Thanks Tim et al,
I have some follow-up questions:
* I am performing tractography by defining an individual coordinate
(in mm not voxels). If I use an XYZ that corresponds to one of the
vertices on the 'white.32k' surface, that should correspond to the
same point in the DWI data. Correct?
* Would the rotation affect this? ("just rotated and moved to the
usual orientation"). I was under the impression that the DWI and T1
were also rotated into the usual orientation.
You state:
"The surfaces in T1w are generated first, as we run freesurfer on
the structural scans to generate them."
I assume that these are the ones living in T1w/Native/
"We then apply the FNIRT warpfield to them to get the MNINonLinear
versions."
These live in MNINonLinear/Native
Then you downsample them to 32k... in MNINonLinear/fsaverage_LR32k
The minimal processing pipeline publication (Glasser et al 2013)
then states:
"Finally, this 32k_fs_LR mesh [I'm assuming the one mentioned in the
point above] is transformed from MNI space back to the native volume
space"
The question is:
* Is this now a correct interpretation?
Regards,
Claude
On 24.07.2017 22:38, Timothy Coalson wrote:
On Mon, Jul 24, 2017 at 8:40 AM, Claude Bajada <c.baj...@fz-juelich.de
<mailto:c.baj...@fz-juelich.de>> 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
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Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
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Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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