Transform atlas on fsaverage to native surface

[Anne-Sophie Kieslinger]

Dear all,

I have the following problem: I have a fsaverage surface parcellation in a "volume-encoded surface segmentation file" (.mgz) and want to align/register/transform this parcellation to a single subject's native surface (since I am assuming this is best for single-subject analysis?).

I have looked at the document "hcp-users FAQ #9: How do I map data between FreeSurfer and HCP" but did not find my case (fsaverage group data to native individual data). I have tried to follow A) but my spheres are not already registered. I am not sure which sphere to register to what or if that is the right approach.

1

I am working with dHCP data where there are no "sphere.reg" files (as far as I can tell), only native surface files. 

Could anyone give me any pointers?

Thanks a lot,

Anne-Sophie

[Tim Coalson]

Data that is already on fsaverage is registered, likely with freesurfer.  You don't need to use native mesh for single subject purposes, 164k has plenty of resolution for even anatomical data.  If you don't have a registered sphere (or something related) for that subject, you can't resample data back to the subject's native mesh, because that registered sphere defines the resampling.

Note that "native surface" can be an ambiguous term, as there is the very different concept of "native volume space".  We generally use distortion corrected, rigid aligned "T1w" space instead of scanner space, and we typically generate 32k and 164k standard mesh surfaces in this space.  However, I believe dHCP uses different pipelines than the ones developed by HCP.

Tim

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[Glasser, Matt]

You need to get this into a NIFTI or GIFTI format to use our instructions.  Perhaps ask the dHCP folks you got it from how to do that or FreeSurfer.

Matt.

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