Thanks Matt and Mike, I'll await to hear from Tim re: his thoughts on drifting.

Mike, thanks for confirming that all structural quantities are measured in real 
(native) space. Just a quick follow-up question / comment to ensure my 
understanding. Am I correct in assuming that the quantities have been resampled 
to the MSMALL 32K mesh, it is then just a matter of visualising them on the 
same mesh that has been warped to either native space or MNI space. Is there 
aren't trip different cortical thickness ciftis one for MNI space and the other 
for native. Have I understood correctly?

Regards,
Claude

________________________________________
From: Glasser, Matthew [[email protected]]
Sent: 02 July 2018 17:21
To: Harms, Michael; Bajada, Claude Julien; [email protected]
Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI 
space dedrifting & file structure

Tim Coalson can explain how to dedrift MNI space (which as Mike says is no
longer true MNI space).

Peace,

Matt.

On 7/2/18, 10:10 AM, "[email protected] on behalf of
Harms, Michael" <[email protected] on behalf of
[email protected]> wrote:

>
>Hi,
>Re (1):
>If you want to work with streamlines in MNI space then you have to accept
>the "drift" (volume expansion) that is part of MNI space itself.
>
>Re (2):
>Maps may be resampled to surfaces in MNI space.  But all the FreeSurfer
>structural quantities that we provide in the database/spreadsheet in
>ConnectomeDB are measured in the subject's real (native) space.
>
>Cheers,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>-----------------------------------------------------------
>
>Associate Professor of Psychiatry
>
>Washington University School of Medicine
>
>Department of Psychiatry, Box 8134
>
>660 South Euclid Ave.                        Tel: 314-747-6173
>
>St. Louis, MO  63110                          Email: [email protected]
>On 7/2/18, 7:14 AM, "[email protected] on behalf of
>Claude Bajada" <[email protected] on behalf of
>[email protected]> wrote:
>
>Dear experts,
>
>I have a few questions:
>
>1) I am currently working on a project using tractography and the HCP
>data. I have used the HCP provided FNIRT based MNI registration in order
>to register individual streamlines from "native" or diffusion space (as
>per post HCP minimal processing pipeline) to MNI space. However, in
>Glasser 2016 supplementary text, it states that the MNI space is drifted
>relative to the mean brain size of individual brains (greatest along the
>x and z axes). I've been told that it is possible to "dedrift" these
>data and I wonder if anyone has experience in doing this and is able to
>point me in the right direction.
>
>2) from what I understand, structural qualities such as cortical
>thickness etc are measured in the individual's real space. However then,
>what I do not understand is the file structure of the HCP data. The
>structural measures such as cortical thickness, curvature and myelin
>maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the
>'native space' directory. Can anyone shed light on this?
>
>Regards,
>
>Claude
>
>
>
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