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<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:49 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 7:53 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Monday, May 29, 2017 at 5:29 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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

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