For tractography of HCP data you would use the surfaces in
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/ and the diffusion data in
${StudyFolder}/${Subject}/T1w/Diffusion, which have the same ACPC rigid
registration to MNI space. If you want your tractography data to be aligned
with MSMAll across subjects, use the surfaces with _MSMAll in the names. If
you want to use MSMSulc, use the surfaces without _MSMAll in the names.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Claude Bajada
<c.baj...@fz-juelich.de<mailto:c.baj...@fz-juelich.de>>
Date: Tuesday, July 25, 2017 at 2:18 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Two questions about surfaces & template spaces |
MSMall & FS
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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