Differences in orientation/voxel size pre- and post-scanner upgrade



I am analyzing data collected pre- and post-scanner upgrade using fMRIPrep for pre-processing and SPM for stats. There are slight differences in the images, and I am unable to run second level analyses in SPM. Is there a way to adjust the dimensions of the post-upgrade images to equate them to the pre-upgrade images?

Here is the corresponding error message and example dimensions:

Running ‘Factorial design specification’
Mapping files :
** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment.
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.

[3.203 0 0 -99.703; 0 3.203 0 -135.703; 0 0 3.21 -81.71] K:\Blevins\R15\Cyberball\SPM\first\controls\sub-21\sham\con_0001.nii
[3.203 0 0 -99.703; 0 3.203 0 -135.703; 0 0 3.21 -81.71] K:\Blevins\R15\Cyberball\SPM\first\controls\sub-21\sham\con_0003.nii
[3.203 0 0 -99.703; 0 3.203 0 -135.703; 0 0 3.2 -81.7] K:\Blevins\R15\Cyberball\SPM\first\controls\sub-27\sham\con_0001.nii
[3.203 0 0 -99.703; 0 3.203 0 -135.703; 0 0 3.2 -81.7] K:\Blevins\R15\Cyberball\SPM\first\controls\sub-27\sham\con_0003.nii

Thank you so very much for any help you can provide!




If you’re working in MNI space, then you should be able to specify --output-space MNI152NLin2009cAsym:res-2, and the voxel sizes will be normalized to 2mm isotropic.