Re: [Freesurfer] I've tried what to do. But, still freeview doesn't work

You’re running MacOS Sonoma (14.X) which was not out when 7.3.2 was released in 2022, i.e., 7.3.2 was not tested on anything newer than MacOS 12.X as listed on the download page under https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads. 7.3.2 release Linux OS: CentOS7, CentOS8, Ubuntu18,

Re: [Freesurfer] recon-all nu_correct error

In our cluster testing, we allocate at least 16G to each recon-all command (see below). We run about 150 of those commands in parallel on the cluster during off-peak usage and it takes about 12 hours for them to complete. $ jobsubmit -A fsm -p basic -t 1-00:00:00 -m 16G "recon-all -all -s

Re: [Freesurfer] Freeview on WSL in Windows 10

Hello Monica, The login page you display is not accessible to the public. We have information about how to get started with WSL on the public wiki pages, e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wslWe talk about installing WSL version 1 and WSL version 2, though it reads like

[Freesurfer] Freesurfer Ubuntu VM updated

The Freesurfer Ubuntu VM has been updated: - Freesurfer 7.2.0 release from July 2021 is installed - download image size now ~8G - expanded image size now ~29G - documentation updated for installing VirtualBox and running the VM image - not much should be needed to do in order to start running

Re: [Freesurfer] Freesurfer commands not found - unable to install

Hello Ashesh, You need someone with admin or root privileges to install tcsh (and I would do csh as well) shells on your machine so those scripts can run, i.e. $ sudo apt-get install tcsh $ sudo apt-get install csh On Oct 25, 2018, at 13:35, Thaker, Ashesh A

Re: [Freesurfer] Difference between 6.0.1 and 6.0.0

Hello Haakon, I don’t there are significant functionality changes in the 6.0.1 patch release. i think there are however changes to fix some run time errors with respect to system libraries found/used on the system running Freesurfer. Someone else who mentors the help list might chime in, but

Re: [Freesurfer] QAtools for Freesurfer version6?

Hello Seonjoo, Could you send along a link to what you ran/tweaked for “QA tools” on freesurfer ? - rob On Oct 4, 2018, at 8:31 PM, Lee, Seonjoo mailto:sl3...@cumc.columbia.edu>> wrote: External Email - Use Caution I tired to use QA tools for freesurfer version6, but did not have

Re: [Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

Sure - or if you want to let us know your office number, I could stop by as well. - rob > On Oct 4, 2018, at 12:10 PM, Vasile, Eduard wrote: > > Hi Rob, > > I have matlab installed on my laptop. I am based in South Central, 149, is > there anywhere I can come to talk to you guys? I am in

Re: [Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. Re: Error during decompression of DICOM JPEG compressed > series (Greve, Douglas N.,Ph.D.) > 2. Re: Error dur

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

It may be complaining about >& for redirection. Try using 2>&1 instead. On Oct 2, 2018, at 4:56 AM, k3...@free.fr wrote: sh: 1: Syntax error: Bad fd number ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Dead Links to 3rd Party Libraries

Hello Joseph, Try this link for the 3rd party libs (to use with the cmake build) http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/ - rob On Sep 20, 2018, at 8:39 PM, Moon, Joseph Young-Joon mailto:moo...@llnl.gov>> wrote: External Email - Use Caution Hi, I’m trying

Re: [Freesurfer] MacOS high Sierra, freesurfer development versiyon build problem! tar.gz

Hello Emre, In the terminal window, try at the $ prompt, $ tar zxpf freesurfer-darwin-OSX-ElCapitan-dev.tar.gz On Sep 14, 2018, at 8:12 PM, emre mailto:z...@hotmail.com>> wrote: tar.gz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] LGI without Matlab license?

The Mathworks offers runtime distribution that contains the libraries you can build your code against w/o needing a Matlab license; you just cannot re-distirbute the files from the distribution w/o permission from The Mathworks. I’ve used it to build code that links against libmat etc. You

Re: [Freesurfer] Unable to copy the license.txt file into $FREESURFER_HOME

Sent you a reply to your direct email, as attachment I wanted to send is too large for list. - rob On Aug 24, 2018, at 12:40 PM, Tsz Wai (Bentley) Lo mailto:lo...@smh.ca>> wrote: External Email - Use Caution Hi FreeSurfer Developers, I am attempting to copy my license.txt into

Re: [Freesurfer] Stats2table_bash.sh script

Hello K, If you type $ asegstats2table --help you will see that you can specify subjects on the command line as, e.g., for bert as —subjects bert or apparently -s bert It looks like the subjects option expects the name for at least one subjects (data), but the help output says you can list

Re: [Freesurfer] Stats2table_bash.sh script

Hello K, If you type $ asegstats2table --help you will see that you can specify subjects on the command line as, e.g., for bert as —subjects bert or apparently -s bert It looks like the subjects option expects the name for at least one subjects (data), but the help output says you can list

Re: [Freesurfer] Untar and sh files in dev version

Fri, Aug 10, 2018 at 7:52 PM, Dicamillo, Robert mailto:rdicami...@mgh.harvard.edu>> wrote: Hello Schumman, Try the following command on the tar archive (cut and paste it if you like) $ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz and then take a look at the files. - Rob On Aug 10,

Re: [Freesurfer] Untar and sh files in dev version

Hello Schumman, Try the following command on the tar archive (cut and paste it if you like) $ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz and then take a look at the files. - Rob On Aug 10, 2018, at 10:25 PM, Schumman Resonance mailto:schumm...@gmail.com>> wrote: External

Re: [Freesurfer] A Help Request for Freesurfer Installing

… I forgot to add that the build process listed on the help pages should basically work on Ubuntu, if you want to try building it form source; the instructions there list Ubuntu 14. http://freesurfer.net/fswiki/freesurfer_linux_developers_page - rob On Jul 18, 2018, at 2:46 AM, Maedeh

Re: [Freesurfer] A Help Request for Freesurfer Installing

Hello Maedeh, I recall building Freesurfer on Ubuntu 16.04, but I don’t have access to that machine right now. I will check to see if I have binaries I can send along, and if so, you could try running them on Ubuntu 18. - rob On Jul 18, 2018, at 2:46 AM, Maedeh Khalilian

Re: [Freesurfer] lazy symbol binding errors

Hello David, Please try downloading the following archive, unzip it, and follow the instructions in the README to update the files that have the lazy symbol issue. https://drive.google.com/open?id=1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR -rob On Jul 12, 2018, at 4:48 AM, Davide Momi

Re: [Freesurfer] lazy symbol binding errors

Hello David, Please try downloading the following archive, unzip it, and follow the instructions in the README to update the files that have the lazy symbol issue. https://drive.google.com/open?id=1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR -rob On Jul 12, 2018, at 4:48 AM, Davide Momi

Re: [Freesurfer] recon-all fatal error

Hello Daniel, The docker container may not be properly supporting symbolic links, i.e., apparently you can write files inside the container, but in your log that error is the first instance of the ln command. Could you try running it w/o using a container and see if it gets past the ln

Re: [Freesurfer] recon-all fatal error

Hello Daniel, The docker container may not be properly supporting symbolic links, i.e., apparently you can write files inside the container, but in your log that error is the first instance of the ln command. Could you try running it w/o using a container and see if it gets past the ln

Re: [Freesurfer] questions about freeview quit unexpectly

surfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Jun 26 16:31:39 Jiang-Shizes-MacBook-Pro com.apple.xpc.launchd[1] (com.yourcompany.Freeview.19232[38452]): Service exited with abnormal code: 59 At 2018-06-27 02:33:31, "Dicami

Re: [Freesurfer] questions about freeview quit unexpectly

edback. There is no notification pop up. The GUI of freeview just quit. I am not sure what was wrong with this. DO you have any ideas about this? Thank you . Best wishes Shize At 2018-06-27 00:54:45, "Dicamillo, Robert" mailto:rdicami...@mgh.harvard.edu>> wrote: Hello Shize, Did you s

Re: [Freesurfer] questions about freeview quit unexpectly

Hello Shize, Did you see the Finder bring up a window with a notification that Freeview quit unexpectedly, with some choices to click on for “ignore”, “report”, or “reopen” Freeview?If so, it could help if you select report, cut and paste (or take a screenshot) of the first page of the

Re: [Freesurfer] Recon-all exited with errors

I followed up with Ryan off the list one this one yesterday, i.e., he tried one of the later dev builds which fixes those lib issues. I think recon-all runs for him now w/o the lib errors, but he is getting a non-zero exit from something else. - rob On Jun 19, 2018, at 11:00 AM, Hoopes,

Re: [Freesurfer] crypt_gkey = (null)

mental version? Also both version are the CentOS 6 build. On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert mailto:rdicami...@mgh.harvard.edu>> wrote: Hello Aaron, You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then i

Re: [Freesurfer] crypt_gkey = (null)

Hello Aaron, You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then it would mean encryption is in use (which can be an issue with FreeSurfer). $ cat /proc/sys/crypto/fips_enabled If it returns zero, it could be an issue with a

Re: [Freesurfer] Installing different versions of FreeSurfer on Same computer (error)

Hello Paul, By default, the mac installer will install freesurfer under /Applications/freesurfer. There is an option to change the install location however, see the screenshots under, https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall It sounds like you ran the 5.3 installer - did not use

Re: [Freesurfer] Errors are occurring after FreeSurfer Installation

Hello Stefano, It looks like you do not have permission to write to /usr/local/freesurfer/subjects/bert If multiple people will be using the data there at the same time, then it is probably not a good idea for everyone not to be writing to the same location. An alternative is to set the

Re: [Freesurfer] Trouble getting git-annex files

On May 3, 2018, at 1:35 PM, Dicamillo, Robert <rdicami...@mgh.harvard.edu<mailto:rdicami...@mgh.harvard.edu>> wrote: Hello Ruy, The -r flag to will cause the build to skip some dependencies, e.g., sometimes makefiles will rebuild the world when you don’t need them to, so if you are

Re: [Freesurfer] Trouble getting git-annex files

that is part of Tracula. The main source file is ./freesurfer/trc/dmri_train.cxx. I don’t mind building the whole tree if necessary, but I haven’t been able to do so either. Do you know what the -r flag to make does? Thank you, Ruy On May 2, 2018, at 6:51 PM, Dicamillo, Robert <rdicami...@

Re: [Freesurfer] Trouble getting git-annex files

Hello Ruy, Do you mean the mri_train binary that gets built under ./freesurfer/mri_train ? (I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a ./freesurfer/dmri_train). Things are not necessarily setup so you can cd to ./freesurfer/ and just build what is there in

Re: [Freesurfer] Freesurfer and crypt

("/home/bennet/tmp/freesurfer/sample-001.mgz", O_RDONLY) = 3 I do not believe that this is something that can be 'whitelisted', as this is set in the Linux kernel at boot time. Thanks,-- bennet On Thu, Apr 12, 2018 at 11:29 AM, Dicamillo, Robert <rdicami...@mgh.harvard.edu<mailto:rdicami

Re: [Freesurfer] mri_deface keeps seg faulting

Can you ls /usr/local/freesurfer/stable6/bin If so, you could put that at the start of your path to get the release 6 binaries. -rob On Apr 17, 2018, at 11:39 AM, Warner, Graham Cary > wrote: Hi, I'm trying to deface an MEMPRAGE dataset

Re: [Freesurfer] Freesurfer and crypt

Hello Bennet, Maybe someone else can chime in on this, as I have not worked on a system with FIPS, but perhaps there is a way for the FIPS administrator to white list all the Freesurfer binaries (and the license file), as security exempt. I know some Enterprise/business applications like

Re: [Freesurfer] -make all error

Hello Carissa, There have been some changes to the files related to the “—make all” option. You can try downloading an updated version of the recon-all.makefile from the list of files under, ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/ and replace the

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

If you are running on Ubuntu, I have a build of the freesurfer source checked out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system using gcc 4.9. However, I did not have the test data to run tests, so I must add the disclaimer that the binaries have not gone thru the

Re: [Freesurfer] Building from source #3 -- dynamic binding

Hello Yaroslav, I believe there is already an option that can be set at configure time to build dynamical;ly, though I have not tried it. e.g., maybe it causes the libraries that Freesurfer builds internally to be built as shared instead of static. However, at least in out nightly builds, the

Re: [Freesurfer] Problem running mri_convert

Hello Jay, I think this undefined reference has been fixed in the builds of the freesurfer source for the Mac since the 6.0.0 release. I am just not sure how to get an update to you. But stay tuned. - rob On Mar 22, 2018, at 10:02 PM, Jay Edelman