I have some quality problems with my scans. I'm trying to run recon-all on pediatric brain images but, given the low contrast between cortical regions and the white matter, I do consistently get some problem in the reconstruction of the cortical surface as well as of the segmentation. I was wondering whether there is a tool making use of i.e. the T2 not only to improve the surface (by the way I cannot see the -T2 option in the help of recon -all to do so) but particularly to improve the contrast of the T1. In a nutshell, there is a way to increase quality and contrast by using T1 together with T2 weighted images during recon-all? Another question is how important it is to use the mprage option in recon-all? Thanks,
Francesco Baldacchini
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