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The MR page allows loading the T1-weighted brain MR image of the same patient using the Load MR button.
MR Image Cropping
The MR image will be the basis for determining the stereotactic normalization. Experience has shown that problems may occur if the MR field-of-view is much larger than the template as occurs for instance with sagittal MR acquisitions. Therefore, please use the Crop facility for reducing the MR data set to the relevant portion with skull and brain, but without the neck.
MR Image Segmentation
The MR image will be segmented into gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF). The algorithm uses four parameters:
Denoising strength |
Denoising of the MR image may improve the segmentation of gray matter, white matter and CSF. If a Denoising strength other than None is selected, a non-local means denoising algorithm is applied which preserves structure boundaries unless the strength is too high. |
Sampling |
Density of pixels considered in the calculation. |
Bias Regularization |
Serves for compensating modulations of the image intensity across the field-of-view. Depending on the degree of the modulation, a corresponding setting can be selected from the list. The parameter to the right indicates the FWHM [mm] to be applied. The larger the FWHM, the smoother the variation is assumed. |
Cleanup threshold |
Procedure for rectifying the segmentation along the boundaries. |
It is recommended to use the default settings and only experiment with other parameter values if the segmentation fails. The default settings can be recovered by the 
button.
The actual segmentation is started with the Segment MR action button. Note that the denoising and segmentation process may take several minutes.