Hi,
I am having a bit of a problem with the orientation of a label produced by mri_cor2label. I have an old analyze ROI that I have converted to a nifti volume and then registered to T1.mgz. When I load the ROI volume in tkmedit , the registration looks fine. The label and T1.mgz are in the same orientation and everything matches up. This occurs whether I load the ROI volume as the aux volume or as the main volume.
I then have tried to run mri_cor2label on the ROI volume in order to convert it to a label. When I look at the label with T1.mgz as the main volume, the z and y axises of the label are flipped and so is the left/right orientation. The strange thing is when I load the ROI volume as the main volume and T1.mgz as the aux volume, the label has the correct orientation. Is there a reason why the label only has the correct orientation when its source volume is used as the main volume? Is there any way I can correct this issue?
I am sorry if any of this is unclear. Thanks in advance for any help.
Thanks,
- Tyler