Hi all,
I have collected functional runs and spin echo field maps in the same space with the same acquisition parameters, but when I reconstruct them using dcm2nii I see that the R-to-L extent is 104 voxels and the A-to-P extent is 96 voxels for the functional runs, while it is reversed (104 voxels R-to-L and 96 voxels A-to-P) for the spin echo field maps. The DICOM matrix field 0051,100B says 96*104s for the spin echo field maps and 96p*104 for the functional runs. However the field maps have width: 192 and height: 208 while for the functional data these are flipped.
To use these together I need them to be in the same space, so my question is, how do I reorient them appropriately? Is there a way to do this with dcm2nii or to3d or 3dresample once they've alreayd been reconstructed? Or can I crop the images (I'd rather not)? And for future acquisitions is there a way to prevent this?
Thank you!
Michael
