Hi, I have a very basic issue that I can’t seem to figure out. When I import 2 different NIFTI volumes of the same subject from the same session in Slicer (one is an anatomical 3D MR volume and the other is a function EPI time series) they appear in completely different orientations to each other.
However, they were acquired with the same bounding box parameters and orientations on the scanner, converted from DICOM to NIFTI the same way (dcm2niix), and indeed they appear correctly and perfectly aligned when imported into any neuroimaging software (AFNI, FSL, SPM).
How can I make Slicer behave in the same was as these other (RAS-based) software when importing volumes?
This indeed seems like LPS-RAS issue. When you load the Nifti file, there is a checkbox to show options. Can you set some option that allows keeping (or converting) the orientation? Or if you have the original DICOM files they would probably load properly.
If I select that for either or both scans, then at least both volumes now load in approximately the same orientation! However, they’re still not aligned in the same was as they appear in neuroimaging software…
To test whether this is LPS/RAS issue, load both volumes normally into Slicer (don’t use the option above). Go to transforms module and create a transform in which the first two diagonal values are -1. Then assign one of the volumes to this transform. See if they line up.
