Re: [HCP-Users] values in myelin maps

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 mailto:lisa.kramare...@gmail.com>> Date: Tues

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

Re: [HCP-Users] values in myelin maps

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.

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-re

Re: [HCP-Users] values in myelin maps

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 mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 8:59 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-us

Re: [HCP-Users] values in myelin maps

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 wrote: > I would look for locations in which the FreeSurfer aseg is clearly > labeling things outside of the brain as grey or white matter.

Re: [HCP-Users] values in myelin maps

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 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,

Re: [HCP-Users] values in myelin maps

Yes. Peace, Matt. From: Lisa Kramarenko mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 9:31 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-User