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The initial ASL reference image is created from M0 scans when available, or control images when M0 scans are not available. However, CBF will have a better gray matter-white matter contrast, so, once we have CBF data, it should be a superior reference image for the T1w registration.
I think I'll need to move the CBF workflow into init_asl_fit_wf, so that the coreg aslref can be created fro native-space CBF data instead of the ASL data.
Summary
The initial ASL reference image is created from M0 scans when available, or control images when M0 scans are not available. However, CBF will have a better gray matter-white matter contrast, so, once we have CBF data, it should be a superior reference image for the T1w registration.
Additional details
Thanks to @caugolm for the suggestion.
Next steps
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