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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

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Prof. Dr. Claas Philip Nähle
cp@naehle.net
+49-178-4001619