Hello,

So some of these subjects do have the original dicoms. I took one subject and used to3d, used 3dinfo, and the orientation was RAI. I also looked at the data through the AFNI viewer and everything looked good (right side up, etc.). So I went to the same data that I converted from Analyze to .nii that I described in the previous post and 3dinfo reports as being in LPI, and used 3drefit to change it to RAI. 3dinfo now reports the header has the data stored as RAI however, when I view the data in the AFNI viewer the data is different than it was when it was in LPI, but still appears upside down in the coronal and sagittal views. So the same data (one set converted as described in my previous post, another set made with to3d) both in RAI looks different in the AFNI viewer - so my guess is using to3d is setting fields in the header (other than the orientation field) causing the data to be read differently. Any thoughts as to what field this may be and/or how to fix this?

Since some of the subjects have the original dicoms while others do not, I was thinking of taking one subject's dicoms, using to3d to convert to .nii, and then copying the header information to all the data for all the subjects. However, I could not find a program to do this - it seems like 3drefit -atrcopy does not have an "all attributes" flag and I'm not quite how to use 3dAttribute to copy attributes from one dataset to another (or even if this is possible). So (1) does this sound like a good strategy to apply to my data?, (2) any suggestions for copying all the header attributes from one dataset to another?

Thanks!
David