Hi everyone,
In order to preprocess some MRIs by normalizing them to have zero mean and unit variance, one may run the following in a bash terminal.
mapfile -t mu < <( mrstats -mask brainmask.nii.gz -output mean image.nii.gz )
mapfile -t sigma < <( mrstats -mask brainmask.nii.gz -output std image.nii.gz )
mrcalc image.nii.gz $mu -sub $sigma -div normalized_image.nii.gz
This isn’t a question per se; I emailed Prof. Tournier directly and he gave me the answer and suggested I post it on this forum for others to benefit. A big thank you to Prof. Tournier.
Just a quick note on the above:
My initial suggestion was the following, but for some reason this didn’t work on @pegger0709’s system. I’m listing here in case it works for others (it relies on reading the output of the mrstats call, captured via command substitution into an array variable):
val=( $(mrstats image.mif -mask brainmask.nii.gz -output mean -output std) )
mrcalc image.mif ${val[0]} -sub ${val[1]} -div normalised.mif
I prefer the above since it only requires a single mrstats call to get both the mean and std dev in one pass.
Otherwise, you should be able to do the two-call version using standard command substitution:
mu=$(mrstats image.mif -mask brainmask.nii.gz -output mean)
sigma=$(mrstats image.mif -mask brainmask.nii.gz -output std)
mrcalc image.mif $mu -sub $sigma -div normalised.mif
Ultimately, it all boils down to bash gymnastics - there’s many ways to skin this cat…