Question regarding MNI space


I am hoping to include a covariate in my ANOVA to account for group differences in grey matter volume at the voxel-wise level. Specifically, I used the CAT12 toolbox in SPM to obtain voxel-wise grey matter probability maps for each of my participants and I would like to include these as covariates in my ANOVA (3dMEMA). This way I can control for atrophy in a finer scale versus using the mean GM volumes.

These grey matter probability maps are in a MNI152 space (Template_1_IXI555_MNI152_GS.nii to be exact). I completed my functional pre-processing using the SSwarper (MNI152_2009 template). Would these images be in the same “space” or do I need to convert the grey matter maps into a space that is more similar to SSwarper’s template?

Thank you very much,


Correction, I used 3dMVM for my ANOVA, not 3dMEMA

I don’t know that software package, but I found some limited information online. It would be best to ask the authors for that information. There are many flavors of MNI, and you will need a fairly accurate match to make these voxelwise covariates useful. The MNI152_2009 template we use is the asymmetric 2009c version, but there are several others.

Thank you very much!

If the GM maps are in a different MNI space, would it be possible to convert it into the MNI asymmetric 2009c version using 3dwarp?

Thank you,

3dWarp applies affine transformations, and that’s probably not accurate enough for this application of transforming among MNI variants. 3dQwarp could be used to align one MNI template to another. The warp computed there could be applied to the gray matter or CSF probability maps.

Great, thank you very much.

Just thinking about another possibility as I wait for SPM to get back to me…would I be able to convert the GM probability maps into talairach space using 3dwarp and then convert into the MNI 2009c template, or would this be too many conversions?

Thank you very much.


The generic transformations that you might use for this are very, very approximate, and I wouldn’t recommend them for an application like this where you will need very fine accuracy.

Also, the SPM group isn’t the author of that CAT toolbox package, so I’m not sure the SPM mail server is the best place to ask questions. The author’s email address is listed at the bottom of the project page:

Thank you very much for your help!!