Dear Registration experts,
I have a registration / brainstripping problem with a small volume, high-resolution, double-oblique oriented ToF-MRAngiography, which I want to register to a normally oriented T1-weighted whole brain data-set.
Right now I do a flirt registration of the ToF-MRA to an EPI partialvolume (same orientation, same small volume coverage) which is registered to a "whole brain" EPI (same orientation, covering the whole brain) which is then registered to the normally oriented (ACPC) T1 weighted whole brain volume.
I then take the concatenated transformation matrix from Angio -> partVol EPI -> whole brain EPI -> whole brain T1 to reorient the original angio-volume to the right position on the T1 weighted image. Because of the high spatial resolution of both the T1 and the angio, I do see registration errors. I therefore tried a final registration step in which I used the former transformation matrix as the initialization matrix for the registration of the ToF-MRA to T1, but this worsened the error.
From my various attempts to find out the critical parameters, why this last step fails, I suspect that it is the small volume of the ToF-MRA in combination with the incomplete brain-extraction that excludes a precise registration . Applying bet small Z and -f 0.1 to the ToF-MRA removes the skull but not the CFS/meninges above the cortical surface.
I' d appreciate any suggestions on further options in "bet" to possibly increase the efficiency of brainstripping the angio, or any ideas on alternative routes for registration.
Thanks,
Renate
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Dr. Renate Schweizer,
Biomedizinische NMR Forschungs GmbH am
Max-Planck-Institut fuer biophysikalische Chemie
Am Fassberg 11
37077 Goettingen
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