I have two sets of MRIs with different resolutions (0.9mm3 and 1mm3 isotropic). At the moment I ran the hippocampal segmentation on both so I assume that the volume I obtained from 0.9mm3 was downsampled to 1mm3 after recon-all. I just read that recon-all allows us to keep the resolution using the -cm flag, the question is would the volume I obtain after rerun with -cm from 0.9mm3 scans be comparable with the volume I obtained from the other set (the 1 mm3 scans) or is it better to keep the downsampled ones? 

Some subjects also have high-resolution T2 (0.4x0.4x2 mm3) scans, would running the recon-all with -cm affect the T1+T2 segmentation result as well?

Thank you very much.

Kind regards,

Jacob