I am new in using Slicer. I did AC-PC alignment of Brain DICOM, which was quite easy to do. After that I did harden transform and finally exported the DICOM. When I open this new AC-PC aligned DICOM in Slicer then it comes fine and perfectly aligned but when I open this same DICOM in some other software like Amira/Avizo, it is not aligned.
Please suggest me where I am doing wrong?
Maybe Amira/Avizo is showing you the images in pixel space and ignoring the orientation. You probably need to resample the images in slicer before exporting (e.g. with Resample Image (BRAINS)).
If I do resample Image (BRAINS), what should be my “Reference Image” because after AC-PC alignment, I have only one DICOM dataset?
Use Resample Image (BRAINS) module
Reference Image: Actual image before AC-PC alignment
Pixel Type: Int
Interpolation Mode: Lanczos
Thank you Pieper…