thank you for replying, i reattached the screenshots. they were in my first mail but i think i broke the thread by replying to the wrong adress once, sorry. screenshot 1 is result of "recon-all -all", screenshot 2 is result of "recon-all -all -wsthresh 0". what's weird is that next to the left hemisphere there's some skull left that wasn't even there with default settings.
On Tue, 13 Apr 2010 08:20:40 -0400 (EDT) Allison Stevens <astev...@nmr.mgh.harvard.edu> wrote: > Thanks, Andreas. That clears it up. > > There was no attachment though. Can you send me the screenshots? > > -- > > 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 <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
