Dear Tamara,
Correct. The MNI spaces are defined by some official files that were generated in a certain way based on certain subjects. There are other files, generated with different algorithms and/or different subjects, which are brought into agreement with these MNI spaces, inevitably leading to discrepancies. In general, one can live with that, but in your case, it seems odd to e.g. warp GM files from CAT12 onto the 2009 MNI variant, as this MNI variant already has some "proper" tissue probability maps for GM, WM, CSF.
If your study were about warping between spaces then it's absolutely fine of course. Your initial message sounded different though. As far as I know voxel-wise covariate in AFNI means that you forward one additional individual volume for each of the subjects, with values for each of the voxels. If you try to account for individual GM volume and density, which sounds very reasonable for certain purposes, then you really need individual GM files, which would usually be derived by segmenting anatomical scans. Once that you have individual GM files, you would warp them + the functional data into a certain MNI space with a certain algorithm. If you were to run models based on smoothed fMRI data, the GM files should be smoothed accordingly.
The main point is that the fMRI data and the GM files forwarded to the group model were brought into a certain space *in a certain consistent manner*, that is, using a certain algorithm. Whether you use CAT12 or SPM12 Segment or an AFNI equivalent is up to you.
If you want to use CAT12 for segmentation, which has interesting features, then you could do slice timing, motion correction, coregistration of functional data and anatomies with AFNI, switch to CAT12 for segmentation, apply the derived spatial normalisation parameters onto the GM files and the functional data and smooth in SPM, and switch back to AFNI for the models. The data would then represent the MNI space as seen in the CAT12 files. If you want your data to correspond to "AFNI MNI" one could account for that during the spatial normalisation in SPM12 by adding an additional warping step.
Anyway. So much about the options. Maybe you can provide additional information what you are aiming at.
Best regards
Helmut
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