Dear AFNI experts,

We have acquired two runs of EPI data that differ in orientation. One is acquired in RAI, the other in RAS. I am using uber_subject.py to analyze both runs together. During the alignment step, the script crashes due to the different orientations. I have tried 3drefit -orient RAI on run 2 but this flips the image. When I try 3dresample -input run2 -master run1 it moves the image out of view and while the script runs through the whole analysis, the results don't look good.

This is the error message I get running regularly through the uber_subject.py script:

Input: dx= 1.875 dy= 1.875 dz=-5.000
Base: dx= 1.875 dy= 1.875 dz= 5.000
Input: R-L A-P S-I
Base: R-L A-P I-S
FATAL ERROR: perhaps you could make your datasets match?

In another approach, I have concatenated the two runs via this command: 3dTcat -prefix pb04.rall.scale 'pb04.r01.scale+tlrc.[0..166}' 'pb04.r02.scale+tlrc.[0..167}' --> run 1 is missing the last TR. My questions are: 1) is adding a line of "0" for the missing TR in the dfile.rall.1D a good idea (I concatenated this file, too)? Should I have used "*" instead? 2) while the output looks fine - is this concatenation approach a good idea?

As always, thanks so much!

Nic