Fsnative to fmriprep fsnative space

Software Support
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1

I’ve noticed that the coordinates in the fsnative surfaces output from fmriprep differ from the freesurfer sourcedata fsnative surfaces.

I’m wondering what transformation is used to go from one to the other?

So far I’ve tried:

  1. mris_convert --to-scanner lh.pial lh.pial.surf.gii

Having mri_convert output in scanner space instead of FS tkr space gets you VERY close to the fmriprep output, but there is a slight offset.

  1. Subsequently using wb_command --surface-apply-affine to apply the “_from-fsnative_to-T1w_mode-image_xfm” transformation. This also doesn’t match the fmriprep surface coordinates.

Is there a different command or different transformation matrix output by fmriprep that could be used to do this successfully?

Thanks,
Nathan