I was wondering how I can check the orientation of a volume. I have been using 3dinfo for this and looking at the [-orient xxx].
When I looked at the orientation of one of my images it was ASR. Then I used 3dLRflip (3dLRflip -LR -prefix New volume OLD Volume) to double check the orientation of the volume. After I ran 3dLRflip the new image was still ASR. Shouldn’t the orientation be ASL since it was flipped? Is this the correct way to check the orientation?
3dLRflip changes the data, not the header information/orientation. Note that this changes your dataset, like where a given (x0, y0, z0) location was before and after will appear to be different. You would typically use this if there were a problem in your data you were trying to fix or test.
You could use 3drefit to change the dataset orientation, rather than the data part-- but you should copy the dataset and edit the copied dset, because in this case 3drefit edits the input dset itself. It does not copy it. Again, this is typically only used if you are trying to fix a header/data mismatch.
If you want to have your data look the same after changing the orientation, you can you 3dresample to change both the header and the data together; in this case, (x0, y0, z0) should appear in the same location, while the dset orientation will be different.