Re: [Freesurfer] changing watershed threshold has no effect

-- On Tue, 13 Apr 2010, Andreas Berger wrote: > 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 astevens@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 astevens@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. >>>> >>> >>> >>> > > >