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

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Setting up environment variables

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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

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

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/10.1101/2024.09.26.24314117v1