I have processed the majority of my T1 images using the general recon-all command. After reviewing segmentation, a number of images have the pial surface included in the gray matter. I re-ran an image with the recon-all command combining the T1 and T2 images and it greatly reduced the segmentation errors. Going forward, are there quality differences between those images processed with only recon-all versus those processed with recon-all T1 & T2? Can I still combine images processed with T1 only and those with T1 & T2 in the same analysis? Or, do I need to rerun all scans with the recon-all T1 &  T2 command? 

Thank you,