ok. so basically just go through recon-all output and manually correct whatever might have gone wrong?
best, Lisa On 30 May 2017 at 16:13, Glasser, Matthew <glass...@wustl.edu> wrote: > I would look for locations in which the FreeSurfer aseg is clearly > labeling things outside of the brain as grey or white matter. > > Peace, > > Matt. > > From: Lisa Kramarenko <lisa.kramare...@gmail.com> > Date: Tuesday, May 30, 2017 at 8:59 AM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] values in myelin maps > > Alright, thanks for the quick reply! Should I look for some specific > problem with the surfaces which is to be fixed? I mean I imagine a lot of > things can go wrong with a surface, so that I need to know what exactly to > fix? Or is it something more general like this: http://sites.bu.edu/ > cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality- > control-step-1-fix-pial-surface/ ? > > And does it look like it affect both pial and white matter surfaces, so > that both need to be fixed? > > Sorry for the naive questions and thanks again. > > On 30 May 2017 at 15:51, Glasser, Matthew <glass...@wustl.edu> wrote: > >> Fat saturation reduces the intensity of the fat within the bone marrow, >> which reduces the chance that FreeSurfer will mistake this fat for white >> matter. You would need to have this on during acquisition. As for how to >> fix the surfaces after the fact, I would look at FreeSurfer’s >> documentation. >> >> Peace, >> >> Matt. >> >> From: Lisa Kramarenko <lisa.kramare...@gmail.com> >> Date: Tuesday, May 30, 2017 at 8:49 AM >> >> To: Matt Glasser <glass...@wustl.edu> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: Re: [HCP-Users] values in myelin maps >> >> Yes, this is data of the lab I am in. I assume that I don't have fat >> saturation as I have never heard about it before... If I understand >> correctly it can't be done post-hoc after acquisition and should have been >> done during scanning? Other patients from the same batch (acquired the same >> way) don't have this problem. >> What would be the way to fix the surfaces manually? >> >> Thanks a lot! >> >> On 30 May 2017 at 15:42, Glasser, Matthew <glass...@wustl.edu> wrote: >> >>> Are these of your own data? Do you have fat sat on in your T1w? This >>> looks like most likely surface errors because of not using fat sat and you >>> would need to exclude these subjects or fix the surfaces manually. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Lisa Kramarenko <lisa.kramare...@gmail.com> >>> Date: Tuesday, May 30, 2017 at 7:53 AM >>> To: Matt Glasser <glass...@wustl.edu> >>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: Re: [HCP-Users] values in myelin maps >>> >>> Thanks! >>> Another question I have concerning myelin maps is the following: when I >>> was doing quality control I noticed that some of them look rather weird >>> (see screenshot). Why are some areas grey? And I presume the fact that the >>> values in this grey area are negative, indicates that something is wrong... >>> And are the black parts normal (they still have positive values)? Do you >>> have an idea of what to do? >>> >>> Thanks a lot! >>> >>> Lisa >>> >>> On 29 May 2017 at 15:55, Glasser, Matthew <glass...@wustl.edu> wrote: >>> >>>> They are the ratio of the T1w/T2w images and are a relative measure of >>>> myelin content. See this publication for more details: >>>> >>>> http://www.jneurosci.org/content/31/32/11597.short >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >>>> Kramarenko <lisa.kramare...@gmail.com> >>>> Date: Monday, May 29, 2017 at 5:29 AM >>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> Subject: [HCP-Users] values in myelin maps >>>> >>>> Hello, >>>> >>>> I am not sure what exactly are the values shown for the myelin maps. >>>> E.g. on the screenshot the values are 0.998 to 1.771. I understand that >>>> higher values mean higher myelination and vice versa, but what do they mean >>>> exactly? >>>> Thanks! >>>> >>>> Lisa >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>> >>> >> > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
