Please see the attached images. We would like to know if these steps are correct. If so, should we do something the erode the low values? or is this normal?
Yes, that’s normal. Warping involves regridding, and regridding involves interpolation, and that kind of “ringing” happens all the time, I think. (Hopefully, your main internal structures are well-aligned; you can turn down the opacity of the overlay to check?)
In fact, the recommendation interpolation kernel for the final data set when you have non-integer valued datasets is “wsinc5”, which will exhibit ringing with tiny values outside the brain; the trade off is that the interpolation inside the brain (where we care about data/values) should be as sharp as possible (or, quite sharp relative to most other kernels like cubic splines). If those tiny values bother you, you can probably automask, or dilate then inflate the brain to remove them, for example such as:
Sorry, I missed the aspect that Daniel pointed out in his reply-- while warps can be calculated individually, they should be concatenated and applied as a single warp. That is probably a much more important point than what I had noted… Daniel pointed out quite useful programs for that-- @SSwarper will combine skullstripping with estimating a warp from subject anatomical to template space. We often recommend that now as part of a standard processing stream: it tends to have nice alignments and also skullstrips the data nicely.
–pt
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