Dear Michael Chappell,
Thank you very much for your quick and clear reply. You are right to assume that the oxford_asl runs fine without partial volume correction.
I've tried supplying the structural mask in the same resolution and orientation as the ASL image. The partial volume correction runs until iteration 7 instead of 4, but crashes afterwards (same problem).
You suggested thresholding the partial volume estimates was a cause of the problem, this seems to be true. When I don't threshold the partial volume estimates the partial volume correction runs until the end without problem. Usually I threshold the partial volume estimates with 0.1, as suggested (after applying the transformation matrix from structural to ASL space and performing a warp). This results in multiple voxels with value zero (no tissue), as you said.
What do you think is the best solution? Simply don't threshold the GM and WM pve, or try something else? I am certain that the ASL mask and pve are in good agreement (no misalignment).
Best regards,
Jordi
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