Hello AFNI gurus,

I am trying to overlay these two images to see areas of activation. I set the structural MNI as the underlay and the functional as the overlay. When I do this, afni for flash the correctly overlayed images for a second and then I can only see the MNI image. Then after changing the threshold for the overlay, I see that it is there but for some reason is shifted and minimized. I have no idea why it does this since both images are in the same space. I am working in AFNI version 18.1.26 but have replicated this in other versions as well.

The 3dinfo for both images are:
Dataset File: MNI152_T1_3mm.brain.nii.gz
Identifier Code: XYZ_4uNZnWnhn0gVWKG2mRs6wA Creation Date: Wed Feb 11 09:48:52 2015
Template Space: MNI
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 543,266 (543 thousand [kilo]) bytes
Geometry String: "MATRIX(3,0,0,-90,0,-3,0,126,0,0,3,-72):61,73,61"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -90.000 [R] -to- 90.000 [L] -step- 3.000 mm [ 61 voxels]
A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 3.000 mm [ 73 voxels]
I-to-S extent: -72.000 -to- 108.000 [S] -step- 3.000 mm [ 61 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short: -962 to 8353

----- HISTORY -----
[agrethe@taisen.ucsd.edu: Wed Feb 11 09:48:52 2015] 3dresample -rmode Cu -inset ../../standard/MNI152_T1_2mm.nii.gz -dxyz 3 3 3 -prefix ../../standard/MNI152_T1_3mm.brain.nii.gz

Dataset File: lme_resample2.nii.gz
Identifier Code: XYZ_pxLsZ2IFoIuaeyXJoJS2UA Creation Date: Fri Jul 29 16:36:20 2022
Template Space: MNI
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 13,038,384 (13 million [mega]) bytes
Geometry String: "MATRIX(3,0,0,-90,0,-3,0,126,0,0,3,-72):61,73,61"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -90.000 [R] -to- 90.000 [L] -step- 3.000 mm [ 61 voxels]
A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 3.000 mm [ 73 voxels]
I-to-S extent: -72.000 -to- 108.000 [S] -step- 3.000 mm [ 61 voxels]
Number of time steps = 12 Time step = 1.00000s Origin = 0.00000s
-- At sub-brick #0 'GroupCW_Estimate' datum type is float: -0.000110403 to 0.000161289
-- At sub-brick #1 'GroupCW_t.value' datum type is float: -3.17021 to 3.73328
statcode = fizt
-- At sub-brick #2 'GroupCW_pval' datum type is float: 0 to 0.999949
** For info on all 12 sub-bricks, use '3dinfo -verb' **

----- HISTORY -----
[sunc04@gux01-1: Wed Jul 27 23:27:25 2022] {AFNI_18.1.26:linux_openmp_64} 3drefit -view tlrc -space MNI -substatpar 1 fizt -substatpar 5 fizt -substatpar 9 fizt -sublabel 0 GroupCW_Estimate -sublabel 1 GroupCW_t.value -sublabel 2 GroupCW_pval -sublabel 3 GroupCW_pflip -sublabel 4 VisitFED_Estimate -sublabel 5 VisitFED_t.value -sublabel 6 VisitFED_pval -sublabel 7 VisitFED_pflip -sublabel 8 GroupCW:VisitFED_Estimate -sublabel 9 GroupCW:VisitFED_t.value -sublabel 10 GroupCW:VisitFED_pval -sublabel 11 GroupCW:VisitFED_pflip lme_CW_BN_FAST_FED_StopError-GoCorrect_n_15_0.99_TrueModelFreeOutput.nii.gz
[sunc04@gux01-1: Fri Jul 29 16:36:20 2022] {AFNI_18.1.26:linux_openmp_64} 3dresample -inset lme_CW_BN_FAST_FED_StopError-GoCorrect_n_15_0.99_TrueModelFreeOutput.nii.gz -master MNI152_T1_3mm.brain.nii.gz -prefix lme_resample2.nii.gz

Any help is appreciated.