I am attempting to use the pipelines to look at functional data on the individual surface on my own (not HCP) data. I used the pre, free, and post hcp processing scripts and judging from the myelin maps, the output was good. When I projected the functional activation to the surface (all in native space) using the wb_command -volume-to-surface-mapping, the functional activation was clearly very poorly aligned with the surface, to the extent that half of the brain activation map was missing. There are several t1_w nifti files that I could align the volume to and I am not sure which one to use. There is for example T1w_restore.nii, T1_restore.2.nii.gz, t1w.nii. Are there any guidelines on how to project functional data onto the surface in native space, or is this not the correct approach. Should the data be normalized to MNI and then projected to surface within MNI space. Thank you,
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