Hi!
We do use the @SSwarper function in our normal fMRI pipeline (yes, it is amazing!). But this is for another project where I just want skull-stripped brains in native space (no non-linear warping) since we want to use them for classification in a 3D CNN. If we use non-linear warping we will potentially lose the differencies between the patient group and HC that we are investigating. This is why we are also using the VBM approach (normalize to template but compensate for the non-linear warp with Jacobians to keep individual differencies).

But step 1 is to use "raw" data, i.e. skull-stripped GM maps in native space. And so far all skull-stripping tools we have used leaves a lot of tissue in the areas that I described. Are we screwed on this? Perhaps without warping or manual segmentation we can't avoid these regions?

Or can SSwarper skull-stripp without warping to template space?

EDIT: Stopped beeing lazy and tested. @SSwarper did indeed an excelent job skull-stripping without the need of warping. Thank you, it looks so nice =)



Edited 1 time(s). Last edit at 03/01/2021 04:58AM by Robin.