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From: Hoekstra, Liesbeth Sent: Wed 12/8/2010 11:11 To: freesurfer@nmr.mgh.harvard.edu Subject: talairach and scullstrip, order and control points, questions
L.S.,
Let me start by saying that you've got a wonderful webpage! I'm a beginner in the Freesurfer field. I worked my way into the method (incl. tutorial and talks), but I've still got a couple of questions about the cortical thickness measurement. 1) when starting after autorecon1 with the talairach transformation and the scullstrp, is it enough to just save the transformations (save reg)? (in the tutorial it said, that you have to rerun autorecon-all, but if you just start the procedure, it seems unlikely to me) 2) small parts of the dura in scullstrip procedure, can they be left in place in the new version of Freesurfer (I read something on the qeustions-page, that allmost everything is automatically transformed, but that still manually must be checked if BIG differences remain (id est: big parts of skull remaining, brain is removed) 3) It is a little confusing, in the order of the Freesurfer workflow the control points are set between autorecon 1 and autorecon 2, but if you set them you have to run autorecon-cp (again). Can I set the control points just after the autorecon 2? 4) Can I do autorecon 2 than do the white matter edits , pial edits and final surfex and than rerun autorecon 2 before going to autorecon3 , or do I have to rerun after each individual step?
thanks a lot for your answers, I'm looking forward to it to continue my analysis,
L.Hoekstra
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