Hi! I have a set of EPI data that were oblique, so I ran the data through the AFNI 3dWarp -deoblique command as an initial step for pre-processing. However, I encountered a problem for one participant, which ultimately resulted in my Run 1 and Run 2 task-based functional data not having the same number of voxels along the x-axis. Could you please take a look for me and let me know what might have caused this problem and how I could resolve this issue? Thank you so much!
Here is the original dimension for my Run1 and Run 2 fMRI data:
Run 1:
Data Axes Tilt: Oblique (37.000 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -113.855 [R] -to- 102.707 [L] -step- 3.438 mm [ 64 voxels]
A-to-P extent: -188.762 [A] -to- 27.800 [P] -step- 3.438 mm [ 64 voxels]
I-to-S extent: -124.056 -to- 27.944 [S] -step- 4.000 mm [ 39 voxels]
Run 2:
Data Axes Tilt: Oblique (36.304 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -110.531 [R] -to- 106.032 [L] -step- 3.438 mm [ 64 voxels]
A-to-P extent: -189.005 [A] -to- 27.557 [P] -step- 3.438 mm [ 64 voxels]
I-to-S extent: -125.130 -to- 26.870 [S] -step- 4.000 mm [ 39 voxels]
After I ran 3dWarp -deoblique -prefix $run.warp $run+orig, below is the resulting Run 1 and Run 2 dimension (showing different numbers of voxels on the x-axis, highlighted in red):
Run 1:
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: -113.855 [R] -to- 102.707 [L] -step- 3.438 mm
[ 64 voxels]
A-to-P extent: -147.001 [A] -to- 121.124 [P] -step- 3.438 mm [ 79 voxels]
I-to-S extent: -125.382
-to- 128.993 [S] -step- 3.438 mm [ 75 voxels]
Run 2:
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: -111.612 [R] -to- 108.388 [L] -step- 3.438 mm [ 65 voxels]
A-to-P extent: -149.319 [A] -to- 118.806 [P] -step- 3.438 mm [ 79 voxels]
I-to-S extent: -127.701 -to- 126.674 [S] -step- 3.438 mm [ 75 voxels]