External Email - Use Caution

 You don’t have permission to write to the default location of SUBJECTS_DIR as set in the freesurfer shell environment, i.e., /Applications/freesurfer/7.4.1/subjects.  The example subject data there is on purpose meant to be read only along with the rest of the freesurfer installation.  When it comes time to process your own subject data and write new or modify existing files, then you should set SUBJECTS_DIR to a path you always have write permission to, e.g., in your home directory,  $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects… place your data under $HOME/subjects and run your freesurfer/freeview commands ....

- R. On Jan 23, 2025, at 06:00, Claas Philip Nähle <cp@naehle.net> wrote:        External Email - Use Caution        I am trying to create a 3D brain model from a *.nii file (here: test.niiI), which I have copied to the subjects folder. A) Using the command line, the following error messages appear: Phils-MacBook:~ cnaehle$ recon-all -s brain -all -i /Applications/freesurfer/7.4.1/subjects/test.niimkdir: /Applications/freesurfer/7.4.1/subjects/brain: Permission deniedfs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SIERROR: cannot find brainrecon-all: version check failedfs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SI Phils-MacBook:~ cnaehle$  With:Phils-MacBook:~ cnaehle$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1Phils-MacBook:~ cnaehle$ export SUBJECTS_DIR=$FREESURFER_HOME/subjectsPhils-MacBook:~ cnaehle$ 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 Now, since this is for a 4th grade project for my daughter, it would be great if you could assist me. 1. Permssion denied: I have grant full disc access to Freesurfer and the terminal, but still….2. Error cannot find:  My Understanding is, that -s specifies the desired name of the output file, i. e. It will be created?3. Version check failed: No idea. B) Using the GUI, Freesurfer simply crashes. The crash log report is rather long as usual, but I can easily provide it if necessary. The Nifti file was created from DICOM images using Micron.

Any advice would be greatly appreciated. Regards  Philip ------- Prof. Dr. Claas Philip Nähle cp@naehle.net +49-178-4001619 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1diz10loniHrO26jrUXhHQcZMRcpC86rmU8ogQ0yU3DutFl...