Hello, 

I am PhD student currently working with CT images that contained random mislabeled axes (e.g. Left was marked as Anterior, Posterior was marked as Superior, etc., but there was no consistency across subjects). 

I used MicroGL (Import>Tools>Reorient) function to manually assign labels to reorient the CT scans. After tracing lesion maps on the reoriented CT scans, I ran them through SPM CT normalization (using the clinical toolbox i.e. SPM>Tools>CT normalize) but I am getting an output image with a part of the brain cropped off. 

Below, I have attached an image of the crop-off issue post CT normalization. 

Any suggestions/help on the above issue will be greatly appreciated! 

Thank you.