Hi Andreas: As far as I know, the complete command is:
recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm Sincerely, Gonzalo Rojas Costa Laboratory of Medical Imaging Processing Department of Radiology Clínica Las Condes Santiago Chile > Date: Fri, 26 Mar 2010 11:07:01 +0100 > From: Andreas Berger <andreas.berger...@gmail.com> > Subject: [Freesurfer] changing watershed threshold has no effect > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <68f948a91003260307g4fee4b69s9c04624544df2...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attached screenshot1. since the problem is somewhat generalized in > location, i tried to change the watershed threshold as suggested by > the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean > -wsthresh n), but even 0 seems to have no effect (it looks different, > but not less skull), see screenshot2. am i doing it wrong? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
