Hi, I’m having troubles with symbolic linking via (step 5):
Working with mac os high sierra 10.13.1 and mrtrix version 3.0_RC2-4-g51864ed2.
foreach * : ln -sr IN/dwi_denoised_preproc_bias.mif …/dwiintensitynorm/dwi_input/IN.mif
foreach * : ln -sr IN/dwi_mask.mif …/dwiintensitynorm/mask_input/IN.mif
ln: illegal option – r
usage: ln [-Ffhinsv] source_file [target_file]
ln [-Ffhinsv] source_file … target_dir
link source_file target_file
However, just copying the files works (without the"-sr").
It also seems, that the option -sr is not known, just -s (that produced Alias-files, which ended up in not working for dwiintensitynorm and seemed to be understood as folders at first, but I’m not sure if that was because of DS_Store files which might have been produced by that process).
After copying, I received .DS_Store files. So installing “tree” via
brew install tree
revealed those files. After that I was able to proceed with step 5.