Dear List,
Please let me ask for your professional advices.
I would like to coregistrate 3DMRI (MPRAGE) after electrode
implantation (for invasive evaluation of epilepsy surgery) into one
before electrode implantation (the same patient).
MPRAGE was taken twice: one before the electrode implantation
(MPRAGEbeforeGrid) and the other taken after the subdural electrodes
(MPRAGEwithGrid) were implanted (i.e., grid is on the surface of the
brain). Usually, the brain get somehow distored locally by the grid.
Electrodes were made of platinum and detected as a round signal void.
We used FLIRT, and then FNIRT to do so. It was successful in about
2/3 of the patients.
MPRAGE (both one before and with grid implantation) has 1x1x1 resolution.
We used the T1_2_MNI152_2mm.conf except
--in=MPRAGEwithGrid.nii.gz
--ref=MPRAGEbeforeGrid.nii.gz
--inmask=skull stripped MPRAGEwithGrid.nii.gz
--refmask=bet'ed MPRAGEbeforeGrid
As for --refmask, we used the bet'ed MPRAGEbeforeGrid.
As for --inmask , we bet'ed MPRAGEwithGrid, and then manually trimmed
the edge of the surface (e.g. got rid of the electrode artifact).
Since there were some high intensities within the cortex around the
grid (probably due to the grid), we also thresholded out these high
intensity spots (by fslmatsh -thr (above 2SD intensity for example)).
We did this because there was a tendency of misalignment with FNIRT
in the area with this kind of high intensity on MPRAGE.
FLIRT did actually a good work (for the starting point of FNIRT), but
FNIRT did locally enlarge/warp the lateral parietal area more than we
expected (cortex enlarged out of the lateral parietal surface of
MPRAGEbeforeGrid).
Any suggestions to improve coregistration?
Attached, please find MPRAGEwithGrid (jpeg).
If allowed I could upload/attach other images (FLIRTed, FNIRTed
images, MRIbeforeGrid).
Many thanks in advance.
Riki
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Riki Matsumoto M.D., Ph.D.
Department of Neurology
Kyoto University Graduate School of Medicine
Shogoin, Sakyo, Kyoto, JAPAN 606-8507
Tel: +81-(0)75-751-3772
Fax:+81-(0)75-751-9416 (for large transfer, use +81-(0)75-761-9780)
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