External Email - Use Caution There was an issue with SegmentAAN for some OS's at the time of the beta build, so I suggest you download and do a real install of the current Ubuntu 22 dev build by downloading the package, https://secure-web.cisco.com/1jtCE3QdoKwQOY25B7jTfo4lrPoTLOS3G1L1-wYGn92U7MwvMt6cUIhozqyCkant6kkRnCnRnftgEZSNJtV0BHWprnyXG1kCksyoJzAfv5y65s6boxZVT73EAbGEE5GLSAUa-dBhqZ2zyD6DV0Js0OwjIwPqVkxvlZqTfblcuAVvs-Y6AAWOL85cq8cMGpMyZIKFBpZ62_lkob8-HzZm9Hi6gVlvU5S2i91QDXzTdWIU3b4zRwRBP2LJEhlXYMQGERPmHUprs_Ao0WVuEDM-8fKCvJBKxxIB5BTRRZYyedTypIAXXkNWt3hQ-Toq-nXpkz9Qp1Jy06SOnAdOFG1tHnQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer_ubuntu22-7-dev_amd64.deb … then cd to the download location and install with the apt commands, $ sudo apt remove freesurfer$ sudo apt install ./freesurfer_ubuntu22-7-dev_amd64.deb That should install such that FREESURFER_HOME and the setup off the environment should now be, $ export FREESURFER_HOME=/usr/local/freesurfer/7-dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu22_x86_64-dev-20250112-a90fba7 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /usr/local/freesurfer/7-devFSFAST_HOME /usr/local/freesurfer/7-dev/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /usr/local/freesurfer/7-dev/subjectsINFO: /home/rd521/matlab/startup.m does not exist ... creatingMNI_DIR /usr/local/freesurfer/7-dev/mni $ which run_segmentNuclei.sh /usr/local/freesurfer/7-dev/bin/run_segmentNuclei.sh $ which segmentNuclei/usr/local/freesurfer/7-dev/bin/segmentNuclei Don’t forget to set your SUBJECTS_DIR to some path not under the protected system install path /usr/local which requires sudo permission to write to. So for example you could set SUBJECTS_DIR to be somewhere you always have non-sudo write permission like your home directory, e.g., $ export SUBJECTS_DIR=$HOME/my_subjects We discourage using the tar archive and recommend running the actual installer package since the tar archive does not check for or install dependencies the freesurfer binaries may need to run on the system. - R.On Jan 9, 2025, at 09:33, Todd L Richards <to...@uw.edu> wrote: External Email - Use Caution I have installed the following version of freesurfer on my ubuntu computer freesurfer-linux-ubuntu22_x86_64-8.0.0-beta.tar.gz and I have linked ln -s to my installation of matlab folderand I am trying to use the tool called SegmentAAN which does exist on this version of the and tried to execute this tool for a subject that already has had recon-all -all -s sub-01 run on it successfullybut the SegmentAAN tool gives an error saying that it can't findSegmentNuclei from therun_segmentNuclei.sh: "${exe_dir}"/segmentNuclei $args command Please advise on how to fix this.Todd
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