Hello,
I have whole brain T1 maps and the pseudo T1-weighted images that I created out of them (so they are perfectly aligned). The are all brain extracted using fsl and I am doing my own tissue segmentation (again, using fsl), but in both steps there is much optimization involved, because I want to do it very carefully avoiding partial volume effects (I am looking at the cortical T1 values). I would like to look at the maps in the inflated and flattened spaces. So I have been learning freesurfer over the past week but my problem is with the surface reconstruction and that everything is automated. I don't want freesurfer to do the segmentation for me. I was hoping it would work well because the data is 1x1x1- but the segmentation is not nearly as precise as I need it. Is there a way that I give my already aligned T1 maps and structural images and tissue segmentation and get out the surfaces with T1 values on top of it?