Hi Matthew,
Just FYI, ANTs uses ITK which, when reading a NIFTI-1 image uses only the qform (if valid). So when writing the output, only the qform is written and the sform is unavoidably set to 0.
Using fslcpgeom on both the individual warped ROI and the nodif_brain_mask (previously registered to T1 and used for bedpostx) seems indeed to have solved the problem.
Thanks!!!
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