Hi bob,


I was trying to align the zstat from FSL onto anatomicals(T1 3dSkullstriped), and the zstat are somewhat a bit inferior from the place it should be. So I plan to try to realign the zstat with anat by using the steps here. But I am not sure if this is the way to do since the functinoals that I got is the zstat from FSL.

I checked both the zstat.nii & ana.nii by 3dinfo,
the Data Axes Orientation is RPI (zstat), ASR (ana).
It seems like I have to either reorient zstat or ana in order to register with each other. Is there a command that I can reorient the images?

I checked the alignment, it generally looks fine (I attach it here , the first image), but I am still not sure if this is correct aligned. Since when I scroll it down to some other slice, ( the second image), it looks a bit away from the center.

Shall I still need to 3dAllineate them?
Or can I, take this zstat as my functional data for further analysis? I am trying hard to align the functional from FSL onto anatomicals by afni, but it seems like it's not straightforward.

Thank you in advance
jackie