Dear FreeSurfers, I would like to run the reconstruction process starting from segmentations (grey, white and deep grey matter) obtained with a different software. The ultimate goal is to measure the cortical thickness in correspondence of the regions in the Desikan-Killiany atlas.
I searched for advice in the mailing list archive and I found this: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg11721.html However, it is not up to date and a problem with the incorrect reconstruction of the pial surface is mentioned. I was wondering if somebody has come up with a more detailed idea/description of how doing this. Many thanks, Emma
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