Brainshift Correction
Context |
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How to
To run brainshift correction, you first go through rough coregistration and normalization to template space. Select the patient (arrow 1), tick
Brainshift correction
with a mask,Check Results
and pressRun
.To estimate a transform, choose either
No Mask
,Coarse Mask
orCoarse + Fine Mask
.No Mask
will just use the cropped images to estimate the transformation and is not recommended. By choosing theCoarse Mask
, a larger mask will be applied. If you choose to use both,Coarse + Fine Mask.
The coarse mask (blue mask in the Schönecker publication within the #context panel) will be applied first, followed by the finer (yellow within the #context panel) mask.
In our example, let's see the use of the Coarse Mask
. This will produce the following result:
As highlighted by the yellow arrows, some regions better overlap in this refined transform. The estimated transformation matrix is printed in the top right corner of the figure.
You can use a slice viewer (such as e.g. 3D Slicer to further examine results in detail. The relevant files will be in derivatives/leaddbs/
patient folder/brainshift/anat.
If you think the approach improved results, click
Approve & Close
to apply the transform to your DBS electrode reconstructions. If not, clickDisapprove & Close
. Alternatively, you can change the settings toNo Mask
orCoarse + Fine Mask
and press(Re-)compute coregistration using...
.
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