What's the easiest way to get the preprocessed, but not skull-stripped T1 in stereotaxic space?


I would like to get the preprocessed, but not skull-stripped anatomical T1 image of a subject. The docs say that *T1w_preproc.nii.gz and *T1w_space-MNI152NLin2009cAsym_preproc.nii.gz are the same except for the space they are in but that’s not the only difference since the stereotaxic image is also skull-stripped. I can apply the ANTs transformation to get the native space, preprocessed T1 into stereotaxic space but for that I need to have ANTs and that will also not scale so well if I want to do that for 1000 subjects.

Is there some flag I can set to have the T1 in MNI space without brain extraction? Currently I am not keeping the working directory, should I do that and pick this file up somewhere in there? Or could there in the future be an option to get the stereotaxic T1 with the skull?

The reason I am asking for this is that I find it helpful to have the skull in the T1 to determine non-linear template registration quality since that combines information about tissue segmentation and registration. An over-extracted brain would be easily recognizable because the skull would be “squished into” the brain. The opposite case is also easy to spot due to the “bobble-head” phenomenon of the excess brain volume living outside the fitted brain mask.