Re: [Freesurfer] changing watershed threshold has no effect

-- On Tue, 13 Apr 2010, Andreas Berger wrote: > 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. > > EDIT: forgot to attach the screenshots, sorry once more... > > > On Tue, 13 Apr 2010 08:20:40 -0400 (EDT) > Allison Stevens astevens@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 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. >>>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > >