbuild

External Email - Use Caution

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. That should ensure all 
the file privileges are correct so the files can be executed. You will 
need sudo privileges for these commands.
… open a terminal window and delete the current freesurfer installation …
$ cd /Applications$ sudo rm -rf freesurfer… you will be asked to enter 
your password ...$ cd
Download the 7.4.1 package installer in your browser using the 
link,https://secure-web.cisco.com/1IMDK1N7QCuFHDBAqbwgRc9pMUoAwzPh8gLV8fwqcUUSZYNUAtkffWnRycsKB-8aNNnZecU30n-LThO_rOXYp_BKdmP4uubAna6GBikj7uoKKAxWfyg0ltpvrbJnznjM8ucu72-EvDBWInryq7Ln74QipZqxLutAiwYkTxTfnUkivop9wJVFh0s1PQ9CtingaAKSC8c7Yk7RwvdfDO1oluWK8W6H2YfS_gGIaXQ0DJ6BnDUBKXr0dWCSg_9I_BURx9B-tLkNE3-Ttz90_Xj_KZDRoeRCc0aktbHn95GmKLFrNW7XWArvn-2qLFEOsyJZmqOFvuxWTt9rNdoUoDXxnUQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
In a Finder window, open your downloads folder (or go to wherever you 
downloaded the .pkg file). Then RIGHT CLICK with the mouse on the icon 
for the filefreesurfer-macOS-darwin_x86_64-7.4.1.pkg and select “Open 
With” installer.app (default).  Select “Open” when the installer opens a 
new window asking if you want to do the install. Click thru the installer 
options by selecting “Continue” and accept the license, etc.
… when the install is done, setup the Fresurfer environment in a terminal 
window …
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.4.1
FSFAST_HOME  /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects
MNI_DIR
/Applications/freesurfer/7.4.1/mni
… check python3 is there ...
$ ls 
$FREESURFER_HOME/python/bin/python3/Applications/freesurfer/7.4.1/python/bin/python3
… then try running freesurfer commands again …
- R.

On Oct 12, 2023, at 20:01, 윤혜정 hyejung7...@amc.seoul.kr 
wrote:External Email - Use 
CautionHi,On top of 
the email I sent earlier, I also get the next error line that says:ERROR: 
could not configure recon-all parameters/Applications/freesurfer/bin/fspython: 
line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary 
file/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 
0-Original 
Message-From:hyejung7...@amc.seoul.krto:freesurfer@nmr.mgh.harvard.edu;Cc:Sent:2023.
 10. 13. (금) 08:35 (GMT+09:00)Subject:ERROR: could not configure 
recon-all parametersGood day,I get the following error 
message when I run recon-all:ERROR: could not configure recon-all 
parameters/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary fileI 
went through a bit of the mail archive and unlike the others I don't see ASCII 
error message in mine.Additionally, I was wondering if the 
thickness of MR slices would affect recon-all process at all?I 
appreciate your help.Best 
wishes,Alice___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Hippocampus Segmentation Troubleshoot - Matlab crash

2023-10-09 Thread fsbuild

External Email - Use Caution

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 compiler).
For your existing install of freesurfer 7..1.1, the tested version of the 
Matlab runtime environment to install is R2014b (listed below as the version to 
use in the bash/zsh commands). However, if you were to update to the 
current freesurfer 7.4.1 
release,https://secure-web.cisco.com/1EbuUGpusH65Vnhqyq32iw8lhOzpyphGTkomb1eGIHw58FD4ikSbt9f7VFH4X8deyqrzjKVzFMgqki-n63sKgin2kguxnvVJ0g1kgDFvZDwcE9MYyz4PxA482Uoppvj_xzoJ7FZfWzjxTRMYqj7SGcDj6ClpBf7YSyiSYJPwYvPDbNKVzBl_68uYwiEBaf4tA7hhc2wAcVv-dTmneINRGW4ayp1zoonJKmUYUsD5NNzRTiy0JBh5uS3MTuHXb8gq_Vb9DwI2znfq2inPePbqtqJtHEU4X372cxYJRMx9L8Q6tGQsl51lXryVbRgi7Mq5L7zTZ2UN8gInW9BnhIgczuQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg,
 then you could use the more recent R2019b Matlab runtime.
$ export FREESURFER_HOME=your install path

$ cd $FREESURFER_HOME/bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2014b 
 — change to R2019b if you end up using freesurfer 7.4.1

… answer y to any installer questions …

The output from running that script will list whatDYLD_LIBRARY_PATH 
should be set to. 

Please make sure you have otherwise removed any references to your previous 
matlab environment from DYLD_LIBRARY_PATH, PATH, etc. It might also work 
to add $FREESURFER_HOME/MCRv97/bin/glnxa64 to DYLD_LIBRARY_PATH but I would 
first try what the script prints out as the local paths on your machine.
- R.

On Oct 9, 2023, at 20:21, Mirsol Choi mir...@ualberta.ca 
wrote:External Email - Use 
CautionHi there,I am a Master's 
student who is looking to segment the hippocampus and analyze diffusion data of 
the segments.I am trying to utilize the segmentation functionwith 
this command:segmentHA_T1.sh subj01But I am met with this error saying that 
Matlab has crashed.The crash log is attached to this email.I have 
freesurfer version 7.1.1, running on MacOs 11.7.10.I have followed your website 
instructions to downloadMatlab R2014b.Following the installation process 
of Matlab, I was met with this message:Installing 
Product:MATLABCompiler Runtime - Core 8.4(Oct 08, 2023 11:29:15) 
Installing Product:MATLABCompiler Runtime - GPU 8.4(Oct 08, 2023 
11:29:21)Notes:On the target computer, append the following to your 
DYLD_LIBRARY_PATH environment 
variable:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/bin/maci64:(Oct
 08, 2023 11:29:21) Exiting with status 0(Oct 08, 2023 11:29:21) End - 
Successful.FinishedR2014b installed successfully in 
/Applications/freesurfer/7.1.1/MCRv84And so I have appended the path using this 
code into my bashrc profile:export 
DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/bin/maci64I
 am wondering if I can get some help with running the hippocampus segmentation 
protocol .Thank you so much for your time, I greatly appreciate your 
support.matlab_crash_dump.28607-2___Freesurfer
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Re: [Freesurfer] $FREESURFER_HOME/bin not being added to PATH (tcsh)

2023-10-09 Thread fsbuild

External Email - Use Caution

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, $HOME/.cshrc, then FREESURFER_HOME, 
SUBJECTS_DIR, PATH, etc., should automatically set/modified by source'ing 
SetUpFreeSurfer.csh when you open a new terminal window.  There is no 
need to subsequently set SUBJECTS_DIR or other freesurfer environment variables 
in your shell init file (or in the current terminal window session) unless the 
settings should be different than the defaults. Most people add those 2 
commands to be the last 2 lines in their shell init file.
I would check the defaults set in the current shell environment using only 
those 2 commands above in your shell init file after opening a new terminal 
window,
$ env | sort
… and check FREESURFER_HOME, SUBJECTS_DIR, PATH are set …
The freeview command should already be found in your path, i.e., you should see 
…
$ which freeview/usr/local/freesurfer/7.4.1-1/bin/freeview
- R.

On Oct 9, 2023, at 14:56, Edward Zuniga eazun...@vcu.edu 
wrote:External Email - Use 
CautionHello,I am attempting to 
install FreeSurfer on a Centos 7 workstation using the tcsh shell. Below are 
the contents of my .cshrc file. Should $FREESURFER_HOME/bin be 
automaticallyadded to the PATH? I tried rebooting, and it still is not 
adding it to the PATH. My environment variables appear to be set 
correctly because I see this when opening a new terminal. I 
alsotried modifying the .cshrc file to add the directory to the PATH 
manually, but it still will not stick after rebooting. 
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME  
/usr/local/freesurfer/7.4.1-1FSFAST_HOME
/usr/local/freesurfer/7.4.1-1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR  
 /usr/local/freesurfer/7..4.1-1/subjectsMNI_DIR   
   /usr/local/freesurfer/7.4.1-1/mniFSL_DIR   
   /usr/local/FSL/fsl_6_0_7_4[cogdmd@cari6 
~]$Thanks,Eddie#umask
 002setenv PATH /usr/local/cuda-9.1/bin:$PATHsetenv LD_LIBRARY_PATH 
/usr/local/cuda-9.1/lib64# auto-inserted by @update.afni.binaries :set path = ( 
$path /home/cogdmd/abin )setenv R_LIBS ~/R#FSL Setupsetenv 
FSLDIR /usr/local/FSL/fsl_6_0_7_4setenv PATH 
${FSLDIR}/share/fsl/bin:${PATH}source ${FSLDIR}/etc/fslconf/fsl.csh#Freesurfer 
Setupsetenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1setenv SUBJECTS_DIR 
$FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.cshalias spm12 
'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"'alias conn 
'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath 
/usr/local/SPM/conn; conn"'setenv PATH /home/cogdmd/anaconda3/bin:$PATHsetenv 
ANTSPATH /home/cogdmd/ants-2.4.1/binsetenv PATH ${ANTSPATH}:${PATH}setenv PATH 
/home/cogdmd/.lcmodel:$PATH--Edward
 A. ZunigaSenior Research AnalystVirginia Commonwealth UniversityC. Kenneth and 
Dianne Wright Center for Clinical and Translational ResearchInstitute for Drug 
and Alcohol StudiesCollaborative Advanced Research Imaging (CARI) Facility203 
East Cary Street, Suite 202Richmond, Virginia 23219Phone: (804) 828-4184Fax: 
(804) 
827-2565eazuniga@vcu.edu___Freesurfer
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continue to communicate over unencrypted e-mail.

[Freesurfer] fRe: SAMSEG lesion mask pattern on Mac with M2 processor and GPU

2023-10-07 Thread fsbuild

External Email - Use Caution

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 the Rosetta environment on arm64 Macs. 
Rosetta translates Intel processor instructions to arm64 processor 
instructions; when there is no equivalent arm processor instruction, you get 
the error “illegal instruction”. The remedy for this is to re-write 
and/or re-build the code (to be more portable).
There is an arm64 freesurfer development build including an arm64 python with 
Apple’s tensorflow.  However, the freesurfer python code is not yet 
entirely compatible with arm64 python and all its packages. The 
mri_synthsr script currently does not work with arm64 tensorflow; I don’t know 
about mri_samseg.  You can try the arm64 development build via the link, 
https://secure-web.cisco.com/17oMRv7D8FpOpyCTDI2b6q3ZFH9-liuuaw55Fk0qAsqgBnL3cDmnkVAujZjuxE5eX79DEYS-N-28sS2kPCHZELA_TD9KfXA1gTpkIIQlltrdLjmUYAErTEyV7pXp61dNngBidguhX9Ro7dWKp68cyGlPyIUMglyRLC5Ic8KxVhEd1h6taIbJUs2RF62qX_akkZQzboTafybXKGqtqZO75VJ_VYmF1FbMwq5IEVXbxaM1fZtZ1ZQn6V7EGFGVpOnhJcYCh6SCvDAdGOF8jbC_XE4GUihNWJa4hRA4860MsPxHxc4Or__ON8TElFES-SLctaTntlZ16qO5C18SyRBuAGw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg%26nbsp;
 Please keep in mind this it not a release build and please report any errors.
Fixes for these kinds of issues will become available in the development builds 
via the link above once they are added into the freesurfer development 
stream. We can also notify the list.
- R.
On Oct 7, 2023, at 03:23, Bianka Forgó fbia...@gmail.com 
wrote:External Email - Use 
CautionDear Freesurfer 
Developers,I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) 
with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer 
version 7.4.1.I am trying to use samsegfor cross-sectional MS lesion 
volume analysisby running the following command:run_samseg --input 
Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii 
--pallidum-separate --lesion --lesion-mask-pattern 0 1 --output 
Freesurfer_subjects/FAMUS/samsegI get the error message:zsh: illegal hardware 
instructionrun_samseg --input 
Freesurfer_subjects/FAMUS/T1.nii--lesion0 
1As described in the samsegmanual, one may be prompted to use 
Tensorflow when using this module for the first time. I was not prompted to do 
so but I did install it (and python3 as well) using the instructions 
here:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1tE2yZiNK2sSgfXl2g2jsBKvz4UwOnAafBZo84FMcVUl1GYayXd0hNDmJphJPV5PjstNU56Mv2-ZHz2gHhAMlXY3hWsiVC1FHjeMi3zwh2v7t_xAJuVou-EfEHo44tHTgbXtjVRgAo0DpLGaC8q50HrjvkQVVyuN6wNvj4caVEzxRrcejp5Id1tZxys3U7RcpxmayW_RhSEZaQHfCJ1Q1oyXrUi1TDf4yT6v1xP-orC4T-AL7A03jXfucvl8wdsmShOubje1GwxXexAM8kDz2tCP3gurL_HfDY8e92Qv3usVI1_utdRBWx-wdHAUfywhLR6tzDc_UhJgGLNgh0-ILoA/https%3A%2F%2Fwww.tensorflow.org%2Finstall%2FpipAfter
 this, I still get the above error message.I can also see that there is no 
support for running Tensorflow on Mac withGPU.Does this mean that there's 
no way for me to run this command or is there anything else I can try to solve 
this?Of note, the basic samsegcommand(run_samseg --input 
file [file ...] --output dir [--threads 
threads] [--pallidum-separate]) is runningwithout any 
issues.Thank 
you,Bianka___Freesurfer mailing 
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime

2023-10-04 Thread fsbuild

External Email - Use Caution


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 fs_Install_mcr,



$ cd bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b



 the script should output the paths to the subdirectories with the 
libraries to add to DYLD_LIBRARY_PATH at the end of it output. 



On the target computer, append the following to your DYLD_LIBRARY_PATH 
environment variable:

  

/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64

  

If MATLAB Runtime is to be used with MATLAB Production Server, you do not need 
to modify the above environment variable.




The paths listed for your machine will be different compared to the 
above, but just copy and paste what is listed for the entire series 
of paths into the command,



$ export 
DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64



- R.





On 10/3/23 21:35, Iglesias Gonzalez, Juan E. 
(jiglesiasgonza...@mgh.harvard..edu) wrote:







  External Email - Use 
Caution

  
Dera Lauren,
I am a bit confused: is /Applications/freesurfer/7.3.2/MCRv97 pointing to
/Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97?
Cheers,
/Eugenio



--
Juan Eugenio Iglesias


http://secure-web.cisco.com/1bqVymEumCTwxGQGbfGgRiZlYNLDyBIOW6zSN5FfiWaLUE4avNpS5ndTC_b-lmKjfuDeqfShAhvKEUUBtern_Sf4_Pck3lqfmued-BBIGDQxMxombrQVSz6We941VmXiva7eATA-sFLDzlhGA9SUj-WUv8uTsOQR6F8B9fLkdO9awXdEGopzCxm_xUh-KEmrrnwtQMclAUB3BkuTGoP6IVhuJLHqwGO5B2XJ1EMjailflpgVXZ7scfYxdZehoC1eTc3rSstLQja84-HM5dq_UpKR6qG9Gc4kIjvcUTdjDYNlw03lxL8AFFcWJ1D9wMU6L/http%3A%2F%2Fwww.jeiglesias.com




From:
freesurfer-boun...@nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lauren 
Stephens laure...@stanford.edu

Date: Tuesday, October 3, 2023 at 1:23 PM

To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu

Subject: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime

External Email - Use 
Caution

Hi FreeSurfers,





I have been attempting to runsegmentThalamicNuclei.sh and continue 
getting the error:





ERROR: cannot find Matlab 2019b runtime in location:
  
/Applications/freesurfer/7.3.2/MCRv97
  
It is looking for either:

bin/glnxa64/libmwlaunchermain.so 
(Linux 64b) or

bin/maci64/libmwlaunchermain.dylib (Mac 64b)

The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.
To do so, please run the following command (you might need root permissions):

fs_install_mcr R2019b

For further details, please visit 
https://secure-web.cisco.com/1ECsrk1Jpk7yzuD5ZaV9DNMKMMh3AzKfgXjXeiMKyBiQtU_0DDobyuRoXd5tik5QQw16SItCVsu1pBM7Nyc8Ub42HJuMZdpFFq-4iYV2ww0gK-7eR3ysbWlrca7QgQKSHo6N2HDKRvVylQB4Cm8LHtLAv6WZKbhKhz4f4kgj3cM3-F8Ht_vQpY12KzyhZa4Mmyx4vJ3i_LA23EXpLaBLCYX8Tgk1iIdgolNHULemQK5m_kWFSr5sYROwoMsvR1QlT5yIXs5GP0wxcfH7-L77-Y6B-dPHQlDkCSjPufnJpVeyos6410wv-Ql-q14gsAsUm3Eqxn83xh-_1SWr_5iLlCQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime
Current path setup on our Mac: /Applications/freesurfer/7.3.2/MCRv97





Symbolic
 link setup on our Mac named 
MCRv97:/Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97/bin/maci64/libmwlaunchermain.dylib





However,
 I have already installed the runtime and have alternatively created a 
symbolic link with Matlab we already have installed on our Mac.



I have also confirmed the runtime file exists on the machine

ln: MCRv91/MATLAB_R2016b.app: File exists





We are using FreeSurfer version 7.3.2 on an iMac Pro with Ventura 
13.6.

Any suggestions for how to get the matlab runtime issue resolved in order to 
reun thesegmentThalamicNuclei.sh code.

Thank you,

Lauren Stephens


Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laure...@stanford.edu
P: (650)-725-1716






  




  

  
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The

Re: [Freesurfer] Free surfer quits unexpectedly

2023-10-03 Thread fsbuild

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$ 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 
https://secure-web.cisco.com/1B3JRrCA1-GeI0tKc8qR9oVMx4vfk7xlYLxiqqBDOBuaesSZHdUEoF9qZ0tWGzGysXuBCEyOpSbXvD_sNqeR-owCXvQsiqm26_9KLalRHeelYHSZQBpacOtpGfPVqO2KTCVR22uzOtp0zFueNRfCITldF6fv-mcOBUheFxV8vLVqr5iTe-nNcq-6ZOaO8MmiDu8oUjdUVLpxwzSYpD7qFV5luFGQ4DYq8YkJAn22_0_I3m84W7sEZDUljCB3QSXifOAvmqyywNPtjdCj0KDvfgVqz6baSBBPtmmLdIsDSaBjYPJUA4i_PCdquW0cDjNybWB8c9JsJOtj_SYkg2acvvg/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050
… check the version of Quartz by starting an xterm.When the xterm 
window opens check the version from the upper left hand corner XQuartz 
application pull down menu and check what “About X11” reports.Check 
you have Quartz 2.8.2 or later and then quit the xterm window.
Mac:/tmpwhich xterm/opt/X11/bin/xtermMac:/tmpxterm 
… copy your license.txt file into your home directory.For example 
if you downloaded the license by default into your Downloads folder, then copy 
it from there into $HOME …
Mac:/tmpcd $HOMEMac:~cp -p -f ./Downloads/license.txt .
… set the environment variable FS_LICENSE to point to the license file … later 
you can put this in your shell init file to be the default when you launch a 
new terminal window with your default shell …
Mac:~export FS_LICENSE=$HOME/license.txtMac:~head -1 
$fs_license...@somedomain.com  
  — email you used to register for the license
… setup the freesurfer environment …
Mac:~export 
FREESURFER_HOME=/Applications/freesurfer/7.4.1Mac:~source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME/Applications/freesurfer/7.4.1FSFAST_HOME
  /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR  
/Applications/freesurfer/7.4.1/subjectsMNI_DIR  
  /Applications/freesurfer/7.4.1/mni
… first check freeview with no arguments opens an empty window …
Mac:~which 
freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~freeview
… close the freeview window and try to open a knoen to be good volume file ...
… check the volume file exists …
Mac:~ls -l $SUBJECTS_DIR/bert/mri/T1.mgz-rwxr-xr-x1 
rootwheel4502402 Jul 132021 
/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz*
… try opening the volume file …Mac:~freeview 
$SUBJECTS_DIR/bert/mri/T1.mgz
If the above works try opening one of your own volume or surface files.
BTW - you should update MacOS on your machine from 12.6.7 to 12.7 as there are 
important security fixes in 12.7.
- R.
On Oct 4, 2023, at 00:53, Clara Massaneda Tuneu 
c.massaneda_tu...@blackdog.org.au 
wrote:External Email - Use 
CautionHi,I'm attempting 
to install and run FreeSurfer, but every time I try to load data, the program 
unexpectedly quits. I downloaded the license from the email sent by FreeSurfer 
and followed the instructions of the video tutorial.I've also downloaded 
and installed the latest version of XQuartz before installing and executing 
FreeSurfer. When I tried to open FreeView in my terminal and load the image, 
there was no message in my terminal explaining why the program 
crashes.The version of FreeSurfer that I'm using is 
freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running 
version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of 
memory.I've searched the list, and no similar errors have been reported. 
Does anyone have any thoughts on how to troubleshoot this issue?Thanks 
for your help.Clara 
MT___Freesurfer mailing 
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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] Slow processing of large defect

2023-10-03 Thread fsbuild

External Email - Use Caution

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 swap
what’s in memory out to disk files when only 80% of RAM is in use. But
disk I/O from loading swap files in/out of memory can cause the machine to slow
down or thrash and never finish processing. With no consequential or RAM
hungry applications running on the host, then the host should be able to
essentially run idle with 8G of RAM leaving 24G to assign to the VM.
- R.

On Oct 3, 2023, at 02:01, Pål Gunnar Larsson p...@ous-hf.no
wrote:External Email - Use
CautionThank you for fast
reply..The computer has 32Gb. The virtual machine has 8Gb. According to ‘top’
all is used, except 140Mb. Swap has 1Gb of which 780Mb is used. Does swapping
use lots of CPU? It is 100% most of the time.Fra:fsbuild
fsbu...@contbay.comSendt:3. oktober 2023
04:33Til:freesur...@nmr.mgh.harvard.eduKopi:Pål Gunnar Larsson
p...@ous-hf.noEmne:Re: [Freesurfer] Slow processing of large
defectNot 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 due to lack of RAM - which can cause a
crash. I would try running the VM on a host machine that can provide
more RAM. So if the VM is currently running with 8G, then try doubling it
to 16G (on a host with at least 24 or 32G RAM).- R.On 10/2/23 10:31, Pål Gunnar
Larsson (p...@ous-hf.no)
wrote:External Email - Use
CautionHelloI am running
FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram.I am
running a child-MRI where I got a message about a large defect which would run
slowly or crash. FS is still running after more than 10 days (70%-100% CPU
use), but there are nothing written to disk for 10 days. It is working on
retesselation of defect 162.Is there any reason to wait it out? Or will the
results be unpredictable?BestPål G. LarssonIkke
sensitiv___Freesurfer mailing
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Re: [Freesurfer] Slow processing of large defect

2023-10-02 Thread fsbuild

External Email - Use Caution

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
due to lack of RAM - which can cause a crash. I would try running the
VM on a host machine that can provide more RAM. So if the VM is
currently running with 8G, then try doubling it to 16G (on a host with
at least 24 or 32G RAM).

- R.

On 10/2/23 10:31, Pål Gunnar Larsson (p...@ous-hf.no) wrote:

External Email - Use
Caution

Hello

I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram.

I am running a child-MRI where I
got a message about a large defect which would run slowly or crash. FS
is still running after more than 10 days (70%-100% CPU use), but there
are nothing written to disk for 10 days. It
is working on retesselation of defect 162.
Is there any reason to wait it out? Or will the results be unpredictable?

Best

Pål G. Larsson

Ikke sensitiv

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Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

2023-09-28 Thread fsbuild

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Thanks for reporting this. This posting indicates there is a difference 
in defining that for arm64 compared to intel 
architectures,https://secure-web.cisco.com/1FTmSa1QjGMsQB8Xf5Zs5AKj4Xk9F312HcVmOIIHIT5kDUDgCxaV4sUSYmWuRa96GF1JL06qjFzBNdpYJJmJtR_3GjMMsisKAkzdiR-9ZBMQ0UGgMFV1FMSpcTLB_xGSq00DSHrWzdrEfSjrszCjHWsweQfauiFuLs2xdeD1eT0PtzAhCwyK4YRNAxKIymf3B2xgRChAGuCAADy3dvKEuQlT1yW9e-XxoMNoOtWuuVrBeO2Q9y2k2MYY7UKxEf-GwVuJjm1SXJMEk-xcM_MzGdfRErVA1oHtLUe91iMGr3w5n81jieFowP5WqliBQChGiNpC5ROUEPBKC68P_B7aNafTnqMUUxJHq1nNq-QPVwXU/https%3A%2F%2Fwww.reddit.com%2Fr%2FUbuntu%2Fcomments%2Fpfabeq%2Fsolved_problem_float128_in_arm64%2F%3Frdt%3D45747
We will look into it along with producing an updated arm64 build. You 
could try making the change described in the posting in the SynthSeg code if 
you like.
You will not encounter that error in any existing/previous release, 7.4.1 ... 
7.3.2 as you are using a new arm64 development build which is post the 7.4.1 
release.


- R.



On 9/28/23 07:20, Conrad, Julian (julian.con...@medma.uni-heidelberg.de) wrote:








  
Hello again FreeSurfer Developers,

I'm attempting todo a surface reconstruction from a GRE magnitude image 
using recon-all-clinical.sh
As was stated before, there seem to be issues with the current Mac processors.

so I downloaded the dev version 
(https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW2QZ0blD-OpKmgogA7x9_rAfwfIcEGnZ7E8kgb9XNIzx2xLxQewJp32hJt31QUUAewAp1K7-Yjwk7lXCYxbaGdw8dtRE5zMFil4OqFhzHgZY7gNWOXHrgQ1zq6WrtnIl3Pllv0QaHc4JShUbdyQSVyQNgVymwLgj-PtjkDzhnise1J5RVUUczUi0PIoIHjn-dH5Ex7dw4_Tj8IUVRY1qDYHEdyBacN3YGVr6RlpLul0aH5727rGjfiCIau2iHg42KAJrBDTHZI1-iNSQ3tkbKJHbmkjy3X3wvfogE4XxSKFEkJaGyNNvit377-Ejbu0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg)
 as was suggested by your team. Now it started to run. But I got this error: 


File 
"/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/numpy/__init__.py",
 line 320, in __getattr__
  raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float128'
Error in SynthSeg

(see also attached recon log)

My numpy version is 1.26, python 3.9.6

I tried to change the float specifications using this but this did not do the 
job

https://secure-web.cisco.com/1Nw2CoSnBRIpwTK-GWDBJpxLeD53b5CAywKvOfsawRYQsCt_nqIiIgvTq2J_n4k1ncOfN0_1YRFNw_yiQfCaYvq7eGL7mh7nrzrvKKlQPHdiBDIJjRSrLSwF2ord-O-WSRM-NviF0EKgGiF2UKK3JW3seF0e8OvmTk9PjKYSyYaHsb-tyVc_4U3HLYcI1gW3Vy3wlhNB1UswTFvC6ZytgyLo5yrnncdt-l8NY3IQCvMy0I1eEd39yhIVSSZG1AyUvSGpe1Vl4NWMJKf_finRkqZwY3bVrUdW2uJLPCUjW9uUH-9_ubVjK7HLys9i6T_IQR7zybKx3_HHH_gNPk-lMtA/https%3A%2F%2Flevelup.gitconnected.com%2Ffix-attributeerror-module-numpy-has-no-attribute-float-d7d68c5a4971

Do you have an idea how to fix this?

Will this also occur if I opted for freesurfer 7.3.2? I am a little hesitant do 
install the older version just yet..

Best regards,

Julian





Mit freundlichen Grüßen





Dr. med. Julian Conrad







Oberarzt| senior physician
Sektion Neurodegeneration| Division of Neurodegeneration
Neurologische Klinik| Department of Neurology
Universitätsmedizin Mannheim| University Medicine Mannheim
Medizinische Fakultät Mannheim| Medical Faculty Mannheim
Universität Heidelberg| Heidelberg University
Theodor-Kutzer-Ufer 1 - 3
D-68167 Mannheim
Tel.+49 621 383-9025
E-Mail:julian.con...@umm.de
https://secure-web.cisco.com/1Ys12d1Q7EjaOXQJ3u43f5YMcfnSzuXxz579PUioZIBnkdjMmJeiYqS72gOEML4tmdshTJVb0Gai-r0nSIwt3zUOq1rPOJ6S1vQ8jnIme23u1sHITNH3Z7pJ5bdgTqzfUu9XxZIwLJjaWguptlNBj2AFXeJ1mTOxf7FvCBoU--iGnNTVgrRGx9NtMLmWjaxXd9Vq0g8OSQ9xWjpl2AU6eHRwZcDCZTYIoAGNNJaHMl0I8K_1Pf6Y60cY6ZisRzXXbAWfYZLhjuApKw3uWiibl5Tjq6L-5Vr5S5WYIq_cZF-5VuamILUkdDSFKB-H3R79vIFA606HhbzTCE-C-jJbFSgXbA5HfsQjr3uzHI8-1mNE/https%3A%2F%2Fwww.umm.de%2Fneurologische-klinik%2Fsektion-neurodegeneration%2F





Universitätsklinikum Mannheim GmbH
Geschäftsführer: Freddy Bergmann, Prof. Dr. med. Hans-Jürgen 
Hennes|Aufsichtsratsvorsitzender:
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Von: fsbuild fsbu...@contbay.com

Datum: Mittwoch, 27. September 2023 um 00:55

An: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu

Cc: "Conrad, Julian" julian.con...@medma.uni-heidelberg.de

Betreff: Re: [Freesurfer] Recon

Re: [Freesurfer] Running MATLAB on a MAC PRO

2023-09-26 Thread fsbuild

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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 change it to be whatever 
you installed on your machine.  The 7.4.1 release was tested with R2019b
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

... output showing SUBJECTS_DIR and other environment variables

$ cd $FREESURFER_HOME/bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

I think that sets things up so the libmwm* libraries are in the freesurfer tree 
under the path, $FREESURFER_HOME/MCRv97/bin/glnxa64.- but you should check that 
path.

Then you can try adding the path you verified, e.g., 
$FREESURFER_HOME/MCRv97/bin/glnxa64, to the head of LD_LIBRARY_PATH and 
remove any other entries to a different MATLAB distribution.
- R..



On Sep 26, 2023, at 18:13, Alan Francis alandarkene...@gmail.com 
wrote:External Email - Use 
CautionHi All :I just bought a 
2023 MAC PRO with an M2 Ultra Chip for my lab. It's running macOS Ventura. I 
have installed MATLAB on it but it refuses to run in a terminal or from the 
Applications folder.MATLAB runs perfectly fine on my other Linux machines.The 
MATLAB website has very little, if outdated, help.Have any of you encountered 
this 
problem?Thanks,Alan--|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan
 N. Francis PhDAssistant Professor of NeuroscienceInstitute of 
NeuroscienceUniversity of Texas, School of MedicineRio Grande 
ValleyTexas.
   
   
   
   
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Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

2023-09-26 Thread fsbuild

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Besides patching the python distribution, another option available now is 
the development arm64 build for silicon Macs with an M1, M2 processor. 
But this is not a release build and so has not been tested like a stable 
release. The dev builds are currently ~3 months post the 7.4.1 release 
from back in June of this. year. We’d be happy to hear how it goes if you 
try it. The download links are below.
- 
R.https://secure-web.cisco.com/1aFiKh6YzbcJ_9V-mQth29TZB1SeCRdpmUdrLhAH6aMSmX5br3cwYdWzk2SQFt3E84yhkJiX8UK-RAuZILJgbwlYcKW-x-4lL7J9kQfLfOwFQG5-1tgyI_iripvurrqc6hOck5zgoIIIxfTjCln1LScJweoTJQieoYz1s4N4sXygNQqlfzYbhZ87LIW9VQGRj3pGteAMKpDrA0j70XQIZemwauVs7meaYj1FI3CZslQwLBeuOE_We0NCBttIsDNpUBA9GcXYMgvwYOvTrFJLWmtJC-RFpnOa99GI2QCrpNkkzMnpOxyTP4aWeg48D0LuNDHAP6kU4s-t48OHy1ayF1g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
https://secure-web.cisco.com/1M-Y1AHK0ybK-HgTbS6EGioPOtjnLKD9oxxiz5O9fG-v6vkulEnH6r0CCzH6_gqM7XnDt6h5dVioJARCFIs9drLzcnO1LHyzTb7WUdjqafmNknH1NK83adDrhak3Sn0exMT0arlACB6QxoPP0HHbD3XGSeh1J4lmUFtZL1p-3jhPqgbUtmG6BAvlnt3MD3uJupFP1_-m-dI9r4fGY_ENFKpEor-bOxOjnAEgsUMyTSBmNzqwbq1iJq7SVXWbbGEPMtKUzSaycRQ66l-WnTskj6bJ2pY1NVyvlLLVMcRl5MCn6pFnRIv9hh88VJ_fH706tE7zsAVUDgD3x6G_nVvYcbg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.tar.gz


On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel 
asorby-ad...@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, but 
reposting here for anyone else having the same issue:You may not be 
able to run these commands without sudo/admin permissions on your machine.1) 
Download thetensorflow-2.4.1-py3-none-any.whl from,MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?usp=share_link2)
 Check the download is OK with the md5 command in the terminal window,$ 
md5tensorflow-2.4.1-py3-none-any.whlMD5 
(tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4DO NOT 
PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.3) Setup the 
Freesurfer 7.3.2 environment (shown here as installed via .pkg file under 
/Applications) and verify the path to fspython is from the 7.3.2 release,$ 
export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-darwin-macOS-7.3.2-20220803-878457d ... environment variable 
settings output ...$ which 
fspython/Applications/freesurfer/7.3.2/bin/fspython4) Uninstall the 
existingtensorflowpackage with,$ sudo 
$FREESURFER_HOME/python/bin/python3 -m pip uninstalltensorflow... apart 
from any warnings you should see the output ...Successfully 
uninstalledtensorflow-2.4.15) Install the package downloaded above. 
This command assumes the package is in the current directory where the command 
is run.$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install 
./tensorflow-2.4.1-py3-none-any.whl... apart from warnings and output about 
requirements (which should all be satisfied) .. you should 
seetensorflowwas updated Successfully 
installedtensorflow-2.4.1CHECK THE UPDATE:$ which 
fspython/Applications/freesurfer/7.3.2/bin/fspython$ fspython 
import sys, os importtensorflowYou should see the 
prompt return to "" after the import oftensorflowwith 
no errors reported. Hit Ctrl-D to escape the python session. The 
update should now be complete.Once you have done this you should be able 
to run recon-all via 7.3.2. Hope this 
works!AnnabelFrom:freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, 
Juan E. jiglesiasgonza...@mgh.harvard.eduDate:Tuesday, 26 
September 2023 at 17:35To:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
Recon-all-clinical error: Illegal instruction Error in 
SynthSegExternal Email - Use 
CautionDear Julian,I believe 
this is a problem with SynthSeg not being compatible with the new 
microprocessor in MAC computers. Our software engineers are looking into 
solutions to this.Sorry for the inconvenience,Eugenio--Juan Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1DgebDH1WCLKceFhMcyIutLihRRkTXmu8dVOr_f4V0A6HCTGgJKyfIgRMdsGA0JY6XdTrwJ9fG9ZF0-rGeXJJR5xuIBa9pWzkJy1MlhajNkbUh4zQoyngk61Y8hRRh9IM13qb6kqn_EED7sD_b7NPGyxpBMu96UJ1F9G5j7HJMmMqjXAlpbHLU0UiAYP6rsxQW1ZwkHU2un5V_LBoaWBBc1MFIfXt_bJeLj_mRT0UANYNpBhXYIMiNEvjU8waDvcGl8LvssZu_7hBYMzrZ73aumJwKnWJdCaUAWrBMN6lK6lUpk3mvzSDFQyDqhMlQR7C8OQ4-dV0n3ofYVP6BGgN6Q/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.h

Re: [Freesurfer] Unable to complete all the steps of recon-all

2023-09-25 Thread fsbuild

External Email - Use Caution

If the files can be read from inside the VM from the external drive, then 
I'd think you could copy them into the Linux file system. You would have 
to run the “mount” or some other command in the Linux terminal window to 
determine the path on the exFAT drive to what SUBEJCTS_DIR is there. But 
usually things are mounted under /media
$ mount | grep media… check output ...

Let’s say your path to SUBJECTS_DIR on the exFAT drive as visible in the Linux 
file system is /media/exfat/data/subj034
You need to find a location in Linux where you have enough space to copy the 
data. I will assume using your home directory in the Linux VM below. 
So in the Linux terminal window to use your home directory you could try 
the commands below. NOTE - that if you have spaces in a path or 
directory name on the exFAT drive, then quote them below, e.g., subj 
034 == "subj 034"
$ cd… or ...$ cd $HOME$ pwd/home/developer   — your result will 
differ… see how much disk space you have …$ df -h .… check output … and if you 
have enough space to copy data, if so, make a subdirectory for the copy …$ 
mkdir data_copy$ cd data_copy… try using the tar utility to copy all data from 
the drive …$ (cd /media/exfat/data; tar cpf - subj034) | tar xpf -… may take a 
while depending on speed of drive and size of data …
$ cd subj034… check all the data is there$ ls -lRt * | more… hit q to 
stop output from more command ...
$ pwd/home/developer/data_copy/subj034
… then set SUBJECTS_DIR in the environment or in script, etc. that runs the 
recon-all
$ export SUBJECTS_DIR=/home/developer/data_copy/subj034
- R.
On Sep 25, 2023, at 02:52, Mervin Tee mervin...@nus.edu.sg 
wrote:External Email - Use 
CautionHi R,Thanks for getting 
back, indeed a copy of those files doesn't help because just like what you have 
mentioned at some point a check failed and I could not proceed with the 
remaining steps of recon-all.The command I pasted was obtain from the 
last line of the error log text file where it indicates where the step of which 
the error occurred. But the main error is mostly due to symlink on exFAT 
storage on linux.Hence, the question here is if there is any solution 
that allows me to still work on external exFAT storage. As symlink doesn't 
seems to work on exFAT storage.As my data are bitlocked on an external 
storage, which doesn'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 September 2023 
10:10To:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduCc:Mervin
 Tee mervin...@nus.edu.sgSubject:Re: [Freesurfer] Unable to 
complete all the steps of recon-all- External Email 
-External Email - Use 
CautionI 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 
link name. That test will fail if the soft link has been replaced by an 
actual (duplicate) copy of the file. The expectation is when writing 
output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible 
file system that supports creating all the Linux file system file types 
(including soft links) and support all Linux file privileges.-R.On Sep 24, 
2023, at 01:58, Mervin Tee mervin...@nus.edu..sg 
wrote:External Email - Use 
CautionHi,I'm trying to 
complete my recon-all command. I'm currently working on Ubuntu 22 and 
processing the images from an exFAT drive.After digging a bit, I realised that 
symbolic links cannot be created on exFAT drives. I then came across another 
post that suggest to change all 'ln' to cp instead. While that works for the 
remaining steps. It started exiting with errors at this stage..The stage where 
it stops#@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 
2023The error that was in the error log.CMD mris_preproc --s 
ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage 
--out lh.white.K.fsaverage.mghWhat should I do to resolve this 
issue?Cheers,MervinImportant: This email is confidential and may be 
privileged. If you are not the intended recipient, please delete it and notify 
us immediately; you should not copy or use it for any purpose, nor disclose its 
contents to any other person. Thank 
you.___Freesurfer mailing 
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attempt from "secure-web.cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferImportant: This 
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Re: [Freesurfer] Unable to complete all the steps of recon-all

2023-09-24 Thread fsbuild

External Email - Use Caution

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 link name. That test will
fail if the soft link has been replaced by an actual (duplicate) copy of the
file. The expectation is when writing output e.g., during recon-all, that
SUBJECTS_DIR points to a linux compatible file system that supports creating
all the Linux file system file types (including soft links) and support all
Linux file privileges.
-R.

On Sep 24, 2023, at 01:58, Mervin Tee mervin...@nus.edu.sg
wrote:External Email - Use
CautionHi,I'm trying to
complete my recon-all command. I'm currently working on Ubuntu 22 and
processing the images from an exFAT drive.After digging a bit, I realised that
symbolic links cannot be created on exFAT drives. I then came across another
post that suggest to change all 'ln' to cp instead. While that works for the
remaining steps. It started exiting with errors at this stage.The stage where
it stops#@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08
2023The error that was in the error log.CMD mris_preproc --s
ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage
--out lh.white.K.fsaverage.mghWhat should I do to resolve this
issue?Cheers,MervinImportant: This email is confidential and may be
privileged. If you are not the intended recipient, please delete it and notify
us immediately; you should not copy or use it for any purpose, nor disclose its
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you.___Freesurfer mailing
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[Freesurfer] Native darwin_arm64 development build for silicon Macs

2023-09-23 Thread fsbuild

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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, M3 arm64 
processors without using the Rosetta emulation environment required to 
run Intel binaries. The build also includes Apple's tensorflow modules 
for arm64 python.



https://secure-web.cisco.com/19iU6Duk2zpbfifexEEBWTZjtW6_df80in56MrW1gz_nnhS2QL8nOPoJrf9T8JRpGvMewbyokX2k34pY38cm8HnnSaxd9YfyFNNpRdcRGrmwzJwgwwBaR4Rj3LL7Wb22mzlh2X5vWOOf_zr9K_joFEeiaTwVAIuKM02oYK15fe7YSUS-rNbpCMeE3DMwcAhcj5rv0O592bRTmiobQEgfeTReeS4hrybLF2ooa7VojaTvZAOhhhFBXNA-tzEFqVZnBkmsmFjN4_Lo-X4Q2-Okr6Ep4D3MPAyyNO6OCNcSiObo3otGjElBnC4EalUpfN0QuwAKbUkxJfaTeZU8vQzxdsQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg

https://secure-web.cisco.com/1XTLOzwkVakfd1RBsibgQ7t6YC509CBc7vc-fZFabprKBsGrDK-OerqpwWpLJhc3PrlNRJMrvI0mKoAEJTqCpArXfLulSA8wc2zah22LADu4AJSCA_Yd1tvuBnGPJE-PiYtOsnz79u2m1YMZ5B7ZELGtQRFr7TPPYvIdK2bhVEUFMTL1qZOnP2ZYHhVpQSf47xAD2vdvYK0FQFgd88D7488dsx-juk6t58unFMHXSjRotw7bSEY7kfbE2rYWkEAr20LEWBPNPMDopq5y1ESegrtoYqQ9t1M6iHsKTECx6v69h8usWmTE2hWUVWGsLGL5W2gP2iQNSdAgkUJdBZtKVjg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.tar.gz


The usual caveat applies if you are contemplating switching from a 
previous/older freesurfer build or release to a different freesurfer 
build or release compiled for a different architecture/platform. We 
provide this advice at the bottom of the Freesurfer 7.X release page, 
https://secure-web.cisco.com/1AR0zDCFfQrz2YrY4j9dkUT8euQVsY4AHiC6ltxf0tEGe5uya7AjVULtJZsAw5xrB1enADS7LrttX-s2xae1zOsf1P39MApP0zc2pC3f_IjSwml45mCYHoGmEr989Rf2oHnbDo4z8b13iQ3buR7YV2PPW3wli76EnPfJSaTvbe9a5QxrYkoeahlJoWjXbtIfWt032Mi2lzMb36wjCzpYt377-s6YrXOrlhZCNoYiEeJb2Ikw1Ce1YeyykjKYLvepEB2qRT6kljElwg70oC5FXWvCnJwOTSgRWWTnATRYh5ycgCZctTOc9iyd8Q1rupwAPhv5y-mEl0e4_CT8wmFGGeg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%3A



Important Note:When processing a group of 
subjects for your study, it is essential to process all your subjects 
with the same version of FreeSurfer, on the same OS platform and vendor,
 and for safety, even the same version of the OS. While we continue to 
work to ensure that results match across platforms, there are 
none-the-less system-level libraries that are OS dependent. An exception
 to this rule is that you may view and edit files across any platform or
 version, and run some post-processing tools (outside the recon-all 
stream) if you check with us first (for instance you may run the 
longitudinal processing with newer versions).


As of this writing, development builds are post the 7.4.1 release from 
June 2023. We don't encourage use of dev builds instead of a previous 
release unless the dev build contains a bug fix or new functionality you
 need, i.e., dev builds are not expected to be as stable as releases. 
That being said, please let us know if 
you run into issues when trying the new build. We have not compared 
the performance
 of the arm64 binaries against the Intel binaries.



- R.

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Re: [Freesurfer] freeview upgrade isn’t working/library issue

2023-09-19 Thread fsbuild

External Email - Use Caution

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 existing freesurfer tree (if you need to keep 
it), and then run the .deb freesurfer 7.4.1 installer matching your system 
(Ubuntu 18, 20, 22) which you can download from,
https://secure-web.cisco.com/1W5Z7do8RHfQJIQIHZ9EbWhe5GYVhLQ8shO8lqEwhsAE6gDaexj3KfFN5zXfZdCA7mfyFvRUV606uEVX8q8IDVG0LNCC0MZeeiPwAtx_-ZxvtEW4-pSlPhehcCbUhEw62kOvNMbYel7i60_-I4om9lr8wCgQc4VQO3UDbDmVYy7BHSKG7VWmKi_tDBsO0qgu5TkBA4znCgxcoZom8erNkPY1dTUq2y5hUZ73nRKztQ4HU7CbYVPgsEOkDiB0P7MIm4uK7VAY2YIXUAPB2HVffR_qC0byOa-k5I7Iw2kPda10T0X0yWknO4wH7-RH0OuZWCBOv1vPCtSOENEHGX5Zf0w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
- R.

On Sep 19, 2023, at 15:33, Hoptman, Matthew (NKI) 
matthew.hopt...@nki.rfmh.org 
wrote:External Email - Use 
CautionTO:freesur...@nmr.mgh.harvard.eduFROM:matthew.hopt...@nki.rfmh.orgSUBJECT:
 freeview upgrade isn’t working/library issueHello FreeSurfer 
Developers,I followed the instructions here to upgrade 
freeview:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewI am now getting the 
error:freeview: error while loading shared libraries: 
libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file 
or directoryI saw that it was recommended to install the package 
libvtk7.1, but that isn’t working:E: Unable to locate package libvtk7.1E: 
Couldn't find any package by glob 'libvtk7.1'Any help is appreciated. I 
am using:5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 
x86_64 x86_64 GNU/LinuxThanks,MattIMPORTANT NOTICE: This 
e-mail is meant only for the use of the intended recipient. It may contain 
confidential information which is legally privileged or otherwise protected by 
law. If you received this e-mail in error or from someone who was not 
authorized to send it to you, you are strictly prohibited from reviewing, 
using, disseminating, distributing or copying the e-mail.PLEASE NOTIFY US 
IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR 
SYSTEM. Thank you for your cooperation.IMPORTANT NOTICE: This e-mail is 
meant only for the use of the intended recipient. It may contain confidential 
information which is legally privileged or otherwise protected by law. If you 
received this e-mail in error or from someone who was not authorized to send it 
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distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR 
BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your 
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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

2023-09-16 Thread fsbuild

External Email - Use Caution

Hello Ken,
The output from your linux shell limits in the log show the following,
cputime   unlimitedfilesize  
unlimiteddatasize  unlimitedstacksize  8192 
kbytescoredumpsize 0 kbytesmemoryuse  unlimitedvmemoryuse 
unlimiteddescriptors 1024memorylocked 64 kbytesmaxproc 
  7823maxlocks  unlimitedmaxsignal 
 7823maxmessage 819200maxnice   
0maxrtprio  0maxrttime  unlimited
I would set at least coredumpsize to something non-zero so you can at least get 
a core file saved that could be looked at. By default the limits on 
my Ubuntu 22 system are:
$ ulimit -areal-time non-blocking time (microseconds, -R) unlimitedcore 
file size   (blocks, -c) 
unlimiteddata seg size
(kbytes, -d) unlimitedscheduling priority  
   (-e) 0file size   
   (blocks, -f) unlimitedpending signals
   (-i) 378881max locked memory 
 (kbytes, -l) 64max memory size   
(kbytes, -m) unlimitedopen files  
   
(-n) 1048576pipe size
(512 bytes, -p) 8POSIX message queues (bytes, -q) 
819200real-time priority
 (-r) 0stack size
 (kbytes, -s) 8192cpu time   
   (seconds, -t) unlimitedmax user processes  
   (-u) unlimitedvirtual 
memory   (kbytes, -v) 
unlimitedfile locks
 (-x) unlimited
You can try setting the core file size to unlimited with,
$ ulimit -c unlimited... then check the value was changed to something  0 
...$ ulimit -a
You could increase memory size (and as many shell limits as possible) to 
unlimited to get the max size allowed by the system in the script you use to 
run recon-all, and then try running recon-all again to see if you can 
retrieve a core dump file.
- R.

On Sep 16, 2023, at 09:55, KennethSPrice kennethspr...@protonmail.com 
wrote:External 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, KennethSPrice kennethspr...@protonmail.com 
wrote:External Email - Use 
CautionUpdate: I tried running 
recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: 
segmentation fault (core dumped)" error again. Any clarity on this issue would 
be appreciated.Thanks,K--- Original Message ---On Thursday, 
September 14th, 2023 at 10:41 PM, KennethSPrice 
kennethspr...@protonmail.com wrote:Howdy yall,I ran a subject through 
synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 
5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the 
error "Segmentation fault (core dumped)" during the mri_convert step. Any 
suggestions?Thanks,Ken___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferrecon-all.log___Freesurfer
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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

2023-09-15 Thread fsbuild

External Email - Use Caution

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 MPRAGE scan and got the "mri_convert: 
segmentation fault (core dumped)" error again. Any clarity on this issue would 
be appreciated.Thanks,K--- Original Message ---On Thursday, 
September 14th, 2023 at 10:41 PM, KennethSPrice 
kennethspr...@protonmail.com wrote:Howdy yall,I ran a subject through 
synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 
5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the 
error "Segmentation fault (core dumped)" during the mri_convert step. Any 
suggestions?Thanks,Ken___Freesurfer
 mailing 
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Re: [Freesurfer] ScLimbic issue

2023-09-12 Thread fsbuild

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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 compiled with AVX instructions. So 
either you are running on new ARM based processors or you are running on older 
Intel processors (approx. pre-2011) that do not implement AVX. There is a 
list of Intel processors supporting AVX instructions 
athttps://secure-web.cisco.com/1uW45KoTvgWNrFJTk9Lu8MiuKA56yspFlAr2_SBqEvMsfNPG3ZWUUoweL2QdxZRBTdwxv4h5RQUORU3aV_9AQCDOvE7q0gwTJhDNBVQklY_s00Um6UCrCzE3CiHgNttK5dx1NZW8X2t8jAmHj86_wXEzQ9wSgxQZeMu3te0A7Zg0E9_XMHm0BIa1fljHb-Kao_UuQWscgL4qS7N3vA0lVAmnocneb99d2M5mqLA7H7OrL0XWmzKOW3HnE6w68skwj9rWEI2KojoFKkC5b3Bitz3gaoLqoTawqmtLx-HcQofxZymwFmtZjznqcF9aKf0F4P8cPSkq8KATJnRnO2kLLl_dHfPjFkEombaGNIJK0umY/https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FAdvanced_Vector_Extensions.%26nbsp;
 For Linux machines, the resolution is to run use Intel processors that can 
execute those instructions.
- R.


On Sep 12, 2023, at 16:27, Douglas N. Greve dgr...@mgh.harvard.edu 
wrote:External Email - Use 
Cautionwhat problem? There is 
nothing else in your email and I don't have the previous threads.On 9/12/2023 
10:51 AM, Glass, John 
wrote:External Email - Use 
CautionHello,I am running 
into the exact same problem at my local site running version 7.4.1 on a centos 
7 machine with a build stamp of: 
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460.Has this issue 
been resolved?Thank you,John O. Glass, M.S.Signal Processing 
SupervisorDepartment of Diagnostic ImagingSt. Jude Children's Research 
Hospital262 Danny Thomas Place, Mail Stop 220Memphis, TN 
38105-3678john.gl...@stjude.org(901) 595-3276MailScanner has detected a 
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Re: [Freesurfer] Password for FS Ubuntu virtual machine

2023-09-11 Thread fsbuild

External Email - Use Caution

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 
wrote:External Email - Use 
CautionDear Sapere-Aude,The 
password is: Map.Brain321!Regards,Ynze HokkenOp ma 11 sep. 2023 om 23:21 
schreef 
sapere-a...@tuta.ioExternal
 Email - Use CautionHi,I would 
like the password for the user "developer" in the FreeSurfer 7.2.0 Ubuntu 
virtual 
machine.Thanks!Regards,Sapere-aude___Freesurfer
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Re: [Freesurfer] Screen tearing in FreeView on Ubuntu 22.04

2023-09-07 Thread fsbuild

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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), which you can pick from the downloads available 
underhttps://secure-web.cisco.com/1lN9y7zM2gRNbX1ihQ-zCX4n48mKFb2WobAfhZHbefn_WS3S3qffaAgUqhBenarPoq6R3IMAVkB88L4E12IX59x0GKyWcdQkDT5wUBdAiGfbIjJ_W_A7uNpV1uBhVecDOYYhf7a_nBnTgeWSeP-KiEzC-bh1aHVuqMcFjjjpLMQglKoLQ-PljVP7Bl723qmzAGHo93Rn7yCmjsD0lvAFaP7c01-zct7eHiW-b7xkVLntRWo0PFJjkUZ5gHg-3dmCYpWWyGF1twtceHYZGeH2JlrKDUCZcs0P5rXkrX0W6RIzhH1T5MTWUxVt0MbOR1zZZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
 Just “sudo apt remove freesurfer” and then “sudo apt install 
./freesurfer deb file”. (2) Perhaps something is going on 
with OpenGL drivers and graphics hardware. You could check the latest 
OpenGL drivers are installed and what you are running is compatible with your 
version of Ubuntu Linux.
- R.

On Sep 7, 2023, at 19:40, VINCENT KOPPELMANS 
vincent.koppelm...@utah..edu 
wrote:External Email - Use 
CautionHi all,I am 
encountering the following issue:In FreeView, when I use the mouse to 
navigate, the crosshair is not under the cursor, but about an inch left and 
down from it.When I resize the FreeView window, it starts to tear. See 
the attached screenshot or the Github issue that I opened 
here:https://secure-web.cisco.com/1nxOyRuDDwSL9nzRXpr6kl-rtPsHnh83mO2Az43L890Z8F-HTtAhatdEb-vqsWbvIDftkGIIh_hQ76NLwCPHChEKn8nJTBx6M6-GvTfLDJHp39_sRHS1fQis-nUlDohkEQ6kIbWe7piBMlGfhcfXv3hUxQF37_YxOv2vyD1XP7q6dRoea2HcmsX2T9VB5C6ZqnWCkhO7Bz1UB51NPpN4n4AshNrl2NXQY8K72vWVyIiFe826ZOBl96q3YzvCZWlvBqv7zklk61yeA8XZwQnvSFTVGePzRY5zqn027ii8rIHPWY69f8ZgLdgHI-Cv-sJzf/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F1129My
 environment:OS: Ubuntu 22.04.3 LTS (but this happened with 20.04 as 
well)FreeSurfer: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460FreeView: 3.0; Build Jun 
14 2023 03:48:54 (but this happened with previous versions as 
well)Best,Vincent261422837-033513d0-3922-4a07-95fe-ff30357b5085.png___Freesurfer
 mailing 
listfreesur...@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu
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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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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] registration error (reCAPTCHA not checked)

2023-09-06 Thread fsbuild

External Email - Use Caution

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 that a firewall enabled on your machine
or your ISP would otherwise block javascript from running.
If your current browser does not work, you could do a clean install of some
browser you do not currently have installed on your machine (w/o changing its
default preference settings). Choices for chrome based browsers you
might not already have installed could be Vivaldi or Opera. You could
search for "download Vivaldi" or "download Opera" and go directly to that
vendors web site and download the installer.
- R.

On Sep 6, 2023, at 09:21, lizhao...@sjtu.edu.cn
wrote:External Email - Use
CautionHi there,
I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A
license is required yet I could not get thelicense.txt from my e-mail.
After filling the form fromMailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/registration.html,a
registrationerror occured (see below). Is there something wrong for
my internet? Or what could I do to get the license? A few
words from you may help me a lot. Thanks in
advance.Catch7EDF(09-06-21-20-21).jpgBest!Lizhao
DuInsertPic_799C(09-06-21-20-21).pngSchoolofBiomedicalEngineering,ShanghaiJiaoTonguniversitylizhao...@sjtu.edu.cn___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] MATLAB autorecon3 glibc error

2023-09-05 Thread fsbuild

External Email - Use Caution

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. (Prior to that, it was R2014b - which you 
could try as well - but that would likely contain an even older version of 
glibc).
Assuming that you can write to your own installed version of freesurfer, then 
once you have set FREESURFER_HOME, you can try running the fs_install_mcr 
script included with the freesurfer distribution. See bash shell commands 
below.
- R.

$ export FREESURFER_HOME=your install path
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
… answer y to any installer questions ...
Then I think it should work to find the Matlab libraries by at least start off 
with setting,
$ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64
Please make sure you have otherwise removed any references to your previous 
matlab 2020a environment from PATH, LD_LIBRARY_PATH, etc.
- R.


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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] [COPY] Fwd: Installation Support for Windows (WSL Linux)

2023-09-05 Thread fsbuild

External Email - Use Caution

The Freesurfer WSL wiki page has been updated to show the download, 
install and setup of the freesurfer 7.4.1 Ubuntu 22 package (latest release)..
- R.

On Sep 4, 2023, at 19:51, Michael Mc Laughlin mich...@thecurate.com 
wrote:External Email - Use 
CautionCool!Thanks for 
the update!On Mon, Sep 4, 2023 at 6:17 PM Sabrena Tuy 
stuy2...@sdsu.edu wrote:Hello!After wiping out WSL and Ubuntu, I 
restarted the process with some different instructions guides by an outdated 
page from the website and I believe someone linked it in a response of 
supporting me as well. Fortunately, I was able to figure it out!! Thanks for 
all of your help!Sincerely,Sabrena TuyOn Mon, Sep 4, 2023 at 1:22 AM Michael Mc 
Laughlin mich...@thecurate.com wrote:Hi Sabrena,Once you get it working 
the WSL option works flawlessly but it can be tricky to get over the first 
hurdle. The help instructions are written assuming that you are fluent in 
Linux.Check which version of Ubuntu you have. When you start WSL it will give 
you a message like:Welcome to Ubuntu 22.04.2and downloadthe corresponding 
release of Freesurfer 7.4.1The help doesn't tell you how to download 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 about setting up WSL on the wiki page under,MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1BBLvc8hOj6S4O_4mbyaaPyyXKlrB_xFdTx9JajbnIpE8S5-lTp9yGrzpoOiV3ADBNct5eM-8P2v5s0ZJV0ZLIx5PiTHaShSZM_mJIat7GH-4n-9hPrTKZzr220vjXkk0nh264tYN-r3aabx6bTmZzGQFXZWAd3KJdO5ufuMc6p6iZFIiqqzXEX-gwvPfQBV3NI8CWWMpC0mT7mYNJ5xPyfZVqla6WqkZ_6CIIZVjfmsM9avXUMuGLSNq7y_SZQrlynrbf5VIo2V7WnErsaKZQjQy9Z11r1KS7Oj8IcX4PNbKrgcI9M0ec2wV4Pfv8XNCyHEcGQOe9_GvNaWISz8FXg/https%3A%2F%2Fsurfer.nmr.mgh..harvard.edu%2Ffswiki%2F%2FFS7_wslYou
 are probably running some version of WSL version 2 (WSL2), but since WSL can 
change w/o notice, we can’t guarantee our notes work for every Windows 11 (or 
Windows 10) setup. See the section there "Setup and Install WSL version 
2” including the link to the MS documentation.  If you can get WSL 
working and login to its Ubuntu Linux terminal window, then we can direct you 
how to install the freesurfer 7.4.1 release.If you want to run freeview to view 
brain images with WSL, you will also need to install a 3rd party X-server like 
XMing to MobaXterm as well on your Windows system. Some users have not 
been able to get freeview to work on their system after consulting our wiki 
page notes.An alternative to using WSL is to use a different virtualization 
application like VirtualBox. Some users find VirtualBox easier to setup 
and manage especially compared to getting WSL to work with freeview and viewing 
images. You would download and install the VirtualBox application on your 
Windows machine, and then download and install our Ubuntu 18 Linux OS image 
with Freesurfer pre-installed.  The notes for that are under,MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1OyYdKcf5JD9g74UZ0Jn9zcZYssuDtbBCfIeykPORRRGhPwhsMKkuI7xrj0yXbhYy8BYPZnTLTsAGrGsR-12flUuuKe9MpiV7WwqASzudYsT6MYhYT7T4IXC6EnGGnO-OPc3-8TAvQtEKwvErh9gOO0pPNZL6y038MJkjxS19SHOqCUSGSqpfx2U_8ugP_uZ1mAw5mfre-et2qCP9IaqUfIR_cL3IbUBmLAQ5al45Uv7ASoxle-tvAseRYIUs7HFQyeWLWjqA4uKuYkJfKU-QQ9usKF5Q6TiM1MbYxzpB_XYWtLNs2sZ93uz7IERhvYCqPUUfEEG_NUorF6Y1yLrzqg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67We
 can send you the codes to unlock the VirtualBox image and login. With 
the VirtualBox setup, there is no additional 3rd party X-server setup needed in 
order to view images with freeview.- R.Begin forwarded 
message:From:Sabrena Tuy 
stuy2...@sdsu.eduSubject:[Freesurfer] Installation Support for 
Windows (WSL Linux)Date:September 2, 2023 at 20:18:48 
EDTTo:freesur...@nmr.mgh.harvard.eduReply-To:Freesurfer support 
list 
freesurfer@nmr.mgh.harvard.eduExternal
 Email - Use CautionHello,I am 
a student in an MRI lab at SDSU that uses Freesurfer religiously, and 
unfortunately, I am a Windows (11) user. I have scrolled mindlessly and have 
made some progress on beginning the installation for Freesurfer, but I have 
come to a complete standstill.. Is there any way you can help me install the 
program onto my PC since I will need to use it for my lab 
work?Sincerely,Sabrena TuySincerely,Sabrena 
Tuy___Freesurfer mailing 
listfreesur...@nmr.mgh..harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/15gClFtc6FO3hbdmG0SDPPXtdWvcmG_RhlHC2D9rl-s1ByZvlTbr-W8U5POjz5nIXarjZAO-Lzf3

[Freesurfer] [COPY] Fwd: Installation Support for Windows (WSL Linux)

2023-09-03 Thread fsbuild

External Email - Use Caution

Hello Sabrena,
We have some notes posted about setting up WSL on the wiki page 
under,https://secure-web.cisco.com/1c9KrekHizcdGhd-EUpY8z6zQtrZ7Hnb3DsudqV1c_pPEjJ1H75BRvca6NRs_TRT6TsXulVKkhed9uxHkgEBBOLR3pJ1QadfUPK9NxzguGJR-9ZEdXbrbGgTiLMC3In-V_1eOTIHf0B8pxWbJcjhkapSbXWjqaraZgKCwigULr2pOXXSZBffwbUX8kMFxbI7lqhsp09hkOwjZUWEqA-D_kikevtPV4pp-1tyt230wlx3hRfEFEslJpansh_4yBibdUHv9pMqyR_dNZwNRQpWAWtaSfk1ChYf1ej-pW-xOjqtkmBb1HCTHC9QEg2eD1QI2kiko5M4aVy3zO_PYwX3pVg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_wsl
You
 are probably running some version of WSL version 2 (WSL2), but since 
WSL can change w/o notice, we can’t guarantee our notes work for every 
Windows 11 (or Windows 10) setup. See the section there "Setup and 
Install WSL version 2” including the link to the MS documentation.  If 
you can get WSL working and login to its Ubuntu Linux terminal window, 
then we can direct you how to install the freesurfer 7.4.1 release.
If
 you want to run freeview to view brain images with WSL, you will also 
need to install a 3rd party X-server like XMing to MobaXterm as well on 
your Windows system. Some users have not been able to get freeview to 
work on their system after consulting our wiki page notes.
An
 alternative to using WSL is to use a different virtualization 
application like VirtualBox. Some users find VirtualBox easier to setup
 and manage especially compared to getting WSL to work with freeview and
 viewing images. You would download and install the VirtualBox 
application on your Windows machine, and then download and install our 
Ubuntu 18 Linux OS image with Freesurfer pre-installed.  The notes for 
that are 
under,https://secure-web.cisco.com/1P4pBW1lhSQIuXvY6PhRq81dp468Q3FTax8bdRBv1NVIxscm7cGXVf6lQY9eI8AozTPM6cbqBUJPWiUfbrZVamB5EvGZ5f-6mJSN6H10op1CkJoGH1bzD-0wtqTvJ5DW9jkgFUD0kNsR5bht3LJE4W-mw3HD9dByZzbuVPqUUgvLowzQPPY2L8-ipuYYbDlUWkBhJSxdb6c9SYXJx857gWeFih6GlTHjkwFj1FfnSEGrQr3OtyxqEFo_ZD9xUXJ6MF0ZWguaxQGV54S2zrY22LEz_8UrmN-MEMAF19IBNn3xGKeNHTkSptfVA3CYK7GfOxV6Yk4TvJ3uIr5EZGQMmKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67We
 can send you the codes to unlock the VirtualBox image and login. With 
the VirtualBox setup, there is no additional 3rd party X-server setup 
needed in order to view images with freeview.
- R.
Begin forwarded message:From:Sabrena Tuy stuy2...@sdsu.edu
Subject:[Freesurfer] Installation Support for Windows (WSL Linux)
Date:September 2, 2023 at 20:18:48 EDT
To:freesurfer@nmr.mgh.harvard.edu
Reply-To:Freesurfer support list freesurfer@nmr.mgh.harvard.edu

External Email - Use 
CautionHello,I
 am a student in an MRI lab at SDSU that uses Freesurfer religiously, 
and unfortunately, I am a Windows (11) user. I have scrolled mindlessly 
and have made some progress on beginning the installation for 
Freesurfer, but I have come to a complete standstill.. Is there any way 
you can help me install the program onto my PC since I will need to use 
it for my lab work?Sincerely,Sabrena TuySincerely,Sabrena 
Tuy___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
This is a copy of a message which has been originally sent to: 
"To" field: freesur...@nmr..mgh.harvard.edu
"Copy" field: stuy2...@sdsu.edu
The message has been sent by 
https://secure-web.cisco.com/1q5buhaTDBn7kf7dqnltFmmqQFe0P3mcvBOkBwMIlZP0zwV3w2Cz7qElIzs5rIiyRYsdcUbY45Ai2HBms5DQvCN0ugj4Knx5q2bOaNCEsZN6i76MgW46wC9YS8PsexDeglxuLGKsEMAnkdpl1RqM1aHAqDIf7qCbQ4NOnCzmxB-TT2T9_zGBkThNoOi4kunp3xtGVI6pHg1Y54aJtiTwG96y81Ff2Q_aTmHHeMyffP5tSyqx_tvPXV-HHXg6XcnAnc6aNoj_KSkTEiRU68WLHLCCMFadE9Am3PjpXemoPc0rg7jRfd_VxLOufX2TC3kmGmeKHdpjpTTSCKIixu6TgtA/https%3A%2F%2FTrashMail.com
 and the used account name was: SSL
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Fwd: recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.

2023-08-30 Thread fsbuild

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 included with the freesurfer distribution 
$ export FREESURFER_HOME=your install path
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
… answer y to any installer questions ...
Then I think it should work to find the Matlab libraries by at least start off 
with setting,
$ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64
Please make sure you have otherwise removed from your environment and 
references to the previous Matlab R2022b setup.
- R.

Begin forwarded message:From:Benjamin Cole Sherman 
bshe...@stanford.edu
Subject:[Freesurfer] recon-all error: matlab gives: Unrecognized function 
or variable 'make_outer_surface'.
Date:August 30, 2023 at 12:02:09 EDT
To:"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Reply-To:Freesurfer support list freesurfer@nmr.mgh.harvard.edu

External Email - Use 
CautionHi FreeSurfer Team,I'm 
trying to run recon-all on an MRI nii.gz file and I believe most of the command 
runs as the error doesn't happen until several hours in, however once matlab is 
initiated I consistently get the following output:MATLAB is selecting SOFTWARE 
OPENGL rendering. 
  M A T L A B (R)   
   Copyright 1984-2022 The 
MathWorks, Inc. 
R2022b (9.13.0.2049777) 64-bit (glnxa64) 
  August 
24, 2022Warning: Function iscolumn has the same name as a MATLAB builtin. We 
suggestyou rename the function to avoid a potential name conflict.Warning: 
Function ismatrix has the same name as a MATLAB builtin. We suggestyou rename 
the function to avoid a potential name conflict.Warning: Function isrow has the 
same name as a MATLAB builtin. We suggest yourename the function to avoid a 
potential name conflict.Warning: Function narginchk has the same name as a 
MATLAB builtin. We suggestyou rename the function to avoid a potential name 
conflict.Warning: Function isequaln has the same name as a MATLAB builtin. We 
suggestyou rename the function to avoid a potential name conflict.Warning: 
Function istable has the same name as a MATLAB builtin. We suggest yourename 
the function to avoid a potential name conflict.Warning: Function isfile has 
the same name as a MATLAB builtin. We suggest yourename the function to avoid a 
potential name conflict.Warning: Function isfolder has the same name as a 
MATLAB builtin. We suggestyou rename the function to avoid a potential name 
conflict..Warning: Function isstring has the same name as a MATLAB builtin. We 
suggestyou rename the function to avoid a potential name conflict.For 
online documentation, 
seehttps://secure-web.cisco.com/1A7cHJG7OTQToCpTNsg3ycqt5UEObzYbnyuy3_pfg1wlC1F4jIcVd5Pf6qNpHle7gAqT6177JQQHGrD_FY6ddsPj56KJNkyqORfZ-yq1A_uco2Hs4cdMVZQlYtvfMd8x_lRoSbGgA6HkBbAlHw3Q-AOuQ__pYiP83887FgmXZJoCFrKjnw3CsPha7iaVbaHPnfA7ZxSpDnyTRx8SR9Lf1azZHdNBwnNBsOPaZ1tDgP3AdDr-vLWNWNGjJa4MSRiWI_dpdoFbTBvkXze5zrUv2R0w8MgXoHQdv0b1UtwSdrSJMTpEhgSqbsVxDqMJhG-S3EN862Yz_ti_Gc66ckcWp4w/https%3A%2F%2Fwww.mathworks.com%2FsupportFor
 product information, 
visithttp://secure-web.cisco.com/1PkNE_zNSBM0yzYMjwH_cGeVC4O7UdJdfnliIOnqoaBcy5GHeqYRm_4T9_WR9vGAfol8V0_h_BBmmgtxSeq1hM7DAzUz2W8u9riITxG6WdjCZo6evmQDs2w70OLY4bBtE9v14Mw-xplN4Bax9dYaGZJinqA1-khI72MQgDmD-GNqYeGUSK4_PoYikluiayoPmvJ3sDu83lphtc86T2XqofDnHgRz4xHVDKv4x4IzRF_k90VuY4qtwhiWQcGFroyQqUnRlwBy8MxzppbNN1vt2O5sFg60fZM18Ksgvk1xxX8wXaurrhAhfCK-lB5rJZX3QwumhPOjvG3htgVFHOsYbJA/http%3A%2F%2Fwww.mathworks.com.%26nbsp;;
 Unrecognized function or variable 
'make_outer_surface'.ERROR: make_outer_surface did not 
create output file 
'/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!Command
 exited with non-zero status 1I haven't been able to find anything in the 
support archives so I was hoping you could help us out.1)Freesurfer version: 
freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb84602)Platform: Ubuntu 
20.04.6 LTS3)recon-all.log: see attachedThanks for any help you can 
provide!___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Freeview output viewing error

2023-08-23 Thread fsbuild

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 we cannot guarantee these settings work 
with the current version of the 2nd iteration of WSL, i.e., WSL2, which you are 
running. 
See,https://secure-web.cisco.com/11H-L4FbGidKmZY-de-JntjYeQLAeVrQ1XgpdUHaMqg8CCouWlZ-csPc_4IeioBAVAqHhk45el9cRUZPv7wIb0Fa33nZc9N4PkjKI0dF1RPJVN-he9XBt1Ua6a4QSVeD_w5bZnfOLabOM5n15lkCAJOV069NjUvo7wvfKDC7ihp4tfFZRlqy04d4Ulv8M3XzFbXzHa3_X6PzLyLptMRW0DpSEH15MxILMfCaw2aXqyXv8WbtHT_dWkB1oPK8nKUInT_c31S6utPE9VzRLR2IkzwjB7r2AqOCZO1vkEd_sd-w--NZS1-g316PnttbIo3N5Ia8In0FQw1pQlYDew151jQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
Some people have found Moba X-term to be easier to setup and use compared to 
Xming for the 
X-server.https://secure-web.cisco.com/1wbbTwhirUX48Lj_j7Zcog0e6ACmMB4oLvaYMUSE6loHwKKH6rYEiMDQ_-1MsBcWWJ3dpd-OBkNiaLAOkgjmtSZ7JWjzkEua8MwktH6pGmclIPg9mYSOIZGoNJqa8TyOhIyULOcXHVCIwSrp1q7QmTmYGBmMt1RXf29SR5i7iBMuAElxCOfXtvqo5wRPR9HlFUq9YF3tI-JWR9ZV0DuGS-nlAMxp2FK8AZkA1JIcN9VK9U6c3gbDeHRkrBKUAB3cFvtv5i1SwGP3i-UzJh2-KSIxX1ezMDxvbg_rkI2XjKSvA8qTaTX0hmxVxg3O3Fd1B50G-W2xhwfmR-OPMEtPh0A/https%3A%2F%2Fmobaxterm.mobatek.net
Before trying to run freeview, check that simple X-windows programs like 
“xclock” or “glxgears” run directly from the terminal window inside linux, 
i.e., you should see a clock displayed,$ xclock… and spinning gears ...$ 
glxgears
An alternative to WSL is to run the VirtualBox VM we provide with freesurfer 
7.2.0 pre-installed running on Ubuntu 
18,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-sSQIXzdhv-YwluzAWgB4gG9phXhLQcVB_o2cNHMOGnK9Gp9XWPjB8FgTqezBrM26yU2u5N756v_OP8sEXvbixcSFk6pTTTGbu3wEJMe_5kxVgYIInMdlJVcY40F7nAa8KOLYdDPEcKUtp7gnSXtBSNLE4rpSwwlEQr2t1r_26eI3pnjxD9fv1Z2pFrryslOZVdLTsNVxs6jZcYOZZYcGKMTjoPot6uYkAjYPe0eKi-U441Xz0011uiNKcTTbbhPOQ4bs6_q6eY9BWkFuxm6JBvP1WaMMtWPal2bAZD488thEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
You can upgrade the VM from Ubuntu 18, to 20, etc…. Similarly you can 
uninstall freesurfer 7.2.0 and install the latest 7.4.1 rpm matching the Ubuntu 
OS you are running from the Freesurfer downloads 
page,https://secure-web.cisco.com/1m70yw-FWa8H1WUCpyYEQ2AgIFTjm9W5pcTX0PejadT4Xt5J_YSvLLKb8_hi0_CHsZkjcfaQJCEMoo1FR4a9GG9tUh6CWii4M9OYVfYi_14SBVGd6at8Lq4qJl4P52yuupYfLSlf4et8HVuNu-BSrFq_g6gQPHt7TDv0XpvqiAcUFOZflBvLAt77eCm7hGGXLN1fDoqdOUQwkVMKxE_fQKUtGggn2wVVcPGGKMn0c6cY2qTSjq4IujXwEdI3Q1R9TCQhHO3yRJUrQQ5_fmbPjy10RA6O0dq6U8snOAcvQBrLVHTurrJ96BgrBP2v5L89SDuPgaqSHlT1K2QIOorRFLA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
Advantages to the VM are it will run (thru Virtualbox) on most Linux, Mac, or 
Windows hosts and since the X-server is built into the VM, there is no need to 
install and configure a 3rd party X-server on a Windows host. Some users 
have switched to VirtualBox because they found it easier to use. 
See,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-sSQIXzdhv-YwluzAWgB4gG9phXhLQcVB_o2cNHMOGnK9Gp9XWPjB8FgTqezBrM26yU2u5N756v_OP8sEXvbixcSFk6pTTTGbu3wEJMe_5kxVgYIInMdlJVcY40F7nAa8KOLYdDPEcKUtp7gnSXtBSNLE4rpSwwlEQr2t1r_26eI3pnjxD9fv1Z2pFrryslOZVdLTsNVxs6jZcYOZZYcGKMTjoPot6uYkAjYPe0eKi-U441Xz0011uiNKcTTbbhPOQ4bs6_q6eY9BWkFuxm6JBvP1WaMMtWPal2bAZD488thEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
- R.


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Re: [Freesurfer] ScLimbic issue

2023-08-20 Thread fsbuild

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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 arguments to it, 
i.e. try,
% bash -x `which mri_sclimbic_seg` --s HAB_008_CST_2.4
 and send along the output ...
- R.
On Aug 20, 2023, at 21:31, Jacobs, Heidi I.,PHD hjac...@mgh.harvard.edu 
wrote:mri_sclimbic_seg

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Re: [Freesurfer] ScLimbic issue

2023-08-20 Thread fsbuild

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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 mounted/available on your machine (so don’t use that 
one).
% cat /usr/local/freesurfer/7.4.1/build-stamp.txt
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
% cat /autofs/cluster/freesurfer/centos7_x86_64/7.4.1/build-stamp.txt
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
Both commands work on my test machine, so I will use the first one. Using 
csh to setup the environment,
% setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1
% source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/usr/local/freesurfer/7.4.1
FSFAST_HOME  /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.4.1/subjects
MNI_DIR
/usr/local/freesurfer/7.4.1/mni
FSL_DIR
/usr/pubsw/packages/fsl/current

But your posted output from the source command does not match the output above. 
It is fine to change SUBJECTS_DIR to a different path *after* you run the 
“source” command above, in order to process your own data, e.g.,
% setenv SUBJECTS_DIR/autofs/space/locus_001/users/mv1048/LC_HYP/FS6
I’m wondering if something was added into your shell initialization file in 
your home directory to set FREESURFER_HOME, etc. to be different. For 
csh, that would be your “.cshrc" file.. I would check that file and 
either change or comment out setting FREESURFER_HOME there, etc. But you 
should get the same output listed above from the source command (apart from 
changing SUBJECTS_DIR).
- R.

On Aug 20, 2023, at 18:12, Jacobs, Heidi I.,PHD hjac...@mgh.harvard.edu 
wrote:/autofs/space/locus_001/users/mv1048/LC_HYP/FS6

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Re: [Freesurfer] ScLimbic issue

2023-08-20 Thread fsbuild

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…. 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 full command line and terminal output?On 
8/20/2023 2:57 PM, Jacobs, Heidi I.,PHD 
wrote:External Email - Use 
CautionHello FreeSurfer 
team,I am trying to run the sclimbic tool on our FreeSurfer processed 
images (from the Martinos center).For some unknown reason I keep getting the 
same problem:Excluding seg [853]Using CPUIllegal instruction (core 
dumped)Not sure what this means?I have 
sourced/usr/local/freesurfer/nmr-dev-envand set the 
SUBJECTS_DIR correctly.I tried with the - - s option referring to the 
FreeSurfer processed subject as well as the - - i option, referring to the 
orig.mgz image.Using the nifti image or the mgz image doesn’t make a difference 
either.Any suggestions on what the problem may be or how to resolve 
this?Thank youAll the 
bestHeidi___
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Re: [Freesurfer] ScLimbic issue

2023-08-20 Thread fsbuild

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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 Aug 20, 2023, at 14:57, Jacobs, Heidi I.,PHD hjac...@mgh.harvard.edu 
wrote:External Email - Use 
CautionHello FreeSurfer 
team,I am trying to run the sclimbic tool on our FreeSurfer processed 
images (from the Martinos center).For some unknown reason I keep getting the 
same problem:Excluding seg [853]Using CPUIllegal instruction (core 
dumped)Not sure what this means?I have 
sourced/usr/local/freesurfer/nmr-dev-envand set the 
SUBJECTS_DIR correctly.I tried with the - - s option referring to the 
FreeSurfer processed subject as well as the - - i option, referring to the 
orig.mgz image.Using the nifti image or the mgz image doesn’t make a difference 
either.Any suggestions on what the problem may be or how to resolve 
this?Thank youAll the 
bestHeidi___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all-clinical out of memory error

2023-08-19 Thread fsbuild

External Email - Use Caution

Thanks for the updates. Not that it will likely help with the 
memory underrun, but it should be straightforward to update Freesurfer from 
7.2.0 to 7.4.1 in the VM from the command line.
You can use the Firefox browser in the VM to download the 7.4.1 installer with 
the 
link,https://secure-web.cisco.com/1NY_o7fEYkraJG0kPriDNOoRkAxLu_PnGwgYcRK1s8senK4bwr3tHkHxmqeA1ox3nv4eLHtKcyOszCYG2iNiDyCTypjVT3XBT4kycfC3LAaLKIWG_pEylRH9BHZQnOFmyrxU4noCzlrXuWiIR7PTEMvUVbduD-WGGg2rcqdN3MAN5iUlS-gfsCJyS0RLjqkERAU04kI2dcPPUE4qdvHhb21jI2n67gWL2EmGF-K8eCfEQRxuZsjeV_rYjPbqmbpbTkGuQRTcHfyLiaG4nAG6zCwrWdyy5UgeoP-u_COfxQZJw-siJZHD07V0nL0XMEkfscHmaOjEbQU8yA92IBEvCvA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu18-7.4.1_amd64.deb
In a terminal window, remove the existing freesurfer 7.2.0 installation,$ sudo 
apt remove freesurfer
Then go to where the 7.4.1 installer was downloaded and run,$ sudo apt install 
./freesurfer_ubuntu18-7.4.1_amd64.deb
There was likely a soft link to the previous freesurfer distribution in 
developer's home directory, so to update that,
$ cd $HOME$ rm -f freesurfer$ln -s 
/usr/local/freesurfer/7.4.1 freesurfer$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 for 
the suggestions. Unfortunately it still does not work. I did not 
try the virtual machine, because I could only find version 7.2.0 ova file on 
the freesurfer website. It appears the 7.4.0 version does not yet have a 
virtual machine? I am trying to use recon-all-clinical, which did not 
appear until 7.4.0. The standard recon-all works fine on 1mm scans on my 
16 Gb machine under WSL. But I am trying to explore use of 
recon-all-clinical.It appeared as if WSL was not using any of the available 
swap space, so I tried a few different swap and memory configurations in 
.wslconfig. Then I tried to create a cgroup that would limit physical 
memory and force freesurfer to use swap. This did cause freesurfer to use 
swap space, but it still crashed with out of memory error when the combined 
swap and physical memory got to about 23 Gb (out of a total of 100 Gb virtual 
memory).I then created a total Linux version using Porteus Linux live USB and 
unpacking the freesurfer 7.4.0 tar.gz and finding a few minor 
dependencies. This is a fairly lightweight Linux distro that runs from 
USB so I didn't have to create a dual boot.. The base memory usage was 
about 1.3 Gb before running recon-all-clinical. I also activated a 16 Gb 
swap file with swapon. It didn't work either, even in a pure Linux 
environment. At maximum memory usage, it used only about 7-9% of the 16 
Gb swap space and I think it also crashed at the same place around 21 Gb total 
memory usage with an OOM error.So it appears to be complaining of out of memory 
even when there is ample memory available in the form of swap space. I 
have tried various options for vm.overcommit and vm.swappiness.This seems to 
occur only for a few selected scans. For most of them it works. 
There is a long error chain but this seems to be the relevant line:OOM when 
allocating tensor with shape[1,288,288,192,72] and type float on 
/job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu[[{{node 
model_5/unet_parc_merge_8/concat}}]]It fails there every time.I bit the 
bullet and bought an additional 16 Gb physical RAM for a total of 32 Gb. 
I'll let you know if that works.On Sun, Aug 13, 2023 at 10:11 PM fsbuild 
fsbu...@contbay.com wrote:You might be better off with swapping inside 
the Linux VM instead of on the windows host. Or I don’t see anything 
preventing the Windows host from trying to swap out the entire VM process - 
which I would not expect to be efficient. You only need the application 
running *inside*the*Linux*VM* to be swapped out if necessary (using the Linux 
OS to do that).This should be straightforward to setup using VirtualBox to run 
the Ubuntu Linux VM we provide with Freesurfer already installed, i.e., 
download fromMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1oFOJz1tXGspfsKNscw0jmPq8nuxBXOxbqTB1n-bwDnNM5mUz6pxVbABWcrVY94a9HN8Vx7byh5P0xNvKIFV8N1LW0Hu5cPXmnrNthADHDBuBRiRRp6d195GsQsDZDnJUej2pAr_nxobufSqEyZIhTg2JwjRrtPSmmd77hlBqEaGKfoFaUNBjQYj8gacvos_7DKkXlSOgQ_Ay5gbOgqdQPPEA6fPD8Bn4bYrf7667Fi4iVmRe66YRG32ggib0H07hOhTiyLOd2HIrDpDGnQ3GqJpRCFDHOvFfShQHILWzT-t_G-eXg7rn2Cwh4DvPZrYox56QeaEs6YybYELsOgFtVg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67In
 the screenshot below, the FreeSurfer VM starts with 4G allocated to it. 
So correspondingly, inside the VM the “free” command reports there is ~4G 
available of which only 1G is being used since nothing consequential is 
runni

Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS

2023-08-16 Thread fsbuild

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Since that did not work, I suggest you try some of the other suggestions 
in that posting about changing the permissions on files related to _apt.. 
If you are not a system administrator, then perhaps one could help you 
out. It reads to me like different fixes worked for various people 
depending upon their system. You could check to see if there are any 
Ubuntu system updates available as that might help, but I don’t see any reports 
of that providing a fix.I would expect what you list to happen with 
any binary RPM you download and try to install, i.e., I don’t see this as an 
issue with the freesurfer installer.
- R.

On Aug 16, 2023, at 06:19, Praise Matsekete mtspra...@myuct.ac.za 
wrote:External Email - Use 
CautionGood day,Kindly find 
attached a screenshot of what I tried to do in the terminal as well.Kind 
regards,PraiseFrom:Praise Matsekete 
mtspra...@myuct.ac.zaSent:Wednesday, 16 August 2023 
12:08To:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] Trouble 
installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTSGood day,Thank you so 
much for the help.I tried to "chmod 777" the .deb file 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 fsbuild 
fsbu...@contbay.comSent:Tuesday, 15 August 2023 
21:48To:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.eduCc:Praise Matsekete 
mtspra...@myuct.ac.zaSubject:Re: [Freesurfer] Trouble installing 
Freesurfer 7.4.1 on Ubuntu 22.04.2 LTSCAUTION:This email originated 
outside the UCT network. Do not click any links or open attachments unless you 
know and trust the 
source.External Email - Use 
CautionHello Praise,This 
post,MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://askubuntu.com/questions/908800/what-does-this-apt-error-message-download-is-performed-unsandboxed-as-root-
 indicates it is from a permission problem with _apt on the system (which may 
have been an Ubuntu bug/issue).  One of the more innocuous fixes 
suggested there is to down protect or “chmod 777” the .deb package and then try 
to install it. Other fixes involve changing the permissions of system 
files. I have not seen that error testing the install in a newly made 
Ubuntu 22 docker container.- R.On Aug 15, 2023, at 10:43, Praise Matsekete 
mtspra...@myuct.ac.za wrote:Download is performed unsandboxed as 
rootDisclaimer - University of Cape Town This email is subject to UCT policies 
and email disclaimer published on our website at 
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Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS

2023-08-15 Thread fsbuild

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Hello Praise,
This post,
https://secure-web.cisco.com/13ufO8OPW7q_Ihf7Z4dQTf5tWtAWOGypFw1c5438ElaNLxhEoDf4Onnc197q69zMpEpSOkn2rAFUJpivo_4XlXeFyughVSMqW95z2BDfKqd3Jsi5_dh0YLp86zHRD4fuap73SFKf3JXCRRt1WDRfYe1Bcu10ViBQjsMOs8qWuvI8axXjS3dDXJ3CNj8uIA8hTvhZmKdyDBeK_mcEJS7g4Q_A07RcObhAJsxSa7s3yFJMR8SO3sPseaPLSR9h6goYXIb2w2pGngtR0TR435vPa9FYLSndUzJzIKNCoycHrtmp1hXvRFiHtz5nHfzF06tUxx6LG8wTe4B4tMILslmA4MQ/https%3A%2F%2Faskubuntu.com%2Fquestions%2F908800%2Fwhat-does-this-apt-error-message-download-is-performed-unsandboxed-as-root
- indicates it is from a permission problem with _apt on the system (which may
have been an Ubuntu bug/issue). One of the more innocuous fixes
suggested there is to down protect or “chmod 777” the .deb package and then try
to install it. Other fixes involve changing the permissions of system
files. I have not seen that error testing the install in a newly made
Ubuntu 22 docker container.
- R.

On Aug 15, 2023, at 10:43, Praise Matsekete mtspra...@myuct.ac.za
wrote:Download is performed unsandboxed as root

Re: [Freesurfer] Freesurfer issue

2023-08-11 Thread fsbuild

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 more details, please visit 
https://secure-web.cisco.com/1G4FPb9n4t6EAd65_hmtnkfEITITNTkf9OQlUdDQs6VJF-TWcoQLNA-2EK0Sqjx6GIYs2iyeva7639j3Ctc-WwaYjjxMSlTxYjuIHTYMLRb4YEDnuCe8VSbpScBeLw8e6x-x1DxlctH2DqHVqXERaJsrErPQ2Vdg3AQPHKJujr5n_cCUdvuclqAbcyATPVSalzJufASJzmxuYxRhGmBK4sVdPYcQvyL4ZeiXi3KhLSgBZKNy9p8KVlDwn27hwEtjZPPV73yM4aHys84vzNPSsF-l2xluHNPkBshPzw6zHIK0C3wn5A83ercPmDb_ykMUMS9w1SffX6C9jY2T1flcb7Q/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050

… check the version of Quartz by starting an xterm. When the xterm window 
opens check the version from the upper left hand corner XQuartz application 
pull down menu and check what “About X11” reports. In the example below, 
Quartz 2.8.5 is running on a late 2019 Intel MacBook Pro with MacOS 12.6.7 
(Monterey) installed …
Mac:/tmpwhich xterm
/opt/X11/bin/xtermMac:/tmpxterm 

… check you have Quartz 2.8.2 or later and then quit the xterm window …
… copy your license.txt file into your home directory. For example if you 
downloaded your license attached to the email notification into your Downloads 
folder, then copy it from there into $HOME …
Mac:/tmpcd $HOME
Mac:~cp -p -f Downloads/license.txt .
… set the environment variable FS_LICENSE to point to the license file … later 
you can put this in your shell init file to be the default when you launch a 
new terminal window with your default shell …
Mac:~export FS_LICENSE=$HOME/license.txt
Mac:~head -1 $fs_license...@somedomain.com
  — email you used to register for 
the license
… setup the freesurfer environment …
Mac:~export FREESURFER_HOME=/Applications/freesurfer/7.4.1
Mac:~source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.4.1
FSFAST_HOME  /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects
MNI_DIR
/Applications/freesurfer/7.4.1/mni
… first check freeview with no arguments opens an empty window …
Mac:~ which 
freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~freeview
… close the window and try to open a volume or surface ...

… check the volume file exists …
Mac:~ls -l $SUBJECTS_DIR/bert/mri/T1.mgz
-rwxr-xr-x1 rootwheel4502402 Jul 
132021/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz*
… try opening the volume file …Mac:~freeview 
$SUBJECTS_DIR/bert/mri/T1.mgz
The above works on the Mac configuration listed above.
- R.
On Aug 11, 2023, at 18:59, Irakli Kaloiani ik...@stanford.edu 
wrote:External Email - Use 
CautionDear Freesurfer 
team,Several members of our lab tried setting up Freesurfer (V.7.4.1) and about 
5-6 people have encountered the same problem (all of the on macOS) of freeview 
crashing when we are trying to load the T1 from the folder bertmriT1. 
We already have license file placed in an appropriate folder.Additionally, 
there’s an issue with XQuartz (V.2.8.5) when I am trying to run xclock in 
terminal – “Error: Can't open display:”Do you know what could be an issue? 
Google and stackoverflow wasn’t useful.Your advice would be greatly 
appreciated,Thankfully,IrakliIrakli Kaloiani, M.D.TMS 
LeadBrain Stimulation Lab, Stanford UniversityDepartment of Psychiatry and 
Behavioral SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttp://secure-web.cisco.com/1ZkGWHgZJw-3zmLYe8yrmEG28cyI9K8rL_avCqmNmtLv0PzowdcqIkU8_wBFs-RPZIKE8FSVmCyMtf66YgwBOtHcp6cQcyPkzTrNJD_Bv1NMjzBNmAnpcGifZeCL7_UT59nsxRycdHULmKLtxT0LNwlrQDiHELrH8ZJGmObeK5OU4RCpqNC50_NcY4ANLzQOGpX8u9So2TQrxJ2df6vS6s__9qZODe6QXGgQkXSMAZ7SIJosvZr32QxTh5hXr8EBYPxPOR0v59BNLccUBWvaAsSuaDodIZTT92fYUM6jnWSoWSjma671lo2XpDU8asCnvbVhQ7rU53oqUeV3IStuyOg/http%3A%2F%2Fmed.stanford.edu%2Fbsl.html%28415%29
 446 - 1596___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] ln: failed to create symbolic link 'file': Operation not supported error

2023-08-11 Thread fsbuild

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 symbolic links and so you need to set SUBJECTS_DIR to point to 
path on a Linux file system. I am not aware of linux OS file systems that 
do not support symbolic links.
- R.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Installation tensorflow: protobuf requires Python '>=3.7' but the running Python is 3.6.8

2023-08-11 Thread fsbuild

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 
installed. You can download that and other releases 
from,https://secure-web.cisco.com/1W23QRgkV4lyrjm7TGpfUuJAucD3HfZxXV6cIIM0at6mOX1kLmDTf4M5mIfEG0Mfb_oxQEBpNNV520ph3XBTNdPvxccVI4NNDfmmiChg-hVbawzdUfVVSqyzjB1VvNUDFjkh_m4XXwXdNJdm0NIVSeGQxX60q1PjXHdMMeAPfBiRpS1nfHQLSNujMvIWyoxmFW94HLsFkUr5d2HOLn950v5uAIIHj3YnjLnT5QRl-oou2sZ0H1Jt6780qv_mHWpfF-cjdEVppe1LsgOhUgmnFkKsOVwuyx9Y036BEgjYi0XukiY1I8QqxfabxsunGQ23Iq6FHGrZSa4dZKA6xcczgLQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
We recommend using a release build since those are more thoroughly tested and 
expected to be more stable compared to the development builds (e.g., what you 
listed). But if you need to use something that can only be found in the 
latest development builds, those can be downloaded via the link below. 
The tensorflow version has been updated to 2.13 in development 
builds.https://secure-web.cisco.com/1WgPel729y72zSVXgE1wFN5HV9jv9DpJYQXKCX3e8Iu3y_--pdjDUjT15H8UsELx_5EojWuo_wc3dyLR5zwo1VnXuCzNUSc_yMw-tT66Brn9xJCqVzViUUrKpiNIvhUabXcJ6sqruS3DUArcgcMY_6CCC9WFGt1I_Bg65WPU7EQaSljvkcbig5uIuO7S8kgcCuMKkIchl8meSz9_GKCZ-SDjuxQyApj1H5H40rC2-51n4EdbsqBRhhJtA73facjpHZZIlMf9qljsFDovxsX9C0-PWUrtVj_GX7UP1fSv9oRQCy1uERt_lJx6BB6AOO_TpvLxUqykwld3C-gqhrmtwQg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
The freesurfer builds/releases are tested with the accompanying fspython 
distribution and setup to not encourage modifying that tested setup.  
Since “fspython” is independent of finding “python” in your PATH, then after 
you source the freesurfer environment setup script, I believe it is possible to 
change what python gets run. If you really need to do that, we can 
follow up with you.
- R.


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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] recon-all-clinical out of memory error

2023-08-10 Thread fsbuild

External Email - Use Caution

Hello Matthew,
Thanks for this info.
If it is not too much work, just wondering if you could make a rough estimate 
or compute an average for the *total*memory* in use = (size of physical RAM in 
use by synthseg + size of all swap files resident on disk used by synthseg).
- R.
On Aug 10, 2023, at 16:08, Matthew Lynch matthewl...@gmail.com 
wrote:External Email - Use 
CautionHere is some additional 
follow up. I was able to get recon-all-clinical working in Ubuntu in WSL 
on a 16 Gb machine by increasing the swap and memory allowed in WSL. This 
is done through the .wslconfigfile which is located in the %USERPROFILE% 
folder (e.g. C:\Users\username\). I had to specify a swap size of 32 Gb 
and also specify that WSL is allowed to use 32 Gb (even though the system only 
has 16 Gb -- it will use swap space).Here is the .wslconfigfile I 
used:-[wsl2]# Limits VM memory to use no more than x GB, this can be set as 
whole numbers using GB or MB# This must be set to 32 Gb or so to 
accomodaterecon-all-clinical# If you set a 32 Gb swap but not 32 Gb 
memory allowance, WSL will stop at the memory limit and not use 
swapmemory=32GB# Sets amount of swap storage space to 8GB, default is 25% 
of available RAMswap=32GB# Sets swapfile path location, default is 
%USERPROFILE%\AppData\Local\Temp\swap.vhdx# I believe the double backslash is 
necessaryswapfile=P:\\Users\\username\\WSL\\wsl-swap.vhdx--For information 
on the .wslconfigfile, see:MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1qV7qOd8MV8Me_H9OrBCSVXR30wzEoGDkBeHd3EGrM14KqAV3QgSA3NPSYDCQmZEjI3IBScWH0I4l3nd8okmiZxGDigkkrYLyO8vmtch63i9fBH9ADb6hgH46SuT2KDYJspHszp9mhrrl0AMgFv5b1aEUW-VSCZ5X5JL69gRnhCNObH2-vbK7kUXnwAoGnffh0nYmeZQ5Re955E7SWL6oJgkZwZaIyX5xF1dwo2Nud50cb69HJdnhAqFYounJ-eTXA4LdozmcTGz5xfnVs77f1JZNiDIvS7xIoHFrG8ttVhPjrCp84LTSa2LvsDKU4eXHgYCPpzg2pX6gA5WC_PsqWA/https%3A%2F%2Flearn.microsoft.com%2Fen-us%2Fwindows%2Fwsl%2Fwsl-configOn
 Sat, Jul 29, 2023 at 6:27 AM Matthew Lynch matthewl...@gmail.com 
wrote:I was able to get recon-all-clinical working with 16 Gb computer.I 
thought the problem might be Windows hogging memory, so I created a live 
persistent USB install of lubuntu, using lubuntu 22 as a low resource distro in 
order to minimize memory usage, and installed freesurfer 7.4.0. Even with 
initial memory usage on 1Gb on lubuntu, synthseg still failed with out of 
memory error with 8 Gb swap file. I watched the swap memory fill up and 
then process was killed.I added 16Gb swap using the following instructions, for 
a total swap space of 24 Gb+ 16 Gb memory:MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1eJ0r45kveGk81B9YYbQBd38RPcxAhW6yy1xCpY2JgWABNj1jDLYcbEOyK_mTjZs1jNOU9o8FFfx9J2BZHUQVHx5x-vTaCnVyovnc-nEXs5V3qZ30_38Dg0p9cACa5w1_lKVc9YpaDJACf-4L0hBx6QzEc11mvu9_ygulTf4O-h7dGx8IpranJ1pdCgtC0BBGATBsIsn1MLnoFMOtCXnGww8HwOTQOzCc1i2H__pxiCkp2tkzZLl_J3MCxPJYhNGotULIBJAy9k6io9RAiTaF41ibYapFMgPVpdzJgvqfgx7fns_Q3LIcKTEtM8lsc1yGd2_Tfr1j6EXuSsoOYb3PWg/https%3A%2F%2Faskubuntu.com%2Fquestions%2F178712%2Fhow-to-increase-swap-spaceThis
 worked.On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch 
matthewl...@gmail.com wrote:I do not have access to a computer with 
more RAM. I can run recon-all with 1mm T1 images without any 
problems. How much RAM would recon-all-clinical be expected to 
need? Does it require less RAM if it uses the GPU instead of 
CPU?On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD 
bfis...@mgh.harvard.edu 
wrote:External Email - Use 
CautionCan you try it on a 
computer with more 
ram?From:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfMatthew LynchSent:Thursday, July 13, 2023 1:55 
PMTo:freesur...@nmr.mgh.harvard.eduSubject:[Freesurfer] 
recon-all-clinical out of memory 
errorExternal Email - Use 
CautionI am having trouble 
running the new recon-all-clinical module. I input 5mm T1 axial DICOM 
images and it fails in SynthSeg with what appears to be an out of memory 
error. I am running FreeSurfer 7.4.0 in WSL with Ubuntu 22 on a computer 
with 16 Gb RAM. Can anyone provide any thoughts on how to correct 
this? Thanks in advance!Here is the 
command:recon-all-clinical.sh ./T1AX5MM/119 fsclin 1here is 
the error output:SynthSeg-robust 2.0using CPU, hiding all 
CUDA_VISIBLE_DEVICESusing 1 threadpredicting 1/1the following problem occured 
with image /mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz :Traceback 
(most recent call last): File 
"/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, in 
predict  post_patch_segmentation, post_patch_parcellation, qc_score 
= net.predict([image, shape_input]) File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 70, in error_handler  raise e.with_traceback(filtered_tb) 
from None File

Re: [Freesurfer] Setup Error with Freesurfer

2023-08-10 Thread fsbuild

External Email - Use Caution

Please send along the link to the video you were using so we can check 
the instructions.
The license is just a single file you obtain by filling out the web form, 
https://secure-web.cisco.com/1hH-N_TseC854TUMeRYHcee_7ls4Btyl5Nn0kU16Lq7t0_WRhRklCJAoLikm5uceIyi1hFacTs4IWobBeVIm4-6bpWg5I8b6mI5Lh4aD55bFlM6e2kRQqBG52zhINJnsJ3vLYIItoe-DIcD54-e_BsVP5ks7-QDYOsss343875Dlse9QsqNHQJdYOvBIZ7BVRpmfq7WQXHeCBByIdAG6cPGw3ssjgclE_LpsTMmW6EQ84lkZ2RWEA1N37mwSsENt4nhoczNWHtCmcnGMAXJKgBBnxCOpiJj9ox8Nb_vyesBvW_BI7QD_CkZV0Y98qL_2amjPSDQx6ztKUT8eMlun4Ig/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
 If the form submission is accepted, the screen will be refreshed and you 
will see a new page saying your license has been sent to the email address you 
specified.
Assuming you are on a Mac reading your email, the default location for 
downloads is your Downloads folder. When you receive that email, you can 
save the license.txt file attached to the email to the default location. 
It will be saved to $HOME/Downloads which you can see in the Finder 
Window when you open your Downloads folder - or from the terminal.
Open a new terminal window and check/setup the license.txt file,
$ cd$ pwd/Users/your userid
$ ls -l Downloads/license.txt-rw-r—r--@ 1 userid group 71 Aug 10 
12:53 Downloads/license..txt  — your userid, group, date, etc. 
will differ
Copy that to your home directory with this command (that is a 
spacefollowed by a period at the end of the line). Or you could 
move it in the Finder.
$ cp -p -f Downloads/license.txt .$ ls -l license.txt-rw-r—r--@ 1 
userid group 71 Aug 10 12:53 license..txt  —— your 
date, etc. output will differ
The above only needs to be done once. To tell freesurfer where to find 
the license file, you can use the environment variable FS_LICENSE. You 
set that in your terminal session with the following (using the default zsh = 
bash compatible shell).
$export FS_LICENSE=$HOME/license.txt
I’ll assume you used one to the .pkg installers we provide for the Mac 
releases, which you can download 
fromhttps://secure-web.cisco.com/1W8vsqGghiuM0oaEbdbdwmxzEGH9qLKdqIXhIsl6GKqRgPDAiv3DM5VbrFqFNW9iZia1ozEciC_PmdyfKLETlphofFIMWl6FUnwvhfyITT6goytCKFLhXZ0cPZxgaCIczfQ6i-8uL6AHiTXDsby0p_44rtHnlbLlnALH0cEW_6KCOzTTmVIh063iej0vam3EvRdGd0u5-8kqUg9HjRixn0qW3n4Jm8w_W0Ca2C_4acipdySKzGtrhF_qd5tyhHRpkoApa1eA2yP8GIcGz7pYlcbPbXylyniPeiGTapgt6xT9tZYFk52gvmoRfGRaeVsPR6WU6emaWdgzd10kxOZ25nQ/https%3A%2F%2Fsurfer.nmr..mgh.harvard.edu%2Ffswiki%2Frel7downloads
 If you downloaded the latest 7..4.1 
installer,https://secure-web.cisco.com/1hOOmlU9howzc7Jw9g6LR2G-cR50zejLhJkRg9HTIpsOaCQLhnYDrWyhgpy3sogHQQVDvZzOXQmW4aO0aZ6Gd_0UMAn9OdDcnBQPZ0PbxomWPbduAWRLVigW68SpbyT_bv85QW9TX7MgLaPEQOalmSP4vq8rU3jWELRSqL1XHAbdr2wMGqnT_Y-l_vu7mx56fzRIjCGowuihctOquP8ZQSqHD86E4QMEPasn44wjSBeMhl9sluP21Ifj4k7BC-XmooeFA9pq6SurIoLJsW26dyI2ABrtLm33kNkKsUOAX8X32yUMiXUlXX1iY2B99MqqzdPUGA4Wl1vxc5LCfy5llxA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg,-
 then freesurfer was installed under /Applications/freesurfer/7.4.1
You can navigate to /Applications/freesurfer in the Finder and see what your 
directory is there under Applications/freesurfer. You will need to add 
what you find under /Applications/freesurfer to substitute for 7.4.1 in the 
example below if you did not install the 7.4.1 .pkg.
Check our setup script is there in the installation$ ls -l 
/Applications/freesurfer/7.4.1/SetUpFreeSurfer.sh-rwxr-xr-x1 
rootwheel1350 Jun 14 
00:09/Applications/freesurfer/7.4.1/SetUpFreeSurfer.sh
Once you have verified the above path to the freesurfer installation, then 
setup the freesurfer environment with,
$export FREESURFER_HOME=/Applications/freesurfer/7.4.1   
— change 7.4.1 etc. to be what you installed if different$source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME/Applications/freesurfer/7.4.1FSFAST_HOME
  /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR  
/Applications/freesurfer/7.4.1/subjectsMNI_DIR  
  /Applications/freesurfer/7.4.1/mni
Try running freeview with no arguments and verify that it opens an empty 
window. It should not crash given FS_LICENSE is set above.
… check freeview is there ..$ which 
freeview/Applications/freesurfer/7.4.1/bin/freeview
$ freeview… should open an empty window … then manually quit freeview …
Try opening one of the example subject volume files
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
… and you should see freeview display some images.
- R.
On Aug 10, 2023, at 12:03, Aqeel Mohamed aqeel.t...@gmail.com 
wrote:External Email - Use 
CautionHello,I am a new 
Freesurfer user and am currently struggling to run the freeview software on my 
MacBook Pro Ventura 13.5 OSX.I was following the step-by-step guide video on 
the Freesurfer wiki, but when

Re: [Freesurfer] Use freeview to visualize white and pial surface

2023-08-08 Thread fsbuild

External Email - Use Caution

I could be wrong, but maybe that error is a function of what code path is
being executed, the order of operations to render the graphics, etc. It
may not be as straightforward as either all images are going to work or none
are going to work.
I would try to test on a known/supported system. If you still get the
same errors, then that would help us reproduce it on the systems we have.
- R.

On Aug 8, 2023, at 22:42, DS zky...@126.com
wrote:External Email - Use
CautionHi expert,Thanks for
discussing it. I really appreciate it. That's very helpful. I have forwarded
this message to admin, so that he will install it. But, I have another
question. Before I visualize these images, I previously successfully loaded
lh.white and lh.pial from another subject. If our system is not compatible with
Freeview, why can I show these images from other subjects? Technically, under
the current system, Freeview would not have worked with any images. Do you have
any thoughts? Thank you so much.PS. I agree with your suggestions. We recently
moved fromRHEL 8 toRHEL 9, we have discardedRHEL 8. So, I
guess that's why I met these issues.At 2023-08-09 10:21:46, "fsbuild"
fsbu...@contbay.com
wrote:External Email - Use
CautionThank you for posting
that output. It shows you are running RHEL or Red Hat Enterprise Linux
9.1 (or the officially supported release downstream from CentOS9). That
explains why your version of mesa packages is rev 22.So your best option is to
try installing the 7.4.1 CentOS8 Stream
installer,https://secure-web.cisco.com/142cnesLA-45N-BegLaDTx7pgSNN6br6URDohmLiZMSgsrfzEfa79RqfL6SnuLw9WoJjAeGGujPuT7JYf5mNNXTV-xOzV-DqHUDD5RCr3es5FGacccgKrIVuhc1WiFWx7ANXcGmvRYO59IDT1sZCsijD34nzoDxNwjGbVsAXQiwRs0h-vxi5g15fhef4fyMSExmhRpvKM_TKU5_txLv_PIr8-exZaAKHsfWBdWO9uwHUIPRjl1JUNxk7uBPVm-yaOKtrOpaFhFC0Vx1eXE8eT508hgn_00T0vzP_BDnLmXIMWwjMVBsljYJd2lyw7Ejjr4bQKnCNG53eeQ_phXccPlw/https%3A%2F%2Fsurfer.nmr.mgh..harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-CentOS8-7.4.1-1.x86_64.rpm,
e.g., via,$ sudo yum install ./freesurfer-CentOS8-7.4.1-1.x86_64.rpmAfter a
successful install, you would set FREESURFER_HOME to
/usr/local/freesurfer/7.4.1-1 and then source the freesurfer setup script under
that directory.While it may install just fine, there is no guarantee everything
is going to work correctly with the newer versions of system libraries in RHEL
9. We have not tested on and currently do not officially support
freesurfer running on RHEL 9/CentOS9 Stream.If you continue to have issues, you
might want to inquire to your system administrators if a RHEL 8 or Ubuntu 22
machine is available to run freesurfer on. Barring that, you could create
and run a VM (virtual machine) or container to host one of the linux OS’s we
have installers for under that download link
(https://secure-web.cisco.com/1X9AQaZtJeadUY-H3cja_TNqCr6QrBvjw4KkCn4svX1XWGAQsCKVat5kT1COo4pwScvia_GbE82kCt1RhcgGUIMk254SNsD4cMiA38OHfX-k_DbdCbbaFEGuLXsXEabyPuxOf1db61-SQNLc9mZu_Mx6I3v8429PuRxAj5BnP9P_PynV0m7S6T3q8ttWUkSjVKgo5wN27AOdGPjKQrWH8UQlmCcrAMp2wv9BH2O63MhWZA2An4p6a7H-a91TLc0lIb07JF-QTf88IKNR8Y_F-DHVISl9L4FnF3rgh9_6NKxS4DqaSPbalWMsjAY0jJcaRQLTgiYhhO-r259RjF73hTw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads).
The supported OS's are CentOS 8, 7 and Ubuntu 22, 20, 18. You could host
that VM or container on top of Red Hat Enterprise Linux 9.1 or most any other
OS.RHEL has its own built in virtualization software called “qemu”. You
system, administrators may already have qemu setup and working on your RHEL 9.1
machine. If so, you could ask them to setup qemu to run RHEL 8 and then
install freesurfer-CentOS8-7.4.1-1.x86_64.rpm in that VM.Please note that it is
easier to run Freeview in a VM compared to a container in order to view
images.- R.On Aug 8, 2023, at 20:38, DS zky...@126.com
wrote:External Email - Use
CautionHi expert,Thanks for
your reply. I have contacted our admin to fix the installer issue, as our admin
installed this FreeSurfer. But, at the same time, I try to get the version of
our system by running "cat /etc/os-release", i.e.NAME="Red Hat Enterprise
Linux"VERSION="9.1
(Plow)"ID="rhel"ID_LIKE="fedora"VERSION_ID="9.1"PLATFORM_ID="platform:el9"PRETTY_NAME="Red
Hat Enterprise Linux 9.1
(Plow)"ANSI_COLOR="0;31"LOGO="fedora-logo-icon"CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"HOME_URL="https://secure-web.cisco.com/1ovUBbgYTLCz1nbzkl9474qBgKoMJVy6A6BR-gSZxobrLQ_R6we7_M4qCeJ0Jd3zyjMIOqgp3qbJuwlaCqRo7x_Tfbq4wveSynoRNHxir4YSSFQ65oU_yuVobT4Ge0oA-l-qJW0etVIzOXcn8b5hBFsNu1f2u2JH6ixjlLZzBFIRsRiUpAPkmdOOWjcDB1g2N20l3FnnaOZavct1pX0aI2bV-utnTAC4-YDAEoqXBD1tOUbAtraUOH6h4rPLKPq324zpus0qkI_hMhyr-2pKL2dzNPqapn24Uh4SVP4i3jd26lGotlPV663TvpI701mPDvQVmVhbS7yd6jGndRKDf_w/https%3A%2F%2Fwww.redhat.com%2F"DOCUMENTA

Re: [Freesurfer] Use freeview to visualize white and pial surface

2023-08-08 Thread fsbuild

External Email - Use Caution

Thank
 you for posting that output. It shows you are running RHEL or Red Hat 
Enterprise Linux 9.1 (or the officially supported release downstream 
from CentOS9). That explains why your version of mesa packages is rev 
22.
So
 your best option is to try installing the 7.4.1 CentOS8 Stream 
installer,https://secure-web.cisco.com/13Yh2Zpq9lfBw2Tx4PthJHddojpo9KYHh0CoKByhmEOoIUBDZ6d6J1J1adZQ2ZW57P7cOi0BS0_rTCE_qkWN22jMm1XH5iswu0qJhv-9A6hj3vGhsGGYqk1aPuUOlnZBAy7I71p90AfenWKtNxsWZC40I-F5EW-NIfywhofMoiUOByPesIGrKzSdmiuGxLPRevNK_XJnp_OK0U1peozva8SDfyJPXQMpCZaxVG6SsMci6ON2rPYwBU6GhRKa7aDazzVX7sEg7ugabHE3g0ESWBqS0wiYSTRO9X7ltYrArvvG55I2MqDQ1HfWN_5EW_6WG/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-CentOS8-7.4.1-1.x86_64.rpm,
 e.g., via,
$ sudo yum install ./freesurfer-CentOS8-7.4.1-1.x86_64.rpm
After
 a successful install, you would set FREESURFER_HOME to 
/usr/local/freesurfer/7.4.1-1 and then source the freesurfer setup 
script under that directory.
While
 it may install just fine, there is no guarantee everything is going to 
work correctly with the newer versions of system libraries in RHEL 9. 
We have not tested on and currently do not officially support 
freesurfer running on RHEL 9/CentOS9 Stream.
If
 you continue to have issues, you might want to inquire to your system 
administrators if a RHEL 8 or Ubuntu 22 machine is available to run 
freesurfer on. Barring that, you could create and run a VM
 (virtual machine) or container to host one of the linux OS’s we have 
installers for under that download link 
(https://secure-web.cisco.com/1NdQZ9ARlP_lmvayOFl13KH1foHnEmo3DsGCA8LmwoJi1bvQ4nb6thEKJe36SmFFJ_Gnc-rMzxaLDA1_8-SikL92Cyuu5G2U-AbyykiVBY9gKGGJHb3IbG1oY7b3EfGZopSjYv0P23CmZ22YDr6-aSLS_8mgnP1MWKYXltAEG0EjqBzwdBt6mu271p2rP74vql420P8Lv6jsEo7iqBQR_Tjb5G6qA5xYnSTy4z6nA7DX6pcAIPCwmVkp7gZNMGC3IR7C7tUfiJfRf_M2mLpFEMdsgu4XGgxiuNdtH2Zseo3CyHeRGltfLM7tEk-iOq0KL/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads).
 The 
supported OS's are CentOS 8, 7 and Ubuntu 22, 20, 18. You could host 
that VM or container on top of Red Hat Enterprise Linux 9.1 or most any 
other OS.
RHEL
 has its own built in virtualization software called “qemu”. You 
system, administrators may already have qemu setup and working on your 
RHEL 9.1 machine. If so, you could ask them to setup qemu to run RHEL 8
 and then install freesurfer-CentOS8-7.4.1-1.x86_64.rpm in that VM.
Please note that it is easier to run Freeview in a VM compared to a container 
in order to view images.
- R.
On Aug 8, 2023, at 20:38, DS zky...@126..com 
wrote:External Email - Use 
CautionHi expert,Thanks for 
your reply. I have contacted our admin to fix the installer issue, as our admin 
installed this FreeSurfer. But, at the same time, I try to get the version of 
our system by running "cat /etc/os-release", i.e.NAME="Red Hat Enterprise 
Linux"VERSION="9.1 
(Plow)"ID="rhel"ID_LIKE="fedora"VERSION_ID="9.1"PLATFORM_ID="platform:el9"PRETTY_NAME="Red
 Hat Enterprise Linux 9.1 
(Plow)"ANSI_COLOR="0;31"LOGO="fedora-logo-icon"CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"HOME_URL="https://secure-web.cisco.com/1XApM7qkseMu45J2kbm9Wvmirf5GLxoeehLie2RNWvR3CqvsY_wft0bg62NiNyPK-ZVJDwIxW-ztrqXrJla6XhBwtITwdWvgwr9raojb2B1W_jW0AXmI8D_VuyVf20AsQH-EkshSic4alkGRk_TRWicLgWGiKhkP1TlGnkok-J3JKKxHbqzkm6ZawlfErwuMdz_OwtSxPyCrzsirLtaOYzhehv9lulK0wddekFsWOPyvwbzfGktjjnXkLsFbM7_VhsMVgPwtzlwCyAPLpQbcoNWdlvJRnTj39M1qBtOLbYXM-DLGN-bm4_Tv46ILX5BDa/https%3A%2F%2Fwww.redhat..com%2F"DOCUMENTATION_URL="https://secure-web.cisco.com/1KVP29f2nVxu6VGypY0-4fnWlTeue0RkLc6RYfAmeCs1rW6qhbahUvXiVBwXLjJNVlHY2-9kwIwAR_QeLeNv4a_pF_g57eCOeiQeQoTia3S6JuQcdTRbNw8Smkon6stvwCdNWwTeh-F6IkRNWKZLGm1ZwLZPsQ8pasPrK6-fheJOm5JpgNDfncyba0RYCTB84l_DSQoz4Avuuq4YTYQul8ZVbf94dufzXMiXSIGSVwlwndpHgjObnJ-4uzfnOf3pMP9pHbLwJJVObo51-MbBWINqiFaTJifc334gWlQC_y3BvuKR8dPQb-5qI7MMeGITl/https%3A%2F%2Faccess.redhat.com%2Fdocumentation%2Fred_hat_enterprise_linux%2F9%2F"BUG_REPORT_URL="https://secure-web.cisco.com/1F1bSssRfJjrdP0pSKPbHm6DQ0qWFXYpO2E6CYe7cDWR93eXXem_LtHPnhSgSBb5VfRyURR06iny51MuOsA4SCqchhGotwNZkZ0I5Qe_MppJdPcH1yYpMuLadpx5et-qAV64cOtc72D_ZzLYSgw0fPs-LaG3cuT6YRlHlJucZthGD6TYzDlQLtGRqki7JBwZTUlt29MuUPemkkWIQkjgRD1fw0882FrfuiB8k3QZMpVALww5fV69hCLzjvKekpSkkGKHJm_KfynOmM4A8ex2VzCHyVIlkWK_s81L2QBcsB8qz8JoI_UnRxmg7iLEVAM59/https%3A%2F%2Fbugzilla.redhat.com%2F"REDHAT_BUGZILLA_PRODUCT="Red
 Hat Enterprise Linux 
9"REDHAT_BUGZILLA_PRODUCT_VERSION=9.1REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise 
Linux"REDHAT_SUPPORT_PRODUCT_VERSION="9.1"Once I have any updates, I will let 
you know. Thanks.At 2023-08-09 02:58:47, "fsbuild" fsbu...@contbay.com 
wrote:External Email - Use 
CautionThe output in your 
previous email lists an error from a mesa version 22 header file f

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