Hi Sima, I've run 6 versions of the same scan of the same subject I got some differences too. Not so big as you found but still some differences
Probably it's the -randomness flag in the recon-all Check: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html> cheers ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business 2009/9/4 sima chalavi <sima.chal...@gmail.com> > > Dear Freesurfer experts, > > We performed 6 different (pilot) structural scans from the same subject > and analyzed the data using Freesurfer in order to find the best scan to > be used in our real experiment. > > We have checked the Freesurfer output visually and there do not seem to be > any problem as described in the trouble shooting manual. So all 6 scans > manage to get through the Freesurfer process just fine. > > > However, There are a lot of differences between the numerical results for > the different scans. Please find Attached graphs of (some of ) the results > of segmentation and parcellation of these 6 sequences from the statistical > outputs. > Now, the problem is how to select the best scan from these results. > > Does any body have a standard protocol for assessing images for analysis > or a standard metric, e.g. goodness of fit, from the software that we can > assess without having a gold standard? > > Or any other tip is also appreciated. > > Thanks in advance, > > Sima. > > > > > > > -- > Sima Chalavi, Ph.D. student > > King's College London > Institute of Psychiatry (IoP) > Box P040, > De Crespigny Park > London SE5 8AF. > Tel:+44-2078485702 > > > BCN Neuroimaging Center (NIC) > University Medical Center Groningen > Antonius Deusinglaan 2 > P.O. Box 196 > 9713 AW Groningen > www.neuroimaging-DID.com > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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