Thank you both for your responses,
I think the reason why I could not understand the purpose of:
# reset the orientation to something simple
3dresample -orient RAI -input DSET_01 -prefix DSET_02
is because we may not use the same method to redefine the correct orientation.
What I am doing, is that I identify the brain orientation of y=1 and z=1.
For example in my case:
y=1 correspond to superior (S)
and
z=1 correspond to posterior (P)
original orientation was LPI,
So the new orientation should be either RSP or LSP (I had meaningful results)
Does that seem fine to you?
I was confused with:
# reset the orientation to something simple
3dresample -orient RAI -input DSET_01 -prefix DSET_02
because with my method, 3dresample actually changes the outcome of the “3drefit” since with my image x=1 becomes x=82, y=1 becomes y=64 and z do not change. In consequence, if 3dresemple is applied before orientating the axes base on x=1, z=1, y=1,
-orient RAI
reversed the LR axis (x=1 becomes x=82) since the original orient was LPI.
Three questions related to my original question:
1 - Is the method that I used valid?
2 - if yes,
In my example:
original orientation was LPI
y=1 correspond to the superior part of the brain
z=1 correspond to the inferior part of the brain
the authors said reverse LR
For now this command did work perfectly to reorient SI and PA axis
3drefit -orient LSP -deoblique
except that I still struggle to identify if left and right should be switched?
3 - Maybe ptaylor method with
# reset the orientation to something simple
3dresample -orient RAI -input DSET_01 -prefix DSET_02
help with that issue and I should use it, however, I don’t understand how based on the DSET_02, you define what to put in -orient (of 3drefit) if not based on x=1, z=1…
Sorry of all these questions but I can’t be 100% of what is L and R, without understanding fully the process,
thank you again for your help!