I have run the AROMA and 2mm resampling grid options with FMRIMPREP, for each of the BOLD MRI, I got the brain mask and two output images:
These two images both have the 2mm voxel size but different dimension as stated above.
These two images lines up perfectly, but with a 2mm atlas I have in the MNI space, even with the same dimension, its voxels could not align with the above 2 images. In each of the axis, they are all of by less than a voxel.
I think this is because of the slight difference in the transformation matrices.
Comparing the non-aggressive AROMA output which has the same voxel dimension with my atlas (91x109x91),
the MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz has the following transformation matrix:
2 0 0 -90.5
0 2 0 -126.5
0 0 2 -72.5
0 0 0 1
and the transformation of my atlas:
-2 -0 -0 90
-0 2 -0 -126
0 0 2 -72
0 0 0 1
Could anyone please suggest on how I could solve the problem?
Thank you very much!