Projection from MNI 2mm to native space/bold space

Hi,
I would like to project an ROIs file in MNI space to native space/ bold space of each of my subjects. All subjects were prepossessed using CPAC. Linear transformation file are in mat format.
I am wondering what is the most efficient tool to do the transformation and which transformation file from the CPAC outputs I should use.

Thanks in advance,
Keren

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