Hello all,

I am currently trying to register a confocal stack of just over half a brain (http://imgur.com/a/W8iCc#0) to a full and complete reference brain (http://imgur.com/a/W8iCc#1). Attempting to register the images as-is gives a reasonable result, but there are quite a number of imperfections, many of which have large deformation errors. As such, I thought I'd try to 'help' the process by removing some of the more problematic areas that we're not interested in (http://imgur.com/a/W8iCc#2 and http://imgur.com/a/W8iCc#3) by simply deleting regions in ImageJ (i.e. setting the pixel values to 0). However, this obviously creates sharp edges at the boundaries between the original image data and the regions that I've removed, and this seems to drastically mess-up the registration process, to the point where reformatted images are empty.

Is there any way to pass a mask into the registration procedure, or an alternative that would have the same effect? If not, would I be best off adding Gaussian noise, centred on the average background level of the original image, to the edited images to try and reduce this problem?

Thanks,
Ashley