Hello AFNI gurus!
This question JUST occurred to me - does the input provided to tpattern in 3dTshift assume axial acquisition? Or is alt+z2 referring to the order in which the slices were saved to disk as explained here (message #5)? In other words, if I have acquired interleaved slices but in the sagittal direction, can I still use alt+z2 for tpattern?
Can’t believe I had never thought about this before!
3dTshift infers the slice direction from the z direction (k dimension) of the storage orientation. With the exception of the voxshift option, these z slices are used for the relative timing offsets with the various timing patterns like alt+z, alt-z, seq+z, … You can find the dataset orientation with “3dinfo -orient mydset”. The last dimension of the 3-letter code determines the slice direction and order (top to bottom vs bottom to top, left to right vs right to left). So an orientation of RAI implies Inferior to superior axial slices. An orientation of PIR implies left to right sagittal slices.