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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.nii mkdir: /Applications/freesurfer/7.4.1/subjects/brain: Permission denied fs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SI ERROR: cannot find brain recon-all: version check failed fs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SI
Phils-MacBook:~ cnaehle$
With: Phils-MacBook:~ cnaehle$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 Phils-MacBook:~ cnaehle$ export SUBJECTS_DIR=$FREESURFER_HOME/subjects Phils-MacBook:~ cnaehle$ 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/7.4.1 FSFAST_HOME /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects MNI_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