You need the executable compiled with MCRv97. You can update the executable from https://github.com/freesurfer/freesurfer/blob/dev/AANsegment/linux_x86_64/se...
Place it under your $FREESURFER_HOME/bin.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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://www.medrxiv.org/content/10.1101/2024.09.26.24314117v1https://secure-web.cisco.com/1OGqZvw4HW07HIN2nsExN8tLMftzckIh0lNtuThR43ViwwEUpm1VOoLOlBi6BiSy3yFU4zLkPU4UKy84vSN_pDQEkMLo2F1bINAxK8Ih-ngI1aTuwo7GlDoDIRCK4VMlJtyFn29p2ZP6m0nQCeNnuQeDZHzxvbLio3dh0wBX3rJwJLwUkJoZBfbM0SsnV3_hh40zBbGealcOT3qj7tGtE1BAAXKG6V9OSaTyBLrAAbQjIV9EqtnwdydcID5W4NtkRrrX7k5fzwtEYUhSBZLQHMXb5efUZ6sDwErL63NtlW86Rqq7sNQe_YDrBsMo8qDgNft2jEFmM1kWfCln9hxkUcw/https%3A%2F%2Fwww.medrxiv.org%2Fcontent%2F10.1101%2F2024.09.26.24314117v1