on one group of subjects i ran "recon-all -all -clean -wsthresh n", which according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags includes what "-clean-bm" does.
on the other group i ran "recon-all -all -wshthresh n" after deleting everything and converting them from raw invol data to freesurfer format again. as i understand it, "-clean" is not required because no previous data is there to be overwritten/cleaned. to prevent confusion, i am not comparing these two groups, it's just that we have a separate group of subjects of which whe don't have the raw data, so i had to use -clean. i compared using "-wsthresh" against not using it in a few subjects from both groups. as far as the "-clean" flags are concerned, there is no bug: they do change the result, so i assume the previous volume is overwritten as it should, however the results are no improvement (see screenshots). On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) Allison Stevens <astev...@nmr.mgh.harvard.edu> wrote: > Andreas, > I'm not very clear on your response. Did using -clean-bm on the subjects > you had used -clean on when running with -wsthresh, change the skull strip > for the better? > > when you ran it on the already clean data set, you said using -wsthresh 0 > still did not get a good skull strip? > Allison > > -- > > On Fri, 9 Apr 2010, Andreas Berger wrote: > > > Sorry for the slow response, > > > > yes, the "-clean" flag should imply "-clean-bm" (among others) > > > > besides, on one group of the subjects i ran "recon-all -all -wsthresh n" > > after converting them from invol data again, everything from scratch (no > > cleaning required), with the same result. also, the fact that the surfaces > > did change (however not as i hoped) indicates that it's not a problem with > > the flags. > > > > > > > > > > On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) > > Allison Stevens <astev...@nmr.mgh.harvard.edu> wrote: > > > >> Andreas, > >> Did using -clean-bm work? > >> Allison > >> > >> -- > >> > >> On Mon, 29 Mar 2010, Allison Stevens wrote: > >> > >>> Andreas, > >>> Let me know how this turns out. The response you got about the command > >>> (using > >>> -clean-bm) is correct but since you used -clean, that should have worked > >>> just > >>> as well. Can you please let me know if using -clean-bm does anything > >>> differently from -clean? If so, we'll have to investigate this as a > >>> potential > >>> bug. > >>> Thanks, > >>> Allison > >>> > >>> > >> > >> > >> 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. > >> > > > > > > -- Andreas Berger <andreas.berger...@gmail.com> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
