External Email - Use Caution Thank you so much Yujing, It worked!
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu> Date: Monday, 10 March 2025 at 13:24 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Some library issues with segmentAAN You need the executable compiled with MCRv97. You can update the executable from https://secure-web.cisco.com/1-goUNX4MWAn9z-C7SYokU8Ai_lkM4nl7sw_MUSbTD0AswHeWD12jRaf9QZwQajq1j5kvsRHq90iMAQWw_iVxItivir7Qngi5Bsa9gbttF6vYFHPuIycYNbY-1Wk-qgaVniSi6ucG1TjzuQx8Jr2RGvZ4RgOQTzUjFcF4rqXUFDCwbqUdaYYQ1wZ0vc_RxKTv-aB5lvkuKw3mkpU1ix0_Mnq-OMDLTZ4FB_dj87IlZmIJ00qRUR3OfEoTnS942clRQ-4Z_8WaYpqpG1_HQhBDloOy_Dq5HK82TrTq2Ru8eUPCkpfuVGZ7CgqWasKPHJw9etmPCFK1ddhReJMtFwSGyg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2FAANsegment%2Flinux_x86_64%2FsegmentNuclei Place it under your $FREESURFER_HOME/bin. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Payam Sadeghi Shabestari Sent: Monday, March 10, 2025 7:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Some library issues with segmentAAN External Email - Use Caution Hello FS dev team, I tried to run segmentAAN.sh with my ubuntu 20.04.6, and MCRv97, and it failed, so I changed it to MCRv84, but I got messages showing some libraries missing. Could you please help me with that? Best, Payam #@# AAN Nuclei processing Mon Mar 10 10:58:02 UTC 2025 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/8.0.0/MCRv84//runtime/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84//bin/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib/x86_64-linux-gnu:/usr/local/freesurfer/8.0.0/MCRv84/runtime/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84/bin/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84/sys/os/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84/extern/bin/glnxa64 declare -x DBUS_SESSION_BUS_ADDRESS="unix:path=/run/user/1000/bus" declare -x FIX_VERTEX_AREA="" declare -x FMRI_ANALYSIS_DIR="/usr/local/freesurfer/8.0.0/fsfast" declare -x FREESURFER="/usr/local/freesurfer/8.0.0" declare -x FREESURFER_HOME="/usr/local/freesurfer/8.0.0" declare -x FREESURFER_HOME_FSPYTHON="/usr/local/freesurfer/8.0.0" declare -x FSFAST_HOME="/usr/local/freesurfer/8.0.0/fsfast" declare -x FSF_OUTPUT_FORMAT="nii.gz" declare -x FSTIME_LOAD="1" declare -x FS_OVERRIDE="0" declare -x FS_TIME_ALLOW="1" declare -x FUNCTIONALS_DIR="/usr/local/freesurfer/8.0.0/sessions" declare -x GROUP="ubuntu" declare -x HOME="/home/ubuntu" declare -x HOST="sch-mri" declare -x HOSTTYPE="x86_64-linux" declare -x ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS="1" declare -x KMP_BLOCKTIME="1" declare -x KMP_HANDLE_SIGNALS="0" declare -x KMP_STACKSIZE="512k" declare -x LANG="C.UTF-8" declare -x LC_CTYPE="C.UTF-8" declare -x LC_NUMERIC="C" declare -x LD_LIBRARY_PATH=".:/usr/local/freesurfer/8.0.0/MCRv84//runtime/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84//bin/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/8.0.0/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib/x86_64-linux-gnu:/usr/local/freesurfer/8.0.0/MCRv84/runtime/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84/bin/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84/sys/os/glnxa64:/usr/local/freesurfer/8.0.0/MCRv84/extern/bin/glnxa64" declare -x LESSCLOSE="/usr/bin/lesspipe %s %s" declare -x LESSOPEN="| /usr/bin/lesspipe %s" declare -x LOCAL_DIR="/usr/local/freesurfer/8.0.0/local" declare -x LOGNAME="ubuntu" declare -x LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:" declare -x MACHTYPE="x86_64" declare -x MCR_CACHE_ROOT="/tmp/MCR_661097455/" declare -x MINC_BIN_DIR="/usr/local/freesurfer/8.0.0/mni/bin" declare -x MINC_LIB_DIR="/usr/local/freesurfer/8.0.0/mni/lib" declare -x MKL_DOMAIN_NUM_THREADS="" declare -x MKL_NUM_THREADS="" declare -x MNI_DATAPATH="/usr/local/freesurfer/8.0.0/mni/data" declare -x MNI_DIR="/usr/local/freesurfer/8.0.0/mni" declare -x MNI_PERL5LIB="/usr/local/freesurfer/8.0.0/mni/share/perl5" declare -x MOTD_SHOWN="pam" declare -x NLSPATH="/usr/dt/lib/nls/msg/%L/%N.cat" declare -x OLDPWD="/home/ubuntu/data/subjects_fs_dir/dvob/mri" declare -x OS="Linux" declare -x OSTYPE="linux" declare -x PATH="/usr/local/freesurfer/8.0.0/bin:/usr/local/freesurfer/8.0.0/fsfast/bin:/usr/local/freesurfer/8.0.0/tktools:/usr/local/freesurfer/8.0.0/mni/bin:/usr/local/freesurfer/8.0.0/bin:/usr/local/freesurfer/8.0.0/fsfast/bin:/usr/local/freesurfer/8.0.0/tktools:/usr/local/freesurfer/8.0.0/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin" declare -x PERL5LIB="/usr/local/freesurfer/8.0.0/mni/share/perl5" declare -x PWD="/home/ubuntu/data/subjects_fs_dir/dvob/tmp/BS_basedOn_T1" declare -x REMOTEHOST="10.26.116.49" declare -x SHELL="/bin/bash" declare -x SHLVL="4" declare -x SSH_CLIENT="10.26.116.49 51025 22" declare -x SSH_CONNECTION="10.26.116.49 51025 172.23.72.246 22" declare -x SSH_TTY="/dev/pts/0" declare -x SUBJECTS_DIR="/home/ubuntu/data/subjects_fs_dir" declare -x TERM="xterm-256color" declare -x USER="ubuntu" declare -x VENDOR="unknown" declare -x XAPPLRESDIR="/usr/local/freesurfer/8.0.0/MCRv84//X11/app-defaults" declare -x XDG_DATA_DIRS="/usr/local/share:/usr/share:/var/lib/snapd/desktop" declare -x XDG_RUNTIME_DIR="/run/user/1000" declare -x XDG_SESSION_CLASS="user" declare -x XDG_SESSION_ID="391" declare -x XDG_SESSION_TYPE="tty" declare -x XFILESEARCHPATH="/usr/dt/app-defaults/%L/Dt" declare -x _="/usr/local/freesurfer/8.0.0/bin/segmentAAN.sh" declare -x __KMP_REGISTERED_LIB_118134="0x7f8a726e0890-cafe71c2-libiomp5.so" Registering imageDump.mgz to BS mask from ASEG /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) mv: cannot stat 'imageDump_coregistered.mgz': No such file or directory /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) mv: cannot stat 'imageDump_coregistered.mgz': No such file or directory /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) /usr/local/freesurfer/8.0.0/bin//mri_robust_register: /usr/local/freesurfer/8.0.0/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by /usr/local/freesurfer/8.0.0/bin//mri_robust_register) gzip: imageDump_flipped_coregistered_affine.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentNuclei (line 201) MATLAB:badSwitchExpression @#@FSTIME 2025:03:10:10:58:02 run_segmentNuclei.sh N 12 e 12.46 S 1.76 U 7.79 P 76% M 890724 F 0 R 292719 W 0 c 655 w 1073 I 0 O 227192 L 0.00 0.00 0.00 @#@FSLOADPOST 2025:03:10:10:58:15 run_segmentNuclei.sh N 12 0.21 0.05 0.02 0 mv: cannot stat '/home/ubuntu/data/subjects_fs_dir/dvob/mri/arousalNetworkVolumes.v10.txt': No such file or directory All done! To visualize the outputs, run: freeview -v /home/ubuntu/data/subjects_fs_dir/dvob/T1.mgz -v /home/ubuntu/data/subjects_fs_dir/dvob/arousalNetworkLabels.v10.mgz:colormap=lut:lut=/usr/local/freesurfer/8.0.0/average/AAN/atlas/freeview.lut.txt If you have used results from this software for a publication, please cite: Histology-guided MRI segmentation of brainstem nuclei critical to consciousness Olchanyi, M.D., Augustinack, J., Haynes, R., Lewis, L.D., Cicero, N., Destrieux, C., Folkerth, R., Kinney, H.C., Fischl, B., Iglesias, J.E., Edlow, B. medRxiv. Preprint available at medRxiv.org: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11A7tgsb42WBbxuqfBScDRIOQuI-XV1M_7z1Xbmu7G8F6DsqIzMeagQua1NRABQVjh7zX9OiOyzceoNZ9L5tEmsQu9lvIGnzdFeiYDODKQNNCIpFVN3PHGRTpWBVNAuF05y0XXS5QXsQowjslEoypBcJwf1A9ogMs2K6FWMtp-_Pv9ElC-Kkg7qcOJJPrfHqM558c4TrSMivUphGSYUe82TdgqJCesW246Cthuq8OZ771pKpJDlws6THW9rgGgalDIokpcDQ0xel-S7ETPtQDJw_z2uGDJRmPcJrlICGYqdbZplwSNz99E5nryPkUSoyfBv4YhfE8W-6bNciVnsoPyg/https%3A%2F%2Fwww.medrxiv.org%2Fcontent%2F10.1101%2F2024.09.26.24314117v1<https://secure-web.cisco.com/1OGqZvw4HW07HIN2nsExN8tLMftzckIh0lNtuThR43ViwwEUpm1VOoLOlBi6BiSy3yFU4zLkPU4UKy84vSN_pDQEkMLo2F1bINAxK8Ih-ngI1aTuwo7GlDoDIRCK4VMlJtyFn29p2ZP6m0nQCeNnuQeDZHzxvbLio3dh0wBX3rJwJLwUkJoZBfbM0SsnV3_hh40zBbGealcOT3qj7tGtE1BAAXKG6V9OSaTyBLrAAbQjIV9EqtnwdydcID5W4NtkRrrX7k5fzwtEYUhSBZLQHMXb5efUZ6sDwErL63NtlW86Rqq7sNQe_YDrBsMo8qDgNft2jEFmM1kWfCln9hxkUcw/https%3A%2F%2Fwww.medrxiv.org%2Fcontent%2F10.1101%2F2024.09.26.24314117v1>
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