Creation of transfer functions using ilr coordinates.

<p>(A) The user starts with the 2D histogram representation of ilr coordinates 1 and 2 (left side) and concurrent visualization of the original brain data (right side). The user can then interact with and select data as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198335#pone.0198335.g003" target="_blank">Fig 3</a>. (B) The interaction with the 2D histogram results in data-driven shapes, here shaded in pink, green and blue (left side). Voxels selected by those areas are highlighted in corresponding colors against the backdrop of the original brain data (right side). The visualization reveals that the area of the 2D histogram shaded in blue selects brain voxels, while the areas shaded in green and pink select CSF* and blood vessel voxels**/dura mater***, respectively. The arrow with exclamation mark (!) indicates an area affected by T2*w image artifacts.</p

Segmentation performance scores MP2RAGE data set.

<p>The table shows the DICE (larger is better) and AVHD (less is better) for the initial CBS tools and FSL FAST GM segmentations as well as after additional masking, using either the gradient magnitude or the compositional data method.</p

2D histogram representation of three 3D MRI contrast images.

<p>(A) Each voxel is considered as a 3 part composition in 3D real space. The barycentric coordinates of each composition which reside in 3D simplex space are represented in 2D real space after using a isometric log-ratio (ilr) transformation. (B) The ilr coordinates are used to create 2D histograms representing all voxels in the images. The blue lines are the embedded 3D real space primary axes. It should be noted that in this case the ilr coordinates are not easily interpretable by themselves but they are useful to visualize the barycentric coordinates which are interpretable via the embedded real space primary axes. Darker regions in the histogram indicate that many voxels are characterized by this particular scale invariant combination of the image contrasts. In this representation, brain tissue (WM and GM, red dashed lines) becomes separable from non-brain tissue (black dashed lines and arrows).</p

Availability of validation data and code.

<p>Validation data and scripts as well as segmentation software are all openly accessible by following the corresponding links for their repositories.</p

Segmentation performance scores MPRAGE data set.

<p>The table shows the DICE (larger is better) and AVHD (less is better) for the initial SPM 12 and FSL FAST GM segmentations as well as after additional polishing, using either the gradient magnitude or the compositional data method.</p

Creation of 2D transfer functions with pre-defined shapes.

<p>(A) Intensity and (B) gradient magnitude values of of a brain extracted T1w-divided-by-PDw MRI image are represented in a 2D histogram. By moving widgets of pre-defined shape, e.g. a circle, over the (C) 2D histogram and (D) concurrent visualization of selected voxels on a 2D slice of brain, positions of different tissue types in the 2D histogram can be probed and transfer functions can be created. In this example, the different probe positions (yellow, orange and red circles) appear to contain different aspects of GM.</p

2D histogram representation for MRI image of a human brain.

<p>(A) Intensity and (B) gradient magnitude values of a brain extracted T1w-divided-by-PDw MRI image are represented in a (C) 2D histogram. Darker regions in the histogram indicate that many voxels in the MRI image are characterized by this particular combination of image intensity and gradient magnitude. (D) The 2D histogram displays a characteristic pattern with tissue types occupying particular areas of the histogram. Voxels containing CSF, dura mater or blood vessels (black dashed lines and arrows) cover different regions of the histogram than voxels containing WM and GM (red dashed lines). As a result, brain tissue becomes separable from non-brain tissue.</p

Comparison of GM segmentation results for MPRAGE data.

<p>GM segmentation results are shown for one representative subject on a transverse (upper row) and a sagittal slice (lower row) of the brain before and after applying the GraMag and CoDa methods. The original image that is input to the segmentation is shown on the left. The original GM segmentation obtained from SPM 12 is shown in red (middle and right column). GM segmentations after additional polishing with brain mask obtained with either the GraMag (middle column) or the CoDa method (right column) are overlaid in blue. Additional masking removes blood vessels, CSF (arrow *) and most of dura mater (arrow †) voxels from the SPM GM definition. Because of its unique compositional properties, connective tissue from the sagittal sinus can be captured and excluded using the CoDa method (arrow **). An area badly affected by the CoDa mask is also indicated with arrow ***.</p

Creation of 2D transfer functions with data-driven shapes.

<p>(A) The user starts with the 2D histogram representation of image intensity and gradient magnitude (left side) and concurrent visualization of the original brain data (right side). The user can then interact with and select data in the 2D histogram to specify transfer functions. In this example, this was done with the help of a normalized graph cut decision tree. (B) The interaction with the 2D histogram results in data-driven shapes of selected areas, here shaded in pink, green and blue (left side). Voxels selected by those areas are highlighted in corresponding colors against the backdrop of the original brain data (right side). The visualization reveals that the area of the 2D histogram shaded in blue selects brain voxels, while the areas shaded in green and pink select CSF* and blood vessel voxels**/dura mater***, respectively.</p

Comparison of GM segmentation results for MP2RAGE data.

<p>Same conventions as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198335#pone.0198335.g006" target="_blank">Fig 6</a>) but with initial segmentation results obtained with CBS tools instead of SPM 12.</p