External Email - Use Caution You can check the post (quoted below) to verify the setup for the 7.4..1 release. Instead of running the freeview command as listed in the post, you can run the mri_info command with no arguments to get the help info about the command line options. If mri_diff runs and prints out the help output, then the issue is likely your command line arguments. - R.. bash-3.2$ mri_info USAGE: mri_info fname1 <fname2> <options>
--conformed : print whether a volume is conformed stdout --conformed-to-min : print whether a volume is conformed-to-min stdout <rest of output deleted> SETUP ENVIRONMENT https://secure-web.cisco.com/1-xQ9e5Z3VTlXilKkcSpNfmxzfXMzCk-PG0p40zknkFsd-OPflitvKnVBlbPqmZOOFVb9VAQ0M1PT82eJ-TQA5l5vXu3cxmiGQ_qMXFYiU6W_jXNSmGaqA3RbGU1beyO26DOuGjlunX7l_t7p3sBnlGCA8WPnPy5fmpsoKV4dY4ITrs3S59UCZ3IberbbCAyXNGPIhR261f_R6V7uFYU-YpjHa3r0hv9PElrVro7lKsGm-JNW6TmXBe6o5armcI5hCwbyu-rAezm9TjIL9J1eeRnkdiZvqDGt6oWMD0j9ILzFiiHj3UZbJHfsC8hr3mZDxdqSJlibJW8p2rTBT4emBQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76743.html If you setup the Freesurfer environment ... here using bash and not zsh ... hostname ~ bash $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurfer/7.4.1FSFAST_HOME /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/7.4.1/subjectsMNI_DIR /Applications/freesurfer/7.4.1/mni .... and point FS_LICENSE to your license.txt file, e.g., in your $HOME directory .... $ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export FS_LICENSE=license.txt$ head -1 license.txt...@somewhere.com <---- email you used to register .... then try running from the command line ... $ freeview $SUBJECTS_DIR/bert/mri/T1.mgz Please keep in mind you will need to change SUBJECTS_DIR to some other path, e.g., $HOME/subjects $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects .... and put files there if you want to write /modify subject files and data since /Applications/freesurfer/7.4.1/subjects is read only by default (not intended to be used to write data).
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