do I find the files I should inspect in the
{subject_id}/T1w/{subject_id}/mri/ folder?On 30 May 2017 at 16:28, Lisa Kramarenko <lisa.kramare...@gmail.com> wrote: > 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/cnrl >> ab/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
