Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Freesurfer 7.1.1: locale bug and workaround
by fsbuild 13 Oct '20

13 Oct '20

External Email - Use Caution Hello Alex, After you have set FREESURFER_HOME and source’d the shell setup script, please try running the binaries you suspect directly from the command line, e.g., with —help option, and see if you get the same error, e.g. $ mri_ca_label —help<help output deleted> $ mri_ca_normalize —help<help output deleted> It would also be interesting to know what locales have been setup/installed on your machine from the output of the locale command, which might display something like, $ locale -aC C.utf8 en_AU en_AU.utf8en_BW en_BW.utf8 en_CA en_CA.utf8 en_DK en_DK.utf8 en_GB en_GB.iso885915 en_GB.utf8… many other countries …POSIX - R. On Oct 12, 2020, at 06:58, Alex Craven <alex.craven(a)uib.no> wrote:        External Email - Use Caution        Greetings,Several binaries in the Freesurfer 7.1.1 release appear to ignore (or misinterpret) system-wide locale settings. This causes a large number of errors to be reported throughout the recon process, particularly on startup. The commands appear to complete successfully despite the reported errors.The errors are displayed as:error: No such file or directoryerror: Could not set locale...repeated dozens of times.A probably not exhaustive list of affected components:mri_ca_labelmri_ca_normalizemri_ca_registermri_convertmri_em_registermri_remove_neckmris_calcstrace output for one such command suggests that it's attempting to load the en_US locale, on a system where that is locale is not configured, and where system-wide settings indicate the something else should be used (eg: LANG=en_AU.UTF-8)openat(AT_FDCWD, "/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 3fstat(3, {st_mode=S_IFREG|0644, st_size=8896640, ...}) = 0mmap(NULL, 8896640, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f727c65d000close(3)                                = 0openat(AT_FDCWD, "/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 3fstat(3, {st_mode=S_IFREG|0644, st_size=2995, ...}) = 0read(3, "# Locale name alias data base.\n#"..., 4096) = 2995read(3, "", 4096)                       = 0close(3)                                = 0openat(AT_FDCWD, "/usr/lib/locale/en_US/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)openat(AT_FDCWD, "/usr/lib/locale/en/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)openat(AT_FDCWD, "/usr/lib/locale/en_US.utf8/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)openat(AT_FDCWD, "/usr/lib/locale/en.utf8/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)write(2, "error: ", 7error: )                  = 7write(2, "No such file or directory", 25No such file or directory) = 25write(2, "\n", 1)                       = 1write(2, "error: ", 7error: )                  = 7write(2, "Could not set locale\0", 21Could not set locale^@)  = 21write(2, "\n", 1)                       = 1System info:Debian 9.1.0 base system, using freesurfer-linux-centos7_x86_64-7.1.1Linux fmri-proc1 4.9.110-arc #1 SMP Tue Aug 14 17:45:49 CEST 2018 x86_64 GNU/LinuxWorkaround:Generating the en_US.UTF-8 locale, by adding/uncommenting the line "en_US.UTF-8 UTF-8" in /etc/locale..gen and re-running locale-gen effectively hides this problem.Best regards,Alex._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Installing Freesurfer
by fsbuild 13 Oct '20

13 Oct '20

External Email - Use Caution ... Sorry, I should have said - if you expanded the tar archive under $HOME/Downloads, then $ ls $HOME/Downloads/freesurfer … would show you something like … ASegStatsLUT.txt  diffusion/              FreeSurferEnv.sh  mni@                  SetUpFreeSurfer.sh*            subjects/average/          docs/                   fsafd/            python/               Simple_surface_labels2005.txt  tkmeditParcColorsCMAbin/              etc/                    fsfast/           SegmentNoLUT.txt      Simple_surface_labels2009.txt  trctrain/build-stamp.txt   FreeSurferColorLUT.txt  lib/              sessions/             sources.csh*                   WMParcStatsLUT.txtDefectLUT.txt     FreeSurferEnv.csh       matlab/           SetUpFreeSurfer.csh*  sources..sh* .... and then you would do $ export FREESURER_HOME=$HOME/Downloads/freesurfer … then the same as before ... $ cat $FREESURFER_HOME/SetUpFreeSurfer.sh$ source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. On Oct 13, 2020, at 04:58, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Rio,I’m not sure why the paths you list include "$home/username”.Usually the absolute path listed by the environment variable HOME ends with the subdirectory named with your username.  So your Downloads folder is usually referenced as $HOME/DownloadsIf you expanded the tar archive there, then the command,$ ls $HOME/Downloads… would show you something like ...ASegStatsLUT.txt  diffusion/              FreeSurferEnv.sh  mni@                  SetUpFreeSurfer.sh*            subjects/average/          docs/                   fsafd/            python/               Simple_surface_labels2005.txt  tkmeditParcColorsCMAbin/              etc/                    fsfast/           SegmentNoLUT.txt      Simple_surface_labels2009.txt  trctrain/build-stamp.txt   FreeSurferColorLUT.txt  lib/              sessions/             sources.csh*                   WMParcStatsLUT.txtDefectLUT.txt     FreeSurferEnv.csh       matlab/           SetUpFreeSurfer.csh*  sources.sh*- and you would set FREESURFER_HOME as,$ export FREESURFER_HOME=$HOME/DownloadsIf you have permission to read the SetUpFreeSurfer.sh file, then you should see the file contents echoed to the terminal when you run,$ cat $FREESURFER_HOME/SetUpFreeSurfer.sh- and then it should work to do, e.g., in bash shell,$ source $FREESURFER_HOME/SetUpFreeSurfer.sh- R..On Oct 12, 2020, at 22:57, Rio Yamaguchi <ryamaguchi..c(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer team,I'm attempting to install freesurfer and am encountering a few problems.When I type in the command:$ source $FREESURFER_HOME/SetUpFreeSurfer.shIt comes back as saying:no such file or directory foundI have done the two previous commands as specified;$ export FREESURFER_HOME=$home/username/Downloads/freesurfer [which is the correct path to the freesurfer directory]$ export SUBJECTS_DIR=$FREESURFER_HOME/subjectsAlso, if I "ls" the files in $home/username/Downloads/freesurferthere is a file "SetUpFreeSurfer.sh" thus I am unsure why this error occurs.I've searched the list and whilst some similar errors have been reported. I could not resolve my issue. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1..1.tar.gz2) Platform: Ubuntu 18.04 Any help would be greatly appreciated.Thank you!Kind regards,Rio_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Installing Freesurfer
by fsbuild 13 Oct '20

13 Oct '20

External Email - Use Caution Hello Rio, I’m not sure why the paths you list include "$home/username”. Usually the absolute path listed by the environment variable HOME ends with the subdirectory named with your username.  So your Downloads folder is usually referenced as $HOME/Downloads If you expanded the tar archive there, then the command, $ ls $HOME/Downloads … would show you something like ... ASegStatsLUT.txt  diffusion/              FreeSurferEnv.sh  mni@                  SetUpFreeSurfer.sh*            subjects/average/          docs/                   fsafd/            python/               Simple_surface_labels2005.txt  tkmeditParcColorsCMAbin/              etc/                    fsfast/           SegmentNoLUT.txt      Simple_surface_labels2009.txt  trctrain/build-stamp.txt   FreeSurferColorLUT.txt  lib/              sessions/             sources.csh*                   WMParcStatsLUT.txtDefectLUT.txt     FreeSurferEnv.csh       matlab/           SetUpFreeSurfer.csh*  sources.sh* - and you would set FREESURFER_HOME as, $ export FREESURFER_HOME=$HOME/Downloads If you have permission to read the SetUpFreeSurfer.sh file, then you should see the file contents echoed to the terminal when you run, $ cat $FREESURFER_HOME/SetUpFreeSurfer.sh - and then it should work to do, e.g., in bash shell, $ source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. On Oct 12, 2020, at 22:57, Rio Yamaguchi <ryamaguchi.c(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer team,I'm attempting to install freesurfer and am encountering a few problems.When I type in the command:$ source $FREESURFER_HOME/SetUpFreeSurfer.shIt comes back as saying:no such file or directory foundI have done the two previous commands as specified;$ export FREESURFER_HOME=$home/username/Downloads/freesurfer [which is the correct path to the freesurfer directory]$ export SUBJECTS_DIR=$FREESURFER_HOME/subjectsAlso, if I "ls" the files in $home/username/Downloads/freesurferthere is a file "SetUpFreeSurfer.sh" thus I am unsure why this error occurs.I've searched the list and whilst some similar errors have been reported. I could not resolve my issue. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1.tar.gz2) Platform: Ubuntu 18.04 Any help would be greatly appreciated.Thank you!Kind regards,Rio_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Installing Freesurfer
by Rio Yamaguchi 12 Oct '20

12 Oct '20

External Email - Use Caution Dear FreeSurfer team, I'm attempting to install freesurfer and am encountering a few problems. When I type in the command: $ source $FREESURFER_HOME/SetUpFreeSurfer.sh It comes back as saying: *no such file or directory found* I have done the two previous commands as specified; $ export FREESURFER_HOME=$home/username/Downloads/freesurfer [which is the correct path to the freesurfer directory] $ export SUBJECTS_DIR=$FREESURFER_HOME/subjects Also, if I "ls" the files in $home/username/Downloads/freesurfer there is a file "SetUpFreeSurfer.sh" thus I am unsure why this error occurs. I've searched the list and whilst some similar errors have been reported. I could not resolve my issue. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1.tar.gz 2) Platform: Ubuntu 18.04 Any help would be greatly appreciated. Thank you! Kind regards, Rio

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Freesurfer 7.1.1: locale bug and workaround
by Alex Craven 12 Oct '20

12 Oct '20

External Email - Use Caution Greetings, Several binaries in the Freesurfer 7.1.1 release appear to ignore (or misinterpret) system-wide locale settings. This causes a large number of errors to be reported throughout the recon process, particularly on startup. The commands appear to complete successfully despite the reported errors. The errors are displayed as: error: No such file or directory error: Could not set locale ...repeated dozens of times. A probably not exhaustive list of affected components: * mri_ca_label * mri_ca_normalize * mri_ca_register * mri_convert * mri_em_register * mri_remove_neck * mris_calc strace output for one such command suggests that it's attempting to load the en_US locale, on a system where that is locale is not configured, and where system-wide settings indicate the something else should be used (eg: LANG=en_AU.UTF-8) openat(AT_FDCWD, "/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 3 fstat(3, {st_mode=S_IFREG|0644, st_size=8896640, ...}) = 0 mmap(NULL, 8896640, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f727c65d000 close(3) = 0 openat(AT_FDCWD, "/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 3 fstat(3, {st_mode=S_IFREG|0644, st_size=2995, ...}) = 0 read(3, "# Locale name alias data base.\n#"..., 4096) = 2995 read(3, "", 4096) = 0 close(3) = 0 openat(AT_FDCWD, "/usr/lib/locale/en_US/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) openat(AT_FDCWD, "/usr/lib/locale/en/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) openat(AT_FDCWD, "/usr/lib/locale/en_US.utf8/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) openat(AT_FDCWD, "/usr/lib/locale/en.utf8/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) write(2, "error: ", 7error: ) = 7 write(2, "No such file or directory", 25No such file or directory) = 25 write(2, "\n", 1 ) = 1 write(2, "error: ", 7error: ) = 7 write(2, "Could not set locale\0", 21Could not set locale^@) = 21 write(2, "\n", 1 ) = 1 *System info:* Debian 9.1.0 base system, using freesurfer-linux-centos7_x86_64-7.1.1 Linux fmri-proc1 4.9.110-arc #1 SMP Tue Aug 14 17:45:49 CEST 2018 x86_64 GNU/Linux *Workaround:* Generating the en_US.UTF-8 locale, by adding/uncommenting the line "en_US.UTF-8 UTF-8" in /etc/locale.gen and re-running locale-gen effectively hides this problem. Best regards, Alex.

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License Management
by Pawletta, Paul 12 Oct '20

12 Oct '20

External Email - Use Caution Hi, we want to use Freesurfer in our “Virtual Research Environment”, where many users can process their neuroimaging data with prebuilt pipelines. Our question is about the license management for each user. Would it be sufficient to obtain a general license that can be used by all users? - Similar to a central installation of Freesurfer. Thank you, Paul

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question about mri_segment_hypothalamic_subunits
by fsbuild 11 Oct '20

11 Oct '20

External Email - Use Caution Hello Victor, If you used the 7.1.1 installer package, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/…, then it should have installed /Applications/freesurfer/7..1.1 for you.  I believe the same is true for the 7.1.0 installer, i.e., /Applications/freesurfer/7.1.0, and similarly for the 7.0.0 installer.  We set it up that way so the distributions would be separate.  This allows people to switch among/compare the distributions by setting FRESURFER_HOME differently, e.g.,  $ export FREESURFER_HOME=/Applications/freesurfer/7.1.1or$ export FREESURFER_HOME=/Applications/freesurfer/7.1.0etc….. then source’ing the shell setup script for either sh or csh, e.g., for sh$ source $FREESURFER_HOME/SetUpFreeSurfer.sh The installer packages create an uninstall script under each distribution, e.g.,  /Applications/freesurfer/{7.1.1, 7..1.0, 7.0.0}/uninstall.sh.  So if you wanted to start with a clean install you could try running the uninstaller script(s), and then re-install using the .pkg files, e.g.,  to run the 7.1.1 installer, $ sudo /Applications/freesurfer/7.1.1/uninstall.sh  - R. On Oct 8, 2020, at 18:13, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote:Hi Victor,I highly recommend that you keep both installations separate.Cheers,/Eugenio  Juan Eugenio IglesiasSenior research fellowCMIC (UCL), MGH (HMS) and CSAIL (MIT)http://www.jeiglesias.com    From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng@bidmc.harvard.edu>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Date: Thursday, October 8, 2020 at 17:54To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] question about mri_segment_hypothalamic_subunits Hi all,  I installed the most recent dev version of FS7.1, and copied its files over the old FS7.1. I entered sudo mri_segment_hypothalamic_subunits into xquartz, and receive an error:  error: freesurfer has not properly been sourced I am using mac os Catalina 10.15.6. How can I fix this? Victor ZengBeth Israel Deaconess Medical CenterKeshavan Lab-- This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer 5.3.0 recon-all error
by Michele Valotti 09 Oct '20

09 Oct '20

External Email - Use Caution I am using freesurfer 5.3.0 (unfortunately this is the version I have to use) and I am encountering an error in the process. I have attached the recon-all.log file. Any pointers to identify the error would be very helpful, Thank you, Michele

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seed point on the CC and Pons
by Jie Zhao 09 Oct '20

09 Oct '20

External Email - Use Caution Hello Freesurfer Experts I am trying to set the correct seed point to cutting the corpus callosum and pons for a macaque subject. It is aimed to remove the brainstem and cerebellum, right? My command line is : recon-all -s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80 The output result is sucessed without errors, but the wm.mgz still include the brainstem and cerebellum in my freeview. I am wondering whether my coordinate used above command is correct ? It is from the Cursor on the right of wm in attached pictures. I know here need talairach coordinate and which one on the Cursor is correct ?Sorry for my ignorance. Any suggestions will be appreciated! Kind Regards Jie

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Seed region in anatomical data for resting state fMRI data
by Kim, Gwang-Won 09 Oct '20

09 Oct '20

Hi there, I obtained a seed region (left superior frontal)from anatomical data to process resting state fMRI data as follows: fcseed-sess -o lh.SFC.dat -segid 1028 -s session -fsd rest. I wonder if what the seed region is the left superior frontal was correct. Question1: Can I display the lh.SFC.dat as MR image (anatomical image) using Freeview? I'd like to obtain ROI region as a seed region from anatomical data to process resting state fMRI data. Question2: How do I make the seed region if I use 8-mm radius spheres centered on a MNI coordinate [x=20, y=20, z=20] as the seed region. Thanks, Gwang-Won

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