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
