Hi Linn, do you mean the brain mask in the cross sectional runs gets worse after you run the longitudinal steps (base and long)? That is not really possible, as these steps don't touch the cross data (only read from it).
If you mean that the brain mask in the long looks worse than in the cross (of same subject time point), then you need to check the brain mask in the base. That one is copied to all the longitudinal runs, so it needs to be accurate in the base. If it is accurate there, but still not in a specific longitudinal run then that indicates a mis-alignment to the base. If that is the case, the first thing I'd try is rename base and all longitudinals and re-run those from scatch to make sure it's not a hick-up (e.g. io problem). Best, Martin On Jun 18, 2013, at 5:16 AM, Linn Mittlestein <linnmit...@gmail.com> wrote: > Dear Freesurfer group. > > I am having some concerns about Freesurfer and the different steps. I have > used version 5.0 for the cross-sectional timepoints, and I am now using > version 5.3 for the longitudinal processing. I am doing therefore the several > different steps involved in longitudinal processing, for example -base, -long > runs and now for the lme analysis with matlab also the smoothing steps etc. I > am very concerned however because looking at the brain masks after these > steps have been done (ie the cross-sectional runs), they look much worse than > they did before the longitudinal editing began; large chunks of surfaces are > missing. Has anybody else reported this problem? Could it be because the > longitudinal steps are now being done with version 5.3 as opposed to 5? > Surely this should not have such a large effect on the brainmasks, as to > completely "deform" them? > > Kind Regards, > > Linn > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu
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