Volume to hcp_s900 surface

neuroimaging
#1

Dear NeroStars,

i am trying to re-sample a volume data (*nii.gz) to the surface, but not sure what is the most proper way to do it.

The volumetric data is a nifti file in MNI152 space, resolution of 4mm. The gray matter voxels are labeled there from 1 to 10k.

The target surface is the HCP_S900 surface, which has 32k vertices on each hemisphere (S900.L.pial_MSMAll.32k_fs_LR.surf.gii for the left hemisphere, and S900.R.pial_MSMAll.32k_fs_LR.surf.gii for the right hemisphere).

Now, I would like to register 10k gray matter voxels to the 64k surface. So far, I tried $wb_command -volume-to-surface-mapping, however, the surface-registered image did not really seem so nice. Is there any way to do the surface registration with freesurfer?

Thanks in advance,
Seyma

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#2

-volume-to-surface-mapping is a reasonable choice (I made a tutorial for using it here https://mvpa.blogspot.com/2018/02/connectome-workbench-making-surface.html), but it’s just going to be a rough approximation. To get higher precision you’ll likely need a pipeline that can do surface preprocessing (e.g., fMRIPrep, HCP pipelines).

But input images at 4 mm isotropic is a pretty low resolution for any sort of surface projection, regardless; I’d expect them to look splotchy.

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