Hi again, a follow up question!

We have linearly collected ascending slices (feet to head) and we are confused about using -z or +z. From previous responses it sounded like -z was correct but +z (from feet to head) is how the data is collected (assuming positive z-axis from feet to head).

When using -tpattern seq-z (and the default -tzero set to 0) we expect the top slice to stay the same which is what we see: the de-spike time course and the tshift time course are identical (i.e. no shift) in the top slice. The shift occurs in the bottom slice. Since we know we start from the bottom -tpattern seq+z makes more sense. The problem here is that with +z the top slice is shifted but it is shifted to the right. The peaks move to the right in the graph. Since the top slice is collected last I would expect them to move to the left. This indicates that +z is wrong for ascending?

The -tpatern seq-z shifts the first (bottom) slice to the right which actually would make it a correct shift but it feel counter intuitive since the actual order is +z, so I would "want" to move the top slice time series to the left.

3dTshift -tzero 0 -quintic -prefix pb02.$subj.r$run.tshift   -tpattern seq+z   pb01.$subj.r$run.despike+orig

tzero zzz    = align each slice to time offset 'zzz';
                  the value of 'zzz' must be between the
                  minimum and maximum slice temporal offsets.
-tpattern ttt = use 'ttt' as the slice time pattern, rather
                  than the pattern in the input dataset header;
                  'ttt' can have any of the values that would
                  go in the 'tpattern' input to to3d, described below:
   seq+z = seqplus   = sequential in the plus direction
   seq-z = seqminus  = sequential in the minus direction

Disregarding the confusion above. We expect the bottom time serie (or top) to not be affected and the top (or bottom) time series just to be shifted in some direction without changing it overall look of the time series. This is what we see. But what is supposed to happen in the middle of the stack? We would expect a smaller shift in some direction, which is kind of what we see, but we also see kind of a modulation of the look of the time series. The peaks of the BOLD signal change their shapes a bit. Is that expected? See attached despike and tshift of a slice in the middle.



Thanks!



Edited 2 time(s). Last edit at 11/16/2017 05:17AM by Robin.