AFNI is changing the signe of an image center

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1

AFNI version=AFNI_24.2.01 (Jul 16 2024) [64-bit]

Dear AFNI experts, 

I recently had a problem with function such as 3drefit or 3dvolreg changing the sign of my image center. Here is an exemple with 3dinfo```

> 3dinfo sub-Roshan_ses-9_task-rest_run-01_bold.nii.gz
> 
> Template Space:  ORIG
> Dataset Type:    Echo Planar (-epan)
> Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
> Storage Mode:    NIFTI
> Storage Space:   183,500,800 (184 million) bytes
> Geometry String: "MATRIX(2,0,0,-63.14847,0,2,0,-27.77728,0,0,2,18.2975):64,64,32"
> Data Axes Tilt:  Plumb
> Data Axes Orientation:
>   first  (x) = Right-to-Left
>   second (y) = Anterior-to-Posterior
>   third  (z) = Inferior-to-Superior   [-orient RAI]
> R-to-L extent:   -63.148 [R] -to-    62.852 [L] -step-     2.000 mm [ 64 voxels]
> A-to-P extent:   -27.777 [A] -to-    98.223 [P] -step-     2.000 mm [ 64 voxels]
> I-to-S extent:    18.297 [S] -to-    80.298 [S] -step-     2.000 mm [ 32 voxels]
> Number of time steps = 700  Time step = 0.70000s  Origin = 0.00000s  Number time-offset slices = 32  Thickness = 2.000
>   -- At sub-brick #0 '?' datum type is short:            0 to         14935
>   -- At sub-brick #1 '?' datum type is short:            0 to         14473
>   -- At sub-brick #2 '?' datum type is short:            0 to         14689
> ** For info on all 700 sub-bricks, use '3dinfo -verb' **
> 
> 
> 3drefit -orient RAI sub-Roshan_ses-9_task-rest_run-01_bold.nii.gz
> 3dinfo sub-Roshan_ses-9_task-rest_run-01_bold.nii.gz
> 
> 
> Template Space:  ORIG
> Dataset Type:    Echo Planar (-epan)
> Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
> Storage Mode:    NIFTI
> Storage Space:   183,500,800 (184 million) bytes
> Geometry String: "MATRIX(2,0,0,-63.14847,0,2,0,-27.77728,0,0,2,-18.2975):64,64,32"
> Data Axes Tilt:  Plumb
> Data Axes Orientation:
>   first  (x) = Right-to-Left
>   second (y) = Anterior-to-Posterior
>   third  (z) = Inferior-to-Superior   [-orient RAI]
> R-to-L extent:   -63.148 [R] -to-    62.852 [L] -step-     2.000 mm [ 64 voxels]
> A-to-P extent:   -27.777 [A] -to-    98.223 [P] -step-     2.000 mm [ 64 voxels]
> I-to-S extent:   -18.297 [I] -to-    43.702 [S] -step-     2.000 mm [ 32 voxels]
> Number of time steps = 700  Time step = 0.70000s  Origin = 0.00000s  Number time-offset slices = 32  Thickness = 2.000
>   -- At sub-brick #0 '?' datum type is short:            0 to         14935
>   -- At sub-brick #1 '?' datum type is short:            0 to         14473
>   -- At sub-brick #2 '?' datum type is short:            0 to         14689
> ** For info on all 700 sub-bricks, use '3dinfo -verb' **

Note the change in I from 18 to -18
tks for your help
2

Howdy-

Well, it isn't a random change. 3drefit will change header info.

What are you aiming to do?

--pt

3

Hey Paul,
you are right, it seems that -oblique_origin keep the center with 3drefit,
however, why is 3dvolreg changing the center?
I am applying several transformations on different images, fMRI, anat
My pipeline keep the center in the anat, and change it with the fMRI images which result in miss alignment
Clément

4

Glad you have a process for the reorientation. What is the problem with the 3dvolreg output? What is the command and the input?