6/22/2023 0 Comments Medinria manual![]() In case one uses other labeling colors than the "blue" segmentation color, the range tool can be used to map those other colors either as belonging to the segment or to remove them by mapping them to a value of 0 intensity. When manually editing an already segmented brain hemisphere volume, region growing is not necessary. does not include the voxels of the desired volume, the minimum and maximum range values can be adjusted before repeating the process. The region growing process is started by clicking the Grow Region button. Note that the intensity of the seed voxel must fall within the specified range, otherwise the segmentation will not spread to neighboring voxels. Running the intensity inhomogeneity correction procedure is highly recommended if not already performed prior to standard cortex sgementation pipelines. ![]() Useful values for white matter are typically in the range of 120-180 but the values depend on the specific anatomical data and the preprocessing performed. Region growing spreads from the voxel to those voxels that are in the intensity range specified by the the Min entry and the Max entry in the Value range. Region growing is prepared by clicking inside the to-be-segmented volume to specify a seed voxel with high enough signal intensity for a region growing operation. This usually involves application of region growing and the range tool to remove voxels with intensity values of no interest. In case the volume is not an (manually edited) VMR resulting from a segmentation pipeline, a desired volume need to be first marked as a segmentation using the tools in the Segmentation tab of the 3D Volume Tools dialog. After preparing the boundary of the segmented structure (see below), the mesh reconstruction process is performed from the 3D Viewer either by using the Reconstruct Mesh From Prepared Volume icon or via the Create Mesh dialog. The segmentation typically represents one cortical hemisphere after manual editing but the procedure is general and can be used for any segmented volume. Here the most basic approach is described using one segmentation labelled with the default "blue" segmentation color (value 240). This can be done using the 3D icon in the Zoom View toolbar for multiple segments. While cortex meshes are reconstructed automatically when running the standard and advanced segmentation pipelines, it is often necessary to reconstruct segmentations that have been manually edited using manual segmentation tools. BrainVoyager v22.0 Reconstructing Edited Brain Volumes
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