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Dear AFNI users-

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Sincerely, AFNI HQ

History of AFNI updates  

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March 01, 2023 06:26PM
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
Subject Author Posted

Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 01, 2023 06:26PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 01, 2023 07:30PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 09:47AM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 11:12AM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 12:00PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 12:14PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 12:25PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 12:34PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 12:44PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 12:55PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 01:00PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 01:08PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 01:40PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 02:38PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 03:00PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 04:44PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 05:19PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 05:37PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

ebaldelo March 02, 2023 06:06PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

rick reynolds March 02, 2023 06:32PM

Re: Translating 3dvolreg 1Dfile to 3dAllineate -1Dparam_apply

Daniel Glen March 13, 2023 10:36AM