Dear A.shamed,

I've been looking at this problem for oblique datasets. It seems there is some confusion here regarding whether the data is oblique. Based upon your 3drotate command, I'll assume it is. I've made good progress with Siemens oblique data. If the angle can be obtained either from the DICOM data or the user has specific knowledge of the acquisition, the problem is relatively simple and follows roughly the steps you followed of 3drotate and 3drefit. You might want to add a 3dZeropad command to avoid rotating real data out of the volume space. Also it's preferable to use the angle rather than the volume registration method if it is known. Because you have already uploaded the data, I'll take a look at that and let you know what I find out.

Remember he who laughs last laughs best.