Hi Tim,

I am trying to follow the drifting procedure below. Can I clarify a few points?

You state:
"Once you have this average, you can invert it (like any other warpfield), and 
then concatenate it after the acpc to MNI warp for each subject, giving you a 
new dedrifted (for the chosen population) template space."

>From this I understand that the multiplication and inversion gives us a warp 
>field that warps the MNI registered subject to the new "drifted" space, 
>correct?

By "concatenate it after the acpc to MNI warp" do you mean multiply the 
acpc2mni warp by the new mni2dedrift? Thus generating an acpc2dedrift?

Second, you state: "By carefully finding the volume of brain masks in acpc 
space and after resampling to this new dedrifted space, you can check for this 
effect"

What exactly am I meant to be checking? I should compare the volume of the mask 
in acpc (native) space and in the drifted space. Should they be roughly the 
same volume? Also you say that I should "carefully find the volume" what 
exactly do you mean by "carefully"

Thanks in advance,

Claude

________________________________________
From: Timothy Coalson [[email protected]]
Sent: 02 July 2018 19:28
To: Glasser, Matthew
Cc: Harms, Michael; Bajada, Claude Julien; [email protected]
Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI 
space dedrifting & file structure

We previously looked at the MNI drift, and found that it is almost entirely an 
affine, even for the nonlinear template.  We have a suspicion that this means 
that it was originally caused by the early MNI linear template, and that the 
issue was known by the time MNI nonlinear templates were released, as it 
implies that the nonlinear template was dedrifted, but then an affine was 
deliberately added in order to match the previous MNI linear template.  
However, we have not investigated whether this was the case.

Since all of our anatomical size and shape measurements are computed using a 
rigid acpc space (after gradient distortion correction), this drift in MNI 
space is largely unimportant to many steps of analysis of things like fMRI.  Be 
aware that even with proper dedrifting, any non-rigid volume registration will 
hide differences in brain size (and shape if nonlinear) across subjects, by 
design, so non-rigid volume-registered data won't ever tell you the whole story 
of the anatomical features.  If you want to make some anatomical measurement 
(distance, area, volume), then you should generally measure it in each 
individual's own rigid/acpc space, not in any kind of template space.

Now, on to the explanation: the registration warpfields from each subject's 
rigid acpc ("T1w") space to MNI nonlinear space provide the information needed 
to compute a dedrifted template that matches the population represented by the 
subjects.  Warpfields are displacement vector fields from the output coordinate 
system to the input coordinate system (because of how volume resampling works - 
the output needs to be a regular grid, so you actually need to transform output 
coordinates backwards to the original location).  So, we can take the vector 
fields for each subjects that specify where the MNI-aligned features originally 
were in acpc space, and average those locations for each voxel.  This is simply 
averaging the warpfields that are used to resample volume data from T1w/acpc 
space to MNI space.  Once you have this average, you can invert it (like any 
other warpfield), and then concatenate it after the acpc to MNI warp for each 
subject, giving you a new dedrifted (for the ch
 osen population) template space.

Note, however, that this requires the acpc alignment to have worked well (in 
the HCP pipelines, it is really a rigid registration to an MNI template, not 
specifically using the ac and pc) - if there are any non-matching rotations 
among the rigidly aligned volumes, they can result in causing a shrinkage from 
the true average brain volume.  By carefully finding the volume of brain masks 
in acpc space and after resampling to this new dedrifted space, you can check 
for this effect (it will never be an expansion).  However, the effect may not 
be isotropic, so actually fixing the effect properly requires more thought.  
However, if the acpc alignments are generally close to being the correct 
orientation, this effect should be small.

Note, in particular, that coordinates in this new space will not match MNI 
coordinates, probably not even at (0, 0, 0), you would need to put any 
coordinates through that same average warpfield in order to go between MNI and 
this new space.  You could also tweak the new space by adding a rigid affine to 
the end, so you could line up (0, 0, 0) with MNI space, or similar.

Tim


On Mon, Jul 2, 2018 at 10:21 AM, Glasser, Matthew 
<[email protected]<mailto:[email protected]>> wrote:
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]<mailto:[email protected]>
 on behalf of
Harms, Michael" 
<[email protected]<mailto:[email protected]>
 on behalf of
[email protected]<mailto:[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]<mailto:[email protected]>
>On 7/2/18, 7:14 AM, 
>"[email protected]<mailto:[email protected]>
> on behalf of
>Claude Bajada" 
><[email protected]<mailto:[email protected]>
> on behalf of
>[email protected]<mailto:[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
>
>
>
>--------------------------------------------------------------------------
>----------------------
>--------------------------------------------------------------------------
>----------------------
>Forschungszentrum Juelich GmbH
>52425 Juelich
>Sitz der Gesellschaft: Juelich
>Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
>Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>Prof. Dr. Sebastian M. Schmidt
>--------------------------------------------------------------------------
>----------------------
>--------------------------------------------------------------------------
>----------------------
>
>
>_______________________________________________
>HCP-Users mailing list
>[email protected]<mailto:[email protected]>
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
>________________________________
>The materials in this message are private and may contain Protected
>Healthcare Information or other information of a sensitive nature. If you
>are not the intended recipient, be advised that any unauthorized use,
>disclosure, copying or the taking of any action in reliance on the
>contents of this information is strictly prohibited. If you have received
>this email in error, please immediately notify the sender via telephone
>or return mail.
>
>_______________________________________________
>HCP-Users mailing list
>[email protected]<mailto:[email protected]>
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users


_______________________________________________
HCP-Users mailing list
[email protected]<mailto:[email protected]>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Reply via email to