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Viewing 2 posts - 1 through 2 (of 2 total)
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I am running lead v126.96.36.199 on Matlab 2016a, with SPM 12. In patient directory I have anat_t1.nii and postop_tra.nii from a T1-weighted 3D image with 312 slices.
My preop MRI is coregistered well to MNI space, but the postop_tra.nii is translated posteriorly and to the right so that only the coronal images look normal, but the sagittal and axial views are cutoff.
I ran the coregistration in SPM outside of lead-dbs and then ran the normalization with the “Do not coregister post – to pre- MRI (already coregistered)” option selected and the normalization ran beautifully. Any suggestions on how to troubleshoot the lead-dbs coregistration for my pre- and post- operative MRIs?
you can re-run “Normalize” with a different setting (e.g. “Coreg MRIs: Hybrid SPM & ANTs) in the coreg popup and choosing “(Re-)apply (priorly) estimated normalization.” in the Normalization popup.
Since coregistrations are affine (nonlinear), it’s okay to mix methods in this step IMHO.
If none of the options coregister your images nicely, you could try to manually coregister the postops to preops e.g. using 3DSlicer.
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