Prostate segmentation and surface reconstruction

This page contains instructions on how to perform MRI prostate segmentation and surface reconstruction in MIPAV. The algorithm facilities the validation of multi-parametric MRI with histopathology slides from radical prostatectomy specimens and targeted biopsy specimens. It employs the technique that combines image processing and computer aided design to construct a high resolution 3D prostate surface from MRI images in three orthogonal views with non-isotropic voxel resolution.

The algorithm outline is shown below (TBD).

Image types

The algorithm could be applied to the following image types (TBD).

Sample image dataset

The sample image dataset can be downloaded using this link (TBD). The data included into the data set are MR images obtained from a 3.0 T whole-body MRI system (Achieva, Philips Healthcare).

T2-weighted MR images of the entire prostate were obtained in three orthogonal planes (sagittal, axial and coronal) using the following settings:

• Scan resolution of 0.2734x0.2734x3.0 cubic millimeters,
• Field of view - 140 mm,
• Image slice dimension 512x512.

The center of the prostate is the focal point for the MRI scan. To reduce the scan time, a lower refocusing pulse of 100 degrees was used for sagittal and coronal images, which alters the contrast on these images compared to the axial images.

Applying the algorithm

Applying the algorithm involves the following steps:

1. Opening 3 orthogonal images and delineating VOIs
2. Prostate segmentation using Automatic B-Spline Registration algorithm
3. Prostate surface reconstruction
4. 3D Visualization and STL surface generation

Opening images and delineating VOIs

Open an axial image. Use File > Open image (A) from disk menu. If you are using the test image dataset provided, open the img_ax_83.xml file.

Draw 3 polygon/polyline VOIs. Use the Polygon/Polyline VOI tool from the MIPAV toolbar.

Please, follow this sequence while delineating VOIs: draw the first VOI on the middle slice, draw the second one on the apex slice, and draw the last VOI on the base slice.

For example, for the test image dataset provided:

1. Draw the mid slice VOI first, on slice #12;
2. Then draw the apex VOI, on slice #6;
3. And finally, draw the last VOI on the base slice #19.