Freesurfer March 2025

freesurfer@nmr.mgh.harvard.edu

49 participants
63 discussions

Longitudinal samseg not working - TypeError: transform() got an unexpected keyword argument 'affine'
by Paola Di Filippo 11 Mar '25

11 Mar '25

External Email - Use Caution Hi everyone, I am trying to launch longitudinal samseg with the lesion flag for an MS subject, in Freesurfer 8.0. I followed instructions, cross sectional samseg for the same subject at T0 worked fine, but now I am having troubles, described as follows: MBP-di-Paola:~ paoladifilippo$ export FS_LICENSE=$HOME/license.txt MBP-di-Paola:~ paoladifilippo$ export FREESURFER_HOME=/Applications/freesurfer/8.0.0 MBP-di-Paola:~ paoladifilippo$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/8.0.0 FSFAST_HOME /Applications/freesurfer/8.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.0.0/subjects MNI_DIR /Applications/freesurfer/8.0.0/mni MBP-di-Paola:~ paoladifilippo$ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/runtime/maci64:$FREESURFER_HOME/MCRv97/bin/maci64:$FREESURFER_HOME/MCRv97/sys/os/maci64:$FREESURFER_HOME/MCRv97/extern/bin/maci64 MBP-di-Paola:~ paoladifilippo$ cd /Users/paoladifilippo/RM.OCT.NFL/A.C/LONGITUDINAL.SAMSEG MBP-di-Paola:LONGITUDINAL.SAMSEG paoladifilippo$ run_samseg_long --timepoint A.C.2.4.91.MRI.12.9.22_t1_reg.mgz A.C.2.4.91.MRI.12.9.22_flair_reg.mgz --timepoint A.C.2.4.91.MRI.13.2.23_t1_reg.mgz A.C.2.4.91.MRI.13.2.23_flair_reg.mgz --timepoint A.C.2.4.91.MRI.20.09.23_t1_reg.mgz A.C.2.4.91.MRI.20.09.23_flair_reg.mgz --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /Users/paoladifilippo/RM.OCT.NFL/A.C/LONG.SAMSEG.OUTPUT/ Assuming an identity transformation between base and each time point WARNING:tensorflow:From /Applications/freesurfer/8.0.0/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term Traceback (most recent call last): File "/Applications/freesurfer/8.0.0/python/scripts/run_samseg_long", line 209, in <module> samsegLongitudinal.segment(saveWarp=args.save_warp, initTransformFile=args.init_reg) File "/Applications/freesurfer/8.0.0/python/packages/gems/SamsegLongitudinal.py", line 181, in segment self.constructAndRegisterSubjectSpecificTemplate(initTransformFile) File "/Applications/freesurfer/8.0.0/python/packages/gems/SamsegLongitudinal.py", line 200, in constructAndRegisterSubjectSpecificTemplate self.sstFileNames = self.generateSubjectSpecificTemplate() File "/Applications/freesurfer/8.0.0/python/packages/gems/SamsegLongitudinal.py", line 835, in generateSubjectSpecificTemplate imageBuffer = image0.transform(affine=self.tpToBaseTransforms[0]) TypeError: transform() got an unexpected keyword argument 'affine' I am working on Apple M4 Pro with 48 GB RAM, MacOS 15.2. Any ideas on how to fix this? Thanks in advance --

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Freesurfer 8.0.0 version: gtmseg
by Miguel Ángel Rivas Fernández 11 Mar '25

11 Mar '25

External Email - Use Caution Dear Freesurfer developers, I have run the recon-all command with version 8.0.0 and now I would like to run the gtmseg command. However, I received the message below. It seems to be looking for the file *talairach.m3z* in the transforms folder, but that is not one of the outputs in the new version. In the latest version of Freesurfer, is it no longer possible to run gtmseg? Is there any way to enable the recon-all from previous versions in version 8, or should I download an older version? setenv SUBJECTS_DIR /input/Freesurfer_outputs/ cd /home/matlab /usr/local/freesurfer//bin/gtmseg --s sub-NDARINVEMZZZWB9 freesurfer-linux-ubuntu20_x86_64-8.0.0-20250204-0f2bd3a gtmseg 8.0.0 Linux test-757bb4cd4-g5rv5 6.4.0-150600.23.30-default #1 SMP PREEMPT_DYNAMIC Sat Dec 7 08:37:53 UTC 2024 (8c25a0a) x86_64 x86_64 x86_64 GNU/Linux xcerebralseg --s sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz ERROR: cannot find /input/Freesurfer_outputs//sub-NDARINVEMZZZWB9/mri/transforms/talairach.m3z ERROR: xcerebralseg --s sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz gtmseg exited with errors Thank you very much Best -- *Miguel Ángel Rivas Fernández*

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Some library issues with segmentAAN
by Payam Sadeghi Shabestari 11 Mar '25

11 Mar '25

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: https://secure-web.cisco.com/1OGqZvw4HW07HIN2nsExN8tLMftzckIh0lNtuThR43Viww…

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Re: [Freesurfer] "mri_segment_hypothalamic_subunits" killed error
by fsbuild 10 Mar '25

10 Mar '25

External Email - Use Caution   An applications process(es) can be killed by the OS when the application requests more resources then the machine has to allocate, e.g., it requests too much memory, CPU resources, etc.   So it could be your Linux machine does not meet the system requirements to run 8.0.0 as listed on the download page, https://secure-web.cisco.com/1XfLimZ9aSU_VUKvX9FsGRHZ_qGVoPimFd5L19Q1cvSCoF… If the total memory on your Linux machine is not greater than 16-24G, and if you don't have more then 2 CPU cores, then the Linux OS plus some Freesurfer commands like mri_segment_hypothalamic_subunits (that make use of tensroflow, keras) might not be able to run. - R. On 3/10/25 07:57, Payam Sadeghi Shabestari (payam.sadeghishabestari(a)uzh.ch) wrote:         External Email - Use Caution         Hi FS dev team,   I tried to run mri_segment_hypothalamic_subunits with my ubuntu 20.04.6 and FS 8.0.0, and MCRv97. I tried both using cpu and gpu, but it returns me the “killed” message when I use 1 thread and another error when I use multiple threads. Could you please help me with that? Best, Payam   ubuntu@sch-mri:~/data/subjects_fs_dir/nalq/mri$ mri_segment_hypothalamic_subunits --s dvob --sd $SUBJECTS_DIR --threads 1 using 1 thread predicting 1/1 Killed ubuntu@sch-mri:~/data/subjects_fs_dir/nalq/mri$ mri_segment_hypothalamic_subunits --s dvob --sd $SUBJECTS_DIR --threads 2 using 2 threads predicting 1/1 terminate called after throwing an instance of 'std::bad_alloc'   what():  std::bad_alloc Aborted (core dumped)       _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/10EQ9krC53_12XYzxHC6HdHgIEt7f-cQEe-AETPMBBGn3K… The 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 https://secure-web.cisco.com/1ezXR_c9HnboqD4n7PzBYWLoG4tcP9ioNq3L6SV9rjkMyH… <https://secure-web.cisco.com/1b7ppWt6UMZVc6U9riBaenK-Ml1AGuj4ZcuZ3jwJT7BXIO-dnQyZyHo1mBONq8MmbKQZbHxkP5r0C7LjfQCtpfK_RlQACz5kv4EOhgxJAY5KQD9PMwylV-Dy5FuKn5lYdeox5kFqYau6DUtyifIhqa1L-FCuLv8urrA9ph605ql4g-tcZen2SGm8NhEklfI7Bk03HaRkSPJe9-YqFxU--bdo-ALGcu7wf7YWxN5DFNthc780ZtGdb5K6noVSEzY38hwqil59znN1k8lnGxz9o6aQjoMeeJL2hK3Zfx-yBlxe_zWhe7Zd49uEe65OU6YteKHi2LrTKaE30fmKhyv9y7Q/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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"mri_segment_hypothalamic_subunits" killed error
by Payam Sadeghi Shabestari 10 Mar '25

10 Mar '25

External Email - Use Caution Hi FS dev team, I tried to run mri_segment_hypothalamic_subunits with my ubuntu 20.04.6 and FS 8.0.0, and MCRv97. I tried both using cpu and gpu, but it returns me the “killed” message when I use 1 thread and another error when I use multiple threads. Could you please help me with that? Best, Payam ubuntu@sch-mri:~/data/subjects_fs_dir/nalq/mri$ mri_segment_hypothalamic_subunits --s dvob --sd $SUBJECTS_DIR --threads 1 using 1 thread predicting 1/1 Killed ubuntu@sch-mri:~/data/subjects_fs_dir/nalq/mri$ mri_segment_hypothalamic_subunits --s dvob --sd $SUBJECTS_DIR --threads 2 using 2 threads predicting 1/1 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)

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Re: [Freesurfer] Problems with Bayesian Segmentation with Histological Atlas "NextBrain"
by fsbuild 09 Mar '25

09 Mar '25

External Email - Use Caution  Hello Lukas and thank you for the feedback. The fireants version included in the 8.0.0 silicon Mac release for fspython is I believe an older version because that is what had been tested with and/or is compatible with the other arm64 packages.  As far as I know, newer versions of fireants have not been tested. The 8.0.0 Mac/Linux installers were tested with the code that mri_histo_atlas_segment_fireants will download  via the instructions, $ cd $BASEPATH… (in Linux): wget https://secure-web.cisco.com/12n1juWI89hxvsaHDfUa2RIDJ71CL6VXTdYe2ZW8P_s8rQ… in MAC): curl -o atlas_simplified.zip https://secure-web.cisco.com/1sEFkCcgarb54UG3YaZK4-VWDWOhf6eZUiWCRhoJQwiVIW… unzip atlas_simplified.zip The ERC_bayesian_segmentation files are not included because of package/size limitations of the installers. - R. On Mar 9, 2025, at 06:46, Lukas von Erdmannsdorff <lukasvonerdmannsdorff(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer Developers,First of all, thank you for the fantastic work on the Histo Atlas Segmentation tool and the amazing updates in FreeSurfer 8!Since I encountered some crashes with mri_histo_atlas_segment_fireants and mri_histo_atlas_segment_fast, I wanted to share the issues I experienced.I downloaded FreeSurfer 8 to my M1 MacBook Pro using the installation package, but it partially contains an older code version compared to the one on GitHub for the NextBrain segmentation with FireAnts. For example, it attempts to import FireAnts packages that are not included, such as GreedyRegistration from fireants.registration. I then installed FreeSurfer 8 directly from GitHub, which worked. However, as soon as EasyReg started, I encountered a thread lock. This also occurred when trying to run the EasyReg step directly as a terminal command.After that, I attempted the installation on Linux. However, in the latest installation package for Ubuntu 18, the ERC_bayesian_segmentation folder was completely missing. I then installed it again directly from GitHub but ran into a similar issue with EasyReg during the mri_histo_atlas_segment_fireants process, even when using only a single thread.I also tried mri_histo_atlas_segment_fast because my data is 1mm isotropic. However, this also did not work, as it failed when starting the registration with SynthMorph. I was able to resolve this by using the spawn method for multiprocessing, preventing issues when processing both hemispheres simultaneously.Additionally, I noticed that mri_TumorSynth is missing, although it is listed on the FreeSurfer wiki page. I hope it will be available in an updated version of FreeSurfer 8.Thanks in advance! Best regards, Lukas von Erdmannsdorff_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1iVlOv9TmGXe1Nc1f75wU746oiUCfNNfUk_BGPVGrTzn9r…

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Re: [Freesurfer] Freesurfer 8.0.0 version: gtmseg
by fsbuild 09 Mar '25

09 Mar '25

External Email - Use Caution  I’m not familiar with the gtmseg command, but I think you can revert to the old recon-all behavior by setting FS_V8_XOPTS=0 on the recon-all command line.  That is listed under recon-all behavior at, https://secure-web.cisco.com/1sfWpao2icNI-saQsKdVISm0uzmYFD95MpfEE… - R. On Mar 8, 2025, at 19:06, Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> wrote:        External Email - Use Caution         Dear Freesurfer developers,I have run the recon-all command with version 8.0.0 and now I would like to run the gtmseg command. However, I received the message below. It seems to be looking for the file talairach.m3z in the transforms folder, but that is not one of the outputs in the new version. In the latest version of Freesurfer, is it no longer possible to run gtmseg? Is there any way to enable the recon-all from previous versions in version 8, or should I download an older version? setenv SUBJECTS_DIR /input/Freesurfer_outputs/ cd /home/matlab /usr/local/freesurfer//bin/gtmseg --s sub-NDARINVEMZZZWB9 freesurfer-linux-ubuntu20_x86_64-8.0.0-20250204-0f2bd3a gtmseg 8.0.0 Linux test-757bb4cd4-g5rv5 6..4.0-150600.23.30-default #1 SMP PREEMPT_DYNAMIC Sat Dec  7 08:37:53 UTC 2024 (8c25a0a) x86_64 x86_64 x86_64 GNU/Linux xcerebralseg --s sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz ERROR: cannot find /input/Freesurfer_outputs//sub-NDARINVEMZZZWB9/mri/transforms/talairach.m3z ERROR: xcerebralseg --s sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz gtmseg exited with errors Thank you very much Best --  Miguel Ángel Rivas Fernández _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard..edu https://secure-web.cisco.com/1pCJSD9v1ks2GRoMKrEozzHYVEm4n7H1Can6zaKV98I3Ue…

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aparc2aseg not working
by Jin Liu 09 Mar '25

09 Mar '25

External Email - Use Caution Hello FreeSurfer team, I’m trying to create a lobe segmentation for white matter. I first created the annotation files using mri_annotation2label with --lobesStrict for each hemisphere, and then tried to map the lobe parcellation onto segmentation volume by using mri_aparc2aseg. But somehow the resulting image was not segmented by lobes. It contains cortical parcellation by lobe, detailed subcortical segmentation by structure, and white matter is marked as a whole (cerebral white matter). I then checked the annotation files created by lobesStrict and they look fine, without any subcortical labels. I wonder where I made a mistake, or if there is an easier way to do lobe segmentation. The code I used is as follows: mri_annotation2label --subject 1300 --hemi lh --labelbase ./1300/label/aparc-lh --lobesStrict ./1300/label/lh.aparc.lobesStrict mri_annotation2label --subject 1300 --hemi rh --labelbase ./1300/label/aparc-rh --lobesStrict ./1300/label/rh.aparc.lobesStrict mri_aparc2aseg --s 1300 --annot aparc.lobesStrict --o ./1300/mri/lobesStrict.mgz Best, Jin

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Re: [Freesurfer] illegal instruction - core dumped with samseg lesion
by fsbuild 09 Mar '25

09 Mar '25

External Email - Use Caution  If you can capture the first 100 or so lines of the core dump file, that could provide some additional information. I don’t see anything in the processor specs that excludes running AVX, SSE, etc. instructions, i.e., it is a recent Intel 14th generation processor, https://secure-web.cisco.com/16RohpBqIB1lAwZpTOwscE_gc2ArnH… being able to run those instructions would result in an illegal instruction error. As of August 2024, that 14th generation processor is also listed here,https://secure-web.cisco.com/1ZbvivIaAcYaPn-cIFZzBkR-9GU_4jH1NhKqB4nXL… perhaps it is crashing from the over voltage firmware bug, i.e., some postings indicate this will cause an illegal instruction error.  Intel has apparently issued a firmware update, but I don’t know how to verify if the processor has it.  Because a CPU could be damaged from over voltage, Intel extended the warranty for affected CPU’s when bought as individually boxed or when the CPU comes installed on a system motherboard as part of an out of the box machine.   You would have to contact the vendor you bought either the individual CPU or machine from to see if you qualify for a replacement.  But I would at least try to make sure the firmware is up to date for the CPU. I think you would see a different error if the VM was not allocated enough RAM or CPU cores, or if the process was running out of swap or disk space.   If you've seen crashes like this when running other perhaps compute intensive software, then that would also point to the firmware issue.. - R. On Mar 7, 2025, at 05:53, Paola Di Filippo <paola.difilippo(a)unifg.it> wrote:Intel(R) Core(TM) i5-14600K

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Problems with Bayesian Segmentation with Histological Atlas "NextBrain"
by Lukas von Erdmannsdorff 09 Mar '25

09 Mar '25

External Email - Use Caution Dear Freesurfer Developers, First of all, thank you for the fantastic work on the Histo Atlas Segmentation tool and the amazing updates in FreeSurfer 8! Since I encountered some crashes with mri_histo_atlas_segment_fireants and mri_histo_atlas_segment_fast, I wanted to share the issues I experienced. I downloaded FreeSurfer 8 to my M1 MacBook Pro using the installation package, but it partially contains an older code version compared to the one on GitHub for the NextBrain segmentation with FireAnts. For example, it attempts to import FireAnts packages that are not included, such as GreedyRegistration from fireants.registration. I then installed FreeSurfer 8 directly from GitHub, which worked. However, as soon as EasyReg started, I encountered a thread lock. This also occurred when trying to run the EasyReg step directly as a terminal command. After that, I attempted the installation on Linux. However, in the latest installation package for Ubuntu 18, the ERC_bayesian_segmentation folder was completely missing. I then installed it again directly from GitHub but ran into a similar issue with EasyReg during the mri_histo_atlas_segment_fireants process, even when using only a single thread. I also tried mri_histo_atlas_segment_fast because my data is 1mm isotropic. However, this also did not work, as it failed when starting the registration with SynthMorph. I was able to resolve this by using the spawn method for multiprocessing, preventing issues when processing both hemispheres simultaneously. Additionally, I noticed that mri_TumorSynth is missing, although it is listed on the FreeSurfer wiki page. I hope it will be available in an updated version of FreeSurfer 8. Thanks in advance! Best regards, Lukas von Erdmannsdorff

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