elham

Thanks Nick; I run the mentioned examples successfully, I understand that after applying the transformation, the intensity of background pixels get negative values (I check it by using histogram of images). I think these negative values cause the dark shadow in the background because when I make the negative values to zero, the shadow disappeared. I want to ask whether this issue is a common thing to happen or not? and also I want to know about the reason of this issue. The transformation file is...

Hi every one I'm beginner in ANTs and I need some help about it. I constructed a MR template using antsMultivariateTemplateConstruction.sh script and then I applied adaptive transformations (during making atlas group for each single) to their extracted CSF with antsApplyTransforms script. After that, I see a dark cubic in the whole of transformed images (in their rendering condition) . when I overlay transformed images on the orginal MR images,they completely cover them with a kind of dark shadow...