Sorry, the recommended sphere for resampling any subject will of course be
that subject's version of that file, not specifically subject 100307's
sphere.
Tim
On Wed, Feb 20, 2019 at 1:31 PM Timothy Coalson <tsc...@mst.edu> wrote:
> On Wed, Feb 20, 2019 at 8:03 AM CHAUMON Maximilien <
> maximilien.chau...@icm-institute.org> wrote:
>
>> Hello,
>>
>> I'm looking at fine changes in MEG forward leadfields and would like to
>> use the 164k meshes in each subject (I know 164k vertices are overkill, but
>> I need this high res rendering for one of my figures). I'm interested in
>> the actual original location of individual vertices in the brain in
>> subject-specific ACPC-aligned headcoordinate space. I don't want any non
>> linear spatial transformation applied to the mesh.
>> So I would like to use the 164k mesh with coordinates without the
>> nonlinear transformation that (as far as I understand) was applied to all
>> the 164k_fs_LR files. Is there an easy way to revert the non linear
>> transformation?
>>
>
> Only the surface files under the MNINonLinear folder have had any
> nonlinear anatomical warp applied. The surface files under T1w all line up
> with the distortion corrected, rigidly aligned T1w image (we don't really
> keep scanner space around, and we often call this distortion corrected
> rigid alignment space "native volume space"). Surface
> registration/resampling does not deform the anatomy, it just tiles the same
> contour in 3D space with a new set of triangles.
>
> Note that averaging the coordinates of vertices across subjects will
> change their location, and this will affect geometry and "foldedness", to a
> degree depending on what registration was used. As long as you stick with
> individual surfaces, you don't need to worry about this.
>
>
>> I would then use the file
>> {Subject}.{Hemi}.midthickness.164k_fs_LR.surf.gii and apply the inverse
>> transformation,
>>
>> Alternatively, is there a way to easily downsample
>> {Subject}.{Hemi}.midthickness.native.surf.gii to 164k vertices? is this
>> then in subject-specific ACPC-aligned headcoordinate space? how could I
>> move to that space?
>>
>
> This is what the existing 164k surfaces in the T1w folder already are.
> Native mesh is commonly ~130k for HCP scans, so 164k is actually a small
> upsampling. We recommend the MSMAll versions, as the same vertex number
> across subjects is more often in the same area than for other registrations.
>
> For reference (since we have already dealt with this resampling for you),
> the recommended sphere to use for resampling from native mesh to any fs_LR
> mesh is "MNINonLinear/Native/100307.L.sphere.MSMAll.native.surf.gii" (and
> the R version, of course). Ignore the fact that it is in the MNINonLinear
> folder, sphere surfaces don't have a volume space, that is just where it
> got put. The standard spheres for fs_LR are in the pipelines
> under global/templates/standard_mesh_atlases/, read the readme file. The
> command to do surface resampling is wb_command -surface-resample.
>
>
>> Does that make sense?
>>
>> Many thanks,
>> Max
>>
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>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
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