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You shouldn’t be getting errors about libcuda (which we do not support). If you have not already done so, please try the script we provide to install the Matlab runtime environment,
$ cd $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2014b - R. On Oct 19, 2022, at 16:41, Alan Francis <alandarkenergy@gmail.com> wrote: External Email - Use Caution Hi Eugenio -Thanks for your reply. We have a Linux Tech. He installed it for me. Should I reinstall the runtime ?Thanks,AlanOn Tue, Oct 18, 2022 at 2:59 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:Dear Alan,How did you install the runtime? Did you follow the instructions in the wiki?Cheers,/EugenioJuan Eugenio IglesiasMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1CU2rXmtEeXSOj0JKFwB3VuWcd145hFeSGV-cS6p3wsULZfg... Oct 18, 2022, at 2:37 PM, Alan Francis <alandarkenergy@gmail.com> wrote: External Email - Use Caution Hi Eugenio -Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help.Thanks,Alancopernicus:~/IMAGING> segmentThalamicNuclei.sh 973770Setting ITK threads to 1#--------------------------------------------#@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022------------------------------------------Setting up environment variables---LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading shared libraries: libicudata.so.52: cannot open shared object file: No such file or directoryCommand exited with non-zero status 127@#@FSTIME 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07@#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69 0.22 0.07127Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxThalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022For more details, see the log file /home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of NeuroscienceUniversity of Texas, School of MedicineRio Grande ValleyTexas. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1elpe2JjxvZ4Lo-xTfcLTjcLXPpUXKRXvDvCfLfJNrWMR-u... mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/114BijDJeA9ze3ZzU7Hd1_nRFQWrlOUbZle3uBgc9CPJ9ze... 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-7MN4BIp5M3Ef13cSzQVtEGvwS4yeQfhmdc4yb2rmc6ebJ... has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tJqHFXPSZkdeGg5_8J1m5U2932-B3u1BJvXvYCerIaEVpl...; .-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of NeuroscienceUniversity of Texas, School of MedicineRio Grande ValleyTexas. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you Eugenio and R. It works great.
On Wed, Oct 19, 2022 at 4:04 PM fsbuild fsbuild@contbay.com wrote:
You shouldn’t be getting errors about libcuda (which we do not support).
If you have not already done so, please try the script we provide to install the Matlab runtime environment,
$ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2014b
- R.
On Oct 19, 2022, at 16:41, Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHi Eugenio -
Thanks for your reply. We have a Linux Tech. He installed it for me. Should I reinstall the runtime ?
Thanks,
Alan
On Tue, Oct 18, 2022 at 2:59 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Alan, How did you install the runtime? Did you follow the instructions in the wiki? Cheers, /Eugenio
Juan Eugenio Iglesias *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1NxrZiMBZIdOtAR8_r0nmuYuSKlfrnrMQ1VsI-DCGLHVaFe6... http://secure-web.cisco.com/1-F2deM4oNalZVW-blsG0oWLgbKUPi9lklFoUJexQqa87w6TBW80F65uV3keXC_JNnhNLjdgs5T3DVG3xGEMIgcb7cMHk2Q_ALBFO9Oi6RrXZyCulsv9K8E_IWAPqNCnI1vFAlkCEf71E98zI0kcYlNH6bHeV9q3ASpBGrbdZM55ULbrYFlerLR3edJIPeSOZkReV7GSq0OlTnO8h6R0G38zKEZdDh-2r98CGtXw-xmmNTNyKlT9K-tpnOb9wFWu5viucqTNIlnzPhcp5yWDmDwUuQyb8g50ui9YFgpCNoMSrr0WMSkbg9zqr7LxhdyS4/http%3A%2F%2Fwww.jeiglesias.com
On Oct 18, 2022, at 2:37 PM, Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHi Eugenio -
Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help.
Thanks,
Alan
copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770 Setting ITK threads to 1 #--------------------------------------------
#@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022
Setting up environment variables
LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading shared libraries: libicudata.so.52: cannot open shared object file: No such file or directory Command exited with non-zero status 127 @#@FSTIME 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07 @#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69 0.22 0.07 127 Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
Thalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022
For more details, see the log file /home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log
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*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine*
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*Texas.*
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*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine*
*Rio Grande Valley*
*Texas.*
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