I am trying to use ICA-AROMA for denoising of my resting state fMRI data. However, registration/normalization using FLIRT and FNIRT does not work well on my data (the images show quite a lot of atrophy and enlarged ventricles), whereas registration in SPM seems to work much better.
I am therefore wondering whether it is possible to perform AROMA on data that was normalized using SPM? So would it make sense to (1) perform registration and normalization in SPM, (2) do a linear transformation of the SPM-normalized images to the MNI152 template and (3) just use the SPM-normalized functional image plus the affine transformation to MNI space as input for AROMA?
Alternatively, is there any way to use the registration information from SPM as input to AROMA (to specify -warp and -affmat)?
Many thanks in advance for your help!