Re: [HCP-Users] Two questions about surfaces & template spaces | MSMall & FS

[Glasser, Matthew]

It is also worth noting that the HCP Pipelines output MSMSulc and MSMAll 
surfaces only (FreeSurfer is worse at aligning function than MSMSulc with more 
distortion).

Matt.

From: 
>
 on behalf of Timothy Coalson >
Date: Monday, July 24, 2017 at 3:38 PM
To: Claude Bajada >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Two questions about surfaces & template spaces | 
MSMall & FS

On Mon, Jul 24, 2017 at 8:40 AM, Claude Bajada 
> wrote:

Dear all,

I have a two questions about the surfaces that live in the HCP data folders:

  1.  MNINonLinear/fsaverage/
  2.  T1w/fsaverageLR32k/

I assume you mean the fsaverage_LR32k folder within each of those folders.

If I have understood the minimal pipeline correctly:

  1.  all the surfaces in MNINonLinear/fsaverage32k/ are the individual's 
surface that was warped into a template space (either FS or MSMAll).
  2.  the surfaces in T1w/fsaverageLR32k/ are the surfaces mentioned in the 
above point that are warped back into the individual's native space

Not exactly.  Volume spaces are a completely orthogonal question to surface 
registration.  Except for some special files, everything in the MNINonLinear 
folder aligns to the MNI template via FNIRT registration.  Everything in T1w 
similarly aligns to the subject's AC-PC rigid aligned space (original size and 
shape of the subject's structural scans, just rotated and moved to the usual 
orientation).

MSMAll, freesurfer, MSMSulc, or any other surface registration does not cause 
any anatomical deformations of the individual's brain.  The standard mesh 
anatomical surfaces you get after surface registration and resampling align 
with the same volumes as the original surfaces.  There is no pre-defined 
anatomical coordinate template in our surface atlases, so we don't need to work 
backward from any template coordinate system.  Instead, we have standard 
spheres that define the standard topology (triangle relationships) - once we 
have the subject's sphere aligned to the standard sphere via template data 
(sulc for MSMSulc or FS; resting state networks, myelin, thickness, etc for 
MSMAll), we can combine the standard sphere's topology with the subject's 
anatomical coordinate data (by resampling the XYZ values), generating the 
subject's standard mesh surfaces.

The surfaces in T1w are generated first, as we run freesurfer on the structural 
scans to generate them.  We then apply the FNIRT warpfield to them to get the 
MNINonLinear versions.

As a side note, group average surfaces ARE significantly deformed from the 
individuals' brain shapes.  Most notably, they contain much less folding, and 
therefore surface area, as all the incompatible or non-corresponding folding 
patterns (when you align based on function, folding becomes less aligned, as 
function isn't always fixed with respect to folds) effectively smooth each 
other out when averaged.  This is why we have correction methods for this when 
doing spatial operations on group average surfaces.

The two questions are:

  1.  Given the above, am I right in assuming that any data that correspond to 
a vertex of a surface in T1w/fsaverageLR32k/ also corresponds to the surface in 
MNINonLinear/fsaverageLR32k/?

 Yes.

> 2. Do you recommend that we the MSMAll surfaces over the FS ones?

Yes, they have considerably better cross subject functional correspondence than 
freesurfer.  That is, if a given vertex index is in area MT in one subject, 
MSMAll will have a considerably higher percentage of other subjects that also 
have that vertex in MT.

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




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Re: [HCP-Users] Two questions about surfaces & template spaces | MSMall & FS

[Timothy Coalson]

On Mon, Jul 24, 2017 at 8:40 AM, Claude Bajada 
wrote:

> Dear all,
>
> I have a two questions about the surfaces that live in the HCP data
> folders:
>
>1. MNINonLinear/fsaverage/
>2. T1w/fsaverageLR32k/
>
> I assume you mean the fsaverage_LR32k folder within each of those folders.

> If I have understood the minimal pipeline correctly:
>
>1. all the surfaces in MNINonLinear/fsaverage32k/ are the individual's
>surface that was warped into a template space (either FS or MSMAll).
>2. the surfaces in T1w/fsaverageLR32k/ are the surfaces mentioned in
>the above point that are warped back into the individual's native space
>
> Not exactly.  Volume spaces are a completely orthogonal question to
surface registration.  Except for some special files, everything in the
MNINonLinear folder aligns to the MNI template via FNIRT registration.
Everything in T1w similarly aligns to the subject's AC-PC rigid aligned
space (original size and shape of the subject's structural scans, just
rotated and moved to the usual orientation).

MSMAll, freesurfer, MSMSulc, or any other surface registration does not
cause any anatomical deformations of the individual's brain.  The standard
mesh anatomical surfaces you get after surface registration and resampling
align with the same volumes as the original surfaces.  There is no
pre-defined anatomical coordinate template in our surface atlases, so we
don't need to work backward from any template coordinate system.  Instead,
we have standard spheres that define the standard topology (triangle
relationships) - once we have the subject's sphere aligned to the standard
sphere via template data (sulc for MSMSulc or FS; resting state networks,
myelin, thickness, etc for MSMAll), we can combine the standard sphere's
topology with the subject's anatomical coordinate data (by resampling the
XYZ values), generating the subject's standard mesh surfaces.

The surfaces in T1w are generated first, as we run freesurfer on the
structural scans to generate them.  We then apply the FNIRT warpfield to
them to get the MNINonLinear versions.

As a side note, group average surfaces ARE significantly deformed from the
individuals' brain shapes.  Most notably, they contain much less folding,
and therefore surface area, as all the incompatible or non-corresponding
folding patterns (when you align based on function, folding becomes less
aligned, as function isn't always fixed with respect to folds) effectively
smooth each other out when averaged.  This is why we have correction
methods for this when doing spatial operations on group average surfaces.

> The two questions are:
>
>1. Given the above, am I right in assuming that any data that
>correspond to a vertex of a surface in T1w/fsaverageLR32k/ also corresponds
>to the surface in MNINonLinear/fsaverageLR32k/?
>
>  Yes.

> 2. Do you recommend that we the MSMAll surfaces over the FS ones?

Yes, they have considerably better cross subject functional correspondence
than freesurfer.  That is, if a given vertex index is in area MT in one
subject, MSMAll will have a considerably higher percentage of other
subjects that also have that vertex in MT.

> 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
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] Two questions about surfaces & template spaces | MSMall & FS

[Claude Bajada]

Dear all,

I have a two questions about the surfaces that live in the HCP data folders:

 1.  MNINonLinear/fsaverage/
 2.  T1w/fsaverageLR32k/

If I have understood the minimal pipeline correctly:

 1.  all the surfaces in MNINonLinear/fsaverage32k/ are the individual's 
surface that was warped into a template space (either FS or MSMAll).
 2.  the surfaces in T1w/fsaverageLR32k/ are the surfaces mentioned in the 
above point that are warped back into the individual's native space

The two questions are:

 1.  Given the above, am I right in assuming that any data that correspond to a 
vertex of a surface in T1w/fsaverageLR32k/ also corresponds to the surface in 
MNINonLinear/fsaverageLR32k/?
 2.  Do you recommend that we the MSMAll surfaces over the FS ones?

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




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