External Email - Use Caution
Hello Behçet, Are you saying the version of the Ubuntu operating system changed and now when you run the same command you get this error about the missing library ?
If so, I would check with your system administrators to see if they have installed the freesurfer 7.1.1 .deb freesurfer package from https://secure-web.cisco.com/1kZqy9BcKMr7diHAAdkyYDg2sSQj5AQELQZUIDe_I964hoH... which matches the version of Ubuntu you are now running. Running the installer package should try to fix that missing library dependency. - R.
On Feb 15, 2023, at 05:36, behçet ayyıldız <behcetayyildizz@gmail.com> wrote: External Email - Use Caution Dear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93Setting ITK threads to 1#--------------------------------------------#@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET------------------------------------------Setting up environment variables---LD_LIBRARY_PATH is .:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory127Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/LinuxDo you guys have any idea how to fix it ?Thanks in advance.-- Behçet Ayyıldız.._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hello, Thank you for your valuable reply. I would ask something before checking it. I forgot to say something, even after the computers change "recon-all" is running, just like it runs before the change, however not the segmentThalamicNuclei.sh command. So yeah, I would also say that the problem is only in the segmentation module of Freesurfer for now. Thanks in advance,
fsbuild fsbuild@contbay.com, 15 Şub 2023 Çar, 13:07 tarihinde şunu yazdı:
Hello Behçet,
Are you saying the version of the Ubuntu operating system changed and now when you run the same command you get this error about the missing library ?
If so, I would check with your system administrators to see if they have installed the freesurfer 7.1.1 .deb freesurfer package from https://secure-web.cisco.com/1ESEXk_LwRBzrrL4Zm69R9ZKqrP8dxwVrKHwrSqSFOLw6vi... which matches the version of Ubuntu you are now running.. Running the installer package should try to fix that missing library dependency.
- R.
On Feb 15, 2023, at 05:36, behçet ayyıldız behcetayyildizz@gmail.com wrote:
External Email - Use CautionDear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.
drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93 Setting ITK threads to 1 #--------------------------------------------
#@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET
Setting up environment variables
LD_LIBRARY_PATH is ..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses..so.5: cannot open shared object file: No such file or directory 127 Linux causal.brain.mri.tu-muenchen.de http://secure-web.cisco.com/1Q7u7_P_NBkc_6lPG6bKTBeKKKlGXijIY3WOh-az_lej5ouUAxdtd4EmKT_u9Ta4ud8eMwDHlMpBMhNFLQGw8LWF4sEDJlyH6Muh82TsilCRK1ngCD8sjyG-bAu8CT6GY9MyisYmh9yQuNzToAjWnufnO_vOtzf99VuFt0fshgezuEzCh7ol77iCiTtL-r6g3DBhNXWLP_G9X0qe-imQVFcZecK19skmK2_yLx7sH-K6ro7bRrWRzE3teegonbBQVv6CgdfZbtEQB51-157E3hXTYNBhNfuMoLwk1ExcuA4yRb2ATsBgCSvv-JLWOJuv_03h2XiPIQvfiWSc1jUKDtA/http%3A%2F%2Fcausal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
Do you guys have any idea how to fix it ?
Thanks in advance.
--
*Behçet Ayyıldız..*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1kWMfU-JL--FBzTTHLBjTT6aABBbpO54SKvPPOw0I_0N5Se...
External Email - Use Caution
Behçet,
This message is the key:
error while loading shared libraries: libncurses..so.5: cannot open shared object file: No such file or directory
FreeSurfer is looking for a supporting library that it expects your operating system installation to have but that is not there.
If you can use `sudo` on your system, then you should be able to install this library with
$ sudo apt-get install libncurses5
If not, then ask your system administrator to install the libncurses5 package. If that is truly the only problem, installing the missing ncurses library should fix it.
On Wed, Feb 15, 2023 at 7:59 AM behçet ayyıldız behcetayyildizz@gmail.com wrote:
External Email - Use CautionHello, Thank you for your valuable reply. I would ask something before checking it. I forgot to say something, even after the computers change "recon-all" is running, just like it runs before the change, however not the segmentThalamicNuclei.sh command. So yeah, I would also say that the problem is only in the segmentation module of Freesurfer for now. Thanks in advance,
fsbuild fsbuild@contbay.com, 15 Şub 2023 Çar, 13:07 tarihinde şunu yazdı:
Hello Behçet,
Are you saying the version of the Ubuntu operating system changed and now when you run the same command you get this error about the missing library ?
If so, I would check with your system administrators to see if they have installed the freesurfer 7.1.1 .deb freesurfer package from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1At8QKM5oUsIZmRsMRNPvhsQysuzVxU0In_cXK4XC9XLDrZ... which matches the version of Ubuntu you are now running.. Running the installer package should try to fix that missing library dependency.
- R.
On Feb 15, 2023, at 05:36, behçet ayyıldız behcetayyildizz@gmail.com wrote:
External Email - Use CautionDear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.
drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93 Setting ITK threads to 1 #--------------------------------------------
#@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET
Setting up environment variables
LD_LIBRARY_PATH is ..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses..so.5: cannot open shared object file: No such file or directory 127 Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
Do you guys have any idea how to fix it ?
Thanks in advance.
--
Behçet Ayyıldız..
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1C2qT0kjSdOsO4Urhs8YV1g41i7E88v5A13FUDYy7LmlSF2...
--
Behçet Ayyıldız..
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1C2qT0kjSdOsO4Urhs8YV1g41i7E88v5A13FUDYy7LmlSF2... 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://secure-web.cisco.com/1ud1ykrOdc9YoV_4X5XaFkvrONTcVWrgb6UukmZdfefvZ1k... https://secure-web.cisco.com/1ud1ykrOdc9YoV_4X5XaFkvrONTcVWrgb6UukmZdfefvZ1kBvYdGCkPoccOy0KuB6ZQRB7QeHYqUF7j-PEfS51jsF2zr5_HJDVLbyZw3XZV21fsqms4lW5K-PbuIWyWmHx37bw3hRujUdFCnaiMl2V8CMPdGTc4mamGSFmzbv8ziVR3sc3KKNgxfprd4Q6E6trvLYS-0G9oLWeSdgp0Jz0lr7Yh1VMH57UKfL9rEm4Hl0-cf_VoYqgs-_euIA_YVPON9Q32qsgIBjcvj27Ls0zmRFHRxyt7vQU9hhweB93_KaXU6PEWFM4gVhQU2f2__ZZfKBOk5Ye41HQOmPUHh4hg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.
External Email - Use Caution
Dear Bennet, Thank you very much for your help and suggestion. I tried it but it didn't work by indicating the following error "*drodriguez* (the ID that I use to login the computers)* is not in the sudoers file. This incident will be reported. * I think I should consult with my system administrator.
Thanks for your suggestion.
Bennet Fauber bennet@umich.edu, 15 Şub 2023 Çar, 14:07 tarihinde şunu yazdı:
External Email - Use CautionBehçet,
This message is the key:
error while loading shared libraries: libncurses..so.5: cannot open
shared object file: No such file or directory
FreeSurfer is looking for a supporting library that it expects your operating system installation to have but that is not there.
If you can use `sudo` on your system, then you should be able to install this library with
$ sudo apt-get install libncurses5
If not, then ask your system administrator to install the libncurses5 package. If that is truly the only problem, installing the missing ncurses library should fix it.
On Wed, Feb 15, 2023 at 7:59 AM behçet ayyıldız behcetayyildizz@gmail.com wrote:
External Email - Use CautionHello, Thank you for your valuable reply. I would ask something before checking
it. I forgot to say something, even after the computers change "recon-all" is running, just like it runs before the change, however not the segmentThalamicNuclei.sh command. So yeah, I would also say that the problem is only in the segmentation module of Freesurfer for now.
Thanks in advance,
fsbuild fsbuild@contbay.com, 15 Şub 2023 Çar, 13:07 tarihinde şunu
yazdı:
Hello Behçet,
Are you saying the version of the Ubuntu operating system changed and
now when you run the same command you get this error about the missing library ?
If so, I would check with your system administrators to see if they
have installed the freesurfer 7.1.1 .deb freesurfer package from MailScanner has detected a possible fraud attempt from " secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1At8QKM5oUsIZmRsMRNPvhsQysuzVxU0In_cXK4XC9XLDrZ... which matches the version of Ubuntu you are now running.. Running the installer package should try to fix that missing library dependency.
- R.
On Feb 15, 2023, at 05:36, behçet ayyıldız behcetayyildizz@gmail.com
wrote:
External Email - Use CautionDear All, I was using Linux Ubuntu to perform my analysis. However, they were
changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.
drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$
segmentThalamicNuclei.sh con_HaJa93
Setting ITK threads to 1 #--------------------------------------------
#@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET
Setting up environment variables
LD_LIBRARY_PATH is
..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
/sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading
shared libraries: libncurses..so.5: cannot open shared object file: No such file or directory
127 Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian
5.10.162-1 (2023-01-21) x86_64 GNU/Linux
Do you guys have any idea how to fix it ?
Thanks in advance.
--
Behçet Ayyıldız..
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "
secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1C2qT0kjSdOsO4Urhs8YV1g41i7E88v5A13FUDYy7LmlSF2...
--
Behçet Ayyıldız..
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1C2qT0kjSdOsO4Urhs8YV1g41i7E88v5A13FUDYy7LmlSF2...
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://secure-web.cisco.com/1ud1ykrOdc9YoV_4X5XaFkvrONTcVWrgb6UukmZdfefvZ1k... < https://secure-web.cisco.com/1ud1ykrOdc9YoV_4X5XaFkvrONTcVWrgb6UukmZdfefvZ1k... .
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1w00bCIy2TE8rC547yu6Ol46KDEv2_z_clcovEOMNz9zkBJ... 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://secure-web.cisco.com/1pvIj_4U6TliLDIHaDxH03jRF17SrSpMmkwRPWiIZfjxQci... < https://secure-web.cisco.com/1pvIj_4U6TliLDIHaDxH03jRF17SrSpMmkwRPWiIZfjxQci... .
freesurfer@nmr.mgh.harvard.edu
-
behçet ayyıldız -
Bennet Fauber -
fsbuild