When I was performing the step of " Global intensity normalisation across subjects", I had 2 problems. My computer system is macOS 10.14.2.
(1) If I type the command
foreach * : ln -sr IN/dwi_denoised_unringed_preproc_unbiased.mif ../dwiintensitynorm/dwi_input/IN.mi
it reported an error about
ln: illegal option -- r usage: ln [-Ffhinsv] source_file [target_file] ln [-Ffhinsv] source_file ... target_dir link source_file target_file
Could you help me to deal with the problem? How to perform correct symbolic linking?
(2) Since the
dwiintensitynorm script performs normalisation on all subjects within a study (using a group-wise registration) and my data contains one patient group and one healthy control group, should I perform the
dwiintensitynorm script within one group seperately, or just perform intensity normalisation of all participants in two groups?