In the anat output folder from FMRIPREP among all other files you will get:
I read from the documents that the T1w image was first skull-stripped before warping into the MNI space.
Therefore, in order to use the composite warp field (sub-XXX_ses-baseline_T1w_target-MNI152NLin2009cAsym_warp.h5) file, does it means that this warp field could only work on a skull-stripped T1w image?
Does applying this warp field to the non-skull-stripped T1w image generate the same result? (I mean for instance, will the gray matter or a particular ROI be warped into the exactly same voxels in the MNI space as if the warp field was applied to a skull-stripped T1w image? )
Or if it doesn’t matter at all, since you could still apply the sub-XXX_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz after applying the warp field to a non-skull-stripped T1w to get the brainmasked voxels anyway?
So, in essence, I am asking whether applying the warp field to both a skull-stripped and non-skull stripped T1w of the same subject and applying the brainmask give you exactly the same image?
Thank you very much!