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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:

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Hi 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


On Oct 18, 2022, at 2:37 PM, Alan Francis <alandarkenergy@gmail.com> wrote:

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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,

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 PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.
                                                                                                           
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|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.
                                                                                                           
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Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.