ENH: Optimize co-registration of T1w to petref, and provide more options for petref generation #185
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ANTS coregistration implementation
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@mathesong - think this is ready for review. Will continue to do more testing locally on my end and test robustness/performance. We may want to consider making ants the default option for co-registration. WDYT? But this should go into a separate PR. |
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Looks good to me! I've been testing this over the weekend on my other dataset too, and unfortunately it's not a silver bullet. I still have failures in ~25%. Some overlapping from before, some not. So better than before, but not quite as robust as I had hoped. I then ran it with the hmc with a 2mm fwhm, and it's saved a few, but they're still causing issues. So I'm not really sure what the default ought to be if we still have issues :\ I suspect that the primary issue is that for this tracer, there's just so much uptake outside the brain in the PET, which makes things messy. There's got to be a solution somewhere... |
mnoergaard
changed the title
This reverts commit f878d27.
…u.mgz Adjust PET co-registration workflow to allow for a different anatomical reference
This PR addresses issue #184 and #177 by adding support for 1) using other reference PET images for e.g. co-registration, and 2) implementing an additional option for performing PET to anatomical co-registration using ANTs. It implements the possibility to use 'twa' which is a time-weighted average of the motion corrected PET data. Furthermore, it also allows the use of 'sum' which is a summed image across time for the motion corrected PET data. Finally, it also allows the use of 'first5min' which is the average of the first 5 minutes of PET data, representing a perfusion-like image. The default is still the template generated from the motion correction using mri_robust_template. Finally, the co-registration is optimized by added the robustfov functionality from FSL to the preprocessed T1w before co-registration. This is to avoid the inclusion of neck and shoulder that will ultimately impact the registration.