Christian, I suspect that in example3-frontal and example2-frontal you have motion artifacts causing increased intensity in the cortex. On the other, example1-horizontal and example1-sagittal seem to have pretty low SNR, specially in GM, but very good GM-WM contrast. I wonder, if they were not acquired after gadolinium injection?
I don't have a recipe to correct either of the problems, but I don't have good experiences with the images after Gd. They seem to have cortex overestimated. Good luck, Martin On Friday 05 September 2008 15:00:17 Christian Scheel wrote: > Dear FS-Experts, > > While checking the results of the autorecon2 process and editing the > brainmask.mgz and wm.mgz I regularly encounter quite a few spots per brain > where - in my eyes - the red pial line seems to get far too close to the > yellow line making the calculated cortex appear too thin in these regions > (see the three examples attached). Sometimes the lines get so close that > hardly any room for the cortex is left. > > I wonder what might be the best way to deal with these spots. Can I simply > ignore them or should I try to remove some parts of the white matter in the > wm.mgz (which will of course add another subjective factor into the > analysis) or is there another way of handling them that i did not think of? > > Any help is greatly appreciated. > > Best wishes, > Christian Scheel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
