I was testing a couple of options to skullstrip some MP2RAGE data, and I noticed that if I don’t deoblique the volume first, 3dSkullStrip changes the Qform and Sform in the header of the file - apparently rounding it up to 1 or down to 0.
See the attached files - the headers (skullstripped volume on the right) and the skullstripped volume (in blue-lightblue) over the original image (the green volume is the result of BET). Note that the voxel offset is also different in the headers.
Is there a way to avoid this behaviour? I am trying to avoid deobliquing the original files, in order to not introduce an extra interpolation in the data. Would overwriting the headers be a good move, or since the change in Qform and Sform happened already, it is too late?