Hi,
I’d like to use SPM to run both first- and second-level analyses, specifically focusing on psychophysiological interactions (PPI). My lab uses fMRIprep as our standard preprocessing pipeline, and we aim to keep both functional and anatomical images in native space (i.e., we do not plan to transform them to MNI space).
Is it possible to import these preprocessed images (in native space) into SPM, or does SPM require that data be in MNI space? If possible, how do you import the correct images from fMRIprep into SPM?
Thanks in advance!
None of the algorithms in SPM’s GLM assumes that the data are in MNI space (e.g. for defining the brain mask), but the ‘glass brain’ view and of course the reported xyz coordinates will not be useful.
So as long as you’re happy to examine the result via the saved images, you’ll be fine. (You can also do inference, and then save the thresholded statistic image, even though the glass brain view will be nonnsense).
-Tom
SPM may complain about gunzipped files and has the annoying (borderline criminal) tendency to dump its output file where it found its input file, so I’d suggest using bids-matlab “copy_to_derivative” to copy / unzipp the files you will work with
https://bids-matlab.readthedocs.io/en/main/api/function_description.html#bids.copy_to_derivative