Hi Afni Experts,
I have a dataset collected at an oblique angle (RPI). When using 3dresample -orient LPI the header shows that the angle is now plumb using 3dinfo. Similarly if I use the 3drefit -deoblique command the dataset is now plumb but in the original RPI orientation when using 3dinfo. However when I use 3dWarp -deoblique the dataset appears in the viewer oblique (similar most likely to the actual acquisition) and now plumb in the RPI orientation according to 3dinfo.
1) In terms of the 3dresample is it essentially performing a similar process to 3drefit in which the data is not moved, but the information of the oblique angle is removed from the fileheader in addition to switching the coordinates to LPI (from RPI)?
2) Using 3dresample in this manner on the input dataset, is the slice timing information still preserved for slice timing correction or could this potentially cause issues and it is better to use 3dresample (or one of these other options )downstream after pre-processing with afni_proc.py? Or should this be performed directly after slice timing correction? If so, which of these tools is recommended?
Thanks,
Ajay
