hi Lysianne and Paul,
hope you don't mind me jumping in here; i'm having a very similar issue with some 7T MP2RAGE data (which i denoised first); see attached after an SSwarper run.
did you find a solution to Lysianne's problem? i've run 3 other subjects from this dataset through SSwarper and they finished fine. note that the final anatQQ*.nii image looks okay *at first glance*, but it seems to have taken this bad native-space skull-strip and performed an extreme warp on the remaining parietal to match the MNI template shape.
so as for this subject, i could start troubleshooting with the 'lpa' cost suggestion, or something like -SSopt -push-to-edge, etc but if you've already arrived at a solution i'd love to try that first because as we know SSwarper takes a while. let me know if you'd like more info or data or scripts (i just ran the most vanilla SSwarper command possible). thanks!
-Sam
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