I am working with arterial spin labeling data and each dataset contains a series of interleaved control and labeled volumes (e.g., C,L,C,L,C,L,C,L,C,L,C,L…). Because the mean signal intensity of the control and labeled volumes is different, the signal appears zig-zagged - which makes motion correction difficult. I would like to use 3dvolreg to perform motion correction of the control and labeled volumes separately, using the first volume as the base for both, but ultimately I need to have produced one motion corrected interleaved dataset in original order. I’ve tried using a sub-brik selector with 3dvolreg ‘[0…$(2)]’ and ‘[1…$(2]’ but as you know this method produces a motion corrected output dataset containing only those selected volumes. Do you have any advice or guidance for how I can use AFNI to accomplish this goal?
Any help is greatly appreciated,