Hello
I am trying to use the output from 3dvolreg to adjust a data set using 3dAllineate -1Dparam_apply.
Reading the program help file: 3dvolreg outputs:
roll = rotation about the I-S axis }
pitch = rotation about the R-L axis } degrees CCW
yaw = rotation about the A-P axis }
dS = displacement in the Superior direction }
dL = displacement in the Left direction } mm
dP = displacement in the Posterior direction }
Question 1) Would 'dL' be x-shift; 'dS' be y-shift; and 'dP' be z-shift?
I ask this because I read in 1dApar2mat help file:
* The 12 parameters are, in the order used on the 1dApar2mat command line
(the same order as output by 3dAllineate):
x-shift in mm
y-shift in mm
z-shift in mm
z-angle (roll) in degrees (not radians!)
x-angle (pitch) in degrees
y-angle (yaw) in degrees
x-scale unitless factor, in [0.10,10.0]
y-scale unitless factor, in [0.10,10.0]
z-scale unitless factor, in [0.10,10.0]
y/x-shear unitless factor, in [-0.3333,0.3333]
Question 2) OR if my understanding of the ordering in question 1 is incorrect. Can someone please show me how to correct the below array using the output of 3dvolreg, to input in 3dAllineate ('C1' is Column 1 which is rolll, 'C2' is Column 2 which is pitch, etc.):
C1 C2 C3 C4 C5 C6 ===> ?
Question 3) How can I easily add columns of zeros to the end of the 1Dfile output by volreg so it can have the required 12 columns for 3dAllineate? Currently, I do this in matlab, but to know how to do in AFNI would be very helpful.
OR is there a more simple way to do what I am trying to do?
Thank you in advance!
Cheers,
Edwin
