You should be able to upscale to 1mm space by using the '-applyisoxfm 1' option in flirt on the 2mm images - e.g.:
flirt -in <2mm image> -ref <1mm target> -applyisoxfm 1 -out <1mm output>
> To whom it may concern:
> I am currently using an ROI atlas defined for the MNI152 T1 2mm brain. I would like to extract these atlas ROIs for tractography in subject brains that have been normalized to the FMRIB158 FA 1mm template. What would be the best method for converting the ROI atlas to fit the 1mm template?
> Thanks in advance.