Dear SCT developers,
I would like to clarify how sct_register_multimodal works. We have structural and functional images acquired with different orientation: sagittal and axial oblique respectively. During the registration step, we are providing the cord segmentations for both images, using centerMass as an algorithm and setting slicewise to 1. It works pretty well.
But I am worried that trying to co-register an oblique volume using 2D transformations only may be sub-optimal. The help page states that:
Hence, this function assumes that orientation of the destination image is axial (RPI). If you need to register two volumes with large deformations and/or different contrasts, it is recommended to input spinal cord segmentations (binary mask) in order to achieve maximum robustness.
My question is whether sct_register_multimodal uses header information about the oblique orientation of the destination image while calculating the transformation? Or should we resample those images to the same orientation to make the registration task easier?
Here are our current registration parameters:
sct_register_multimodal -i T2w.nii.gz -d EPI_combinedRUNs_Spine_moco_mean.nii.gz -iseg T2w_seg.nii.gz -dseg EPI_combinedRUNs_Spine_Mean_seg.nii.gz -param step=1,type=seg,algo=centermass,metric=MeanSquares,iter=5,slicewise=1
Thank you!