What version are you running? The cmd should be -autorecon2-cp -autorecon3 Make sure you put control points in only white matter with no partial volume gm, otherwise things will go very wrong Cheers Bruce
On Nov 23, 2012, at 7:01 AM, Catherine Bois <clb...@york.ac.uk> wrote: > ps. could this have anything to do with the script Ive been using during > reconstruction? If so, what is the correct command line to use in order to > make sure edits to white matter mask/control points and the pial surface are > incorporated during reconstruction? > > Thanks! > > On 23 November 2012 10:06, Catherine Bois <clb...@york.ac.uk> wrote: > Hello, > > I have a question re reconstructing brains (ie after doing the edits and > running them again to ensure the edits went through). Before the > reconstruction, the whole brain was there, however afterwards, large chunks > of the brain is missing. Im worried whether this is something to do with the > edits i have done; ie can control points/white matter edits actually make > parts of the brain "go missing"? Or is it more likely that somewhere along > the process the watershed parameters changed/gone wrong? Has anybody else > experienced this problem? > > Thank you so much for your help > > Regards Cathy > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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