I am trying to work in native space instead of in MNI space.

I would like to transform all my 4D functional data matrices of the same subject to fit the anatomical data (not from the same session).

In the next step I read the nifti into Matlab and use it as a data matrix, so changes of information in the header cannot help me - the transformation should apply to the data itself.

The problem is that my anatomy is in 1x1x1mm resolution, while my functional scan is 3x3x3.3

I would like to keep the original resolution in order to avoid memory issues (right now everything I am trying fails because the data matrix ends up being too large).

This appears to be something very basic, but somehow I found it easier to transform to MNI than to keep the native resolution in the right orientation.

Every help will be much appreciated!

Thank you very much in advance,

Francesca