Brain Extraction Configuration

Brain extraction configuration window.

Note: The Brain Extraction Configuration dialog box can be displayed by selecting Brain extraction from the Modules menu.

Matter parameters

Cumulative cuts [%]

There is an upper and a lower cumulative cut, t_low (0 - t_up) and t_up (t_low - 100) respectively. The unit for these parameters is %. These cuts are used to remove a small number of voxels whose intensity values are very different from the rest of the image series. I.e. a fraction of the distribution accounting for the 0 - t_low % lowest intensity values and a similar fraction accounting for the t_up - 100 % highest intensity values are not considered in the fitting procedure.

Brain/non-brain matter separation (0 - 100) [%]

In many MR image bone tissue appears dark. This value is chosen as a rough initial separation between brain tissue (above) and "background" (below). The value represents a fraction of the range between t_low (0 - t_up) and t_up (t_low - 100) and is given in units of %.

Smoothness parameters [mm]

There are two parameters that determine the smoothing of the mesh surface, r_min (0 - r_max) [mm] and r_max (r_min - 20) [mm] . The unit for these parameters is mm. Structures with radii of curvature < r_min are heavily smoothed while structures with radii > r_max experience little smoothing. The amount of smoothing follows a sigmoid function of radius of curvature.

Fractional intensity threshold (0 - 100) [%]

This parameter represents a fraction of the intensity threshold that separates brain tissue from background in the later stages of the fitting. The iterative update of the tessellated mesh along directions given by surface normals is guided by this parameter.

Threshold gradient (-1 - 1)

The amount of iterative update of the tessellated mesh along directions given by surface normals is guided by this parameter.

Set Centre of Gravity

By default, the centre of gravity used to initiate the iterative search of the image volume is automatically estimated from the input data. If the image volume includes large non-brain regions (e.g. neck), the iteration may not easily converge to a correct extraction of brain. This option enables manual selection of centre of gravity region as well as the initial radius of the search region.

Iterative parameters

Maximum number of iterations

The maximum number of steps used to fit the brain volume.

Maximum number of intersections

The maximum number of surface self-intersections allowed before refitting the brain surface.

Navigation buttons

Help

Display the Users Manual's section on brain extraction.

Reset

Return to the default configuration values.

Close

Close the brain extraction configuration window and abort configuration.

Process

Start brain extraction.

When brain extraction is completed a new image window displaying the segmented image volume is opened.