SEGMENTING HEAD & NECK MR IMAGES Antal Nagy Department of - PowerPoint PPT Presentation

SEGMENTING HEAD & NECK MR IMAGES Antal Nagy Department of Image Processing and Computer Graphics University of Szeged 27th Summer School on Image Processing Timi ş soara, Rom â nia, 2019

Segmenting Head & Neck MR images 2 Introduction • Medical Image • Tomographic Image Acquisition Systems • MR protocols • Segmentation • Delineating certain areas • Organs at Risk (OAR) for radiotherapy • Healthy organs must be protected from radiation • Tumors • Abnormal mass of tissue

Segmenting Head & Neck MR images 3 Tomographic Acquisition Systems • Transmission Tomography • Imaging procedure • Cross-sections of the 3D object are determined from its projection images • Projection images created by rays • Transmitted through and absorbed by the object • Emission Tomography • Whole space is filled with some Courtesy of https://medical-dictionary.thefreedictionary.com homogeneous absorbing material • The function to be reconstructed represents an object emitting radioactive rays into the surrounding space • Observe metabolic processes Courtesy of http://www.whatisnuclearmedicine.com

Segmenting Head & Neck MR images 4 Magnetic Resonance Imaging • Created by using • Powerful magnet • Magnetic protons which align with the field • Radio waves • Knocks down the atoms • Disrupts their polarity • Sensors • Detect the time to return to the original alignment • MRI shows the fluid characteristic of different tissues (soft tissues) • Air and bone are black

Segmenting Head & Neck MR images 5 Magnetic Resonance Imaging • Tissue Characteristics • T1 weighted • Longitudinal movement of protons • Protons in fat realign quickly with high energy • Normal anatomical details • T2 weighted • Transverse movement of proton • Protons in water dephase slowly • Pathological details

Segmenting Head & Neck MR images 6 Liver scan after the „vector - gradient” process Historical Overview 3D Phase and Amplitude images Intensity of gamma radiation SEGAMS nuclear medicine system Kidney study

Segmenting Head & Neck MR images 7 Syllabus • MR Head and Neck • Generating Atlas Studies Information • Study parameters • Segments • Segmentation Methods • Different methods • Preprocessing Steps • Different features • Noise reduction • Inhomogeneity correction • Histogram matching

Segmenting Head & Neck MR images 8 Motivation • Head and neck region is suggested by physicians • There are no tools/results • „Tubular” organs • Starting at a certain slice number • There is a vertical coherence between the slices • Organs • Carotid arteries (left, right) • Jugular veins (left, right) • Trachea • Spinal cord • Parotid glands (left, right) • Sternocleidomastoid muscle (SCM) • Varying size, shape and deformation

Segmenting Head & Neck MR images 9 INPUTS „ If you know the enemy and know yourself, you need not fear the result of a hundred battles ” – Sun Tzu

Segmenting Head & Neck MR images 10 MR Head & Neck Input Images • MR studies used in daily routine • Body Planes • Axial slices • 0.5 mm x 0.5 mm x 7 mm • MR Protocols • T1 FATSAT • T1 FSE • T1 FSPOSTGAD • T2 FRFSE

Segmenting Head & Neck MR images 11 MR Head & Neck Input Images coronal • Body Planes • Sagital • T1 FSE POSTGAD • T2 FRFSE • Coronal • T1 FSE POSTGAD • T2 FRFSE • Physicians use all • Positioning sagital • Sagital and coronal • Reporting • Axial axial

Segmenting Head & Neck MR images 12 MR Head & Neck Input Images • Axial, coronal, and sagital studies are in different spaces • They are created in different time even • Can not be used in same way as the physicians do • Solution Make your own input • Jan Sijbers (Univ. of Antwerp): Superresolution reconstruction of magnetic resonance images

Segmenting Head & Neck MR images 13 Organ Delineation • Contouring the target organs • Carried out • By 2 well trained physicians • Separately • On all studies • On each slices • Using different modalities • T2 FRFSE and T1 FSPostGad • Application • Validating the segmentation algorithms’ results • Creating organ atlas

Segmenting Head & Neck MR images 14 Organ Delineation • Problems • Organs delignated in different ways • On axial slices • Organ boundary • Different interpretation of the head and neck region • Starting and ending slices • Overlapping • Neighboring organs • Pairs of organs • E.g. removed during operation • Tumor deformation

Segmenting Head & Neck MR images 15 PREPROCESSING STEPS Battle with Artifacts

Segmenting Head & Neck MR images 16 Intensity Inhomogeneity within Studies • Multiplicative noise with low frequency • Due to the un-calibrated coils • Solutions • N3 • Nonparametric non-uniform normalization • Retrospective bias correction algorithm • N4 • De-convolving the intensity histogram by a Gaussian • Remapping the intensities • Spatially smoothing this result by a B-spline modeling of the bias field itself • http://stnava.github.io/ANTs/

Segmenting Head & Neck MR images 17 Intensity Inhomogeneity between Studies • The absolute intensity values do not have a fixed meaning on MRI images • Solution • Intensity transformation • Histogram matching • Between two MRI studies • Nyul, L. G., Udupa, J. K., & Zhang, X. (2000). New variants of a method of MRI scale standardization. IEEE Transactions on Medical Imaging, 19(2), 143-150. DOI: 10.1109/42.836373

Segmenting Head & Neck MR images 18 Noise Reduction • Anisotropic diffusion • Edge preserving filtering • Be careful with the parameters • Important details can be washout

Segmenting Head & Neck MR images 19 CREATING ATLAS „ Navigare necesse est …”

Segmenting Head & Neck MR images 20 Task • Problems with manual contouring • Time consuming • Organs hard to delineate on certain modalities • Possibilities of the application of the image registration • Searching for geometry correspondence between images • Image resampling on other image grid • Superimposition • Joint images combined displaying • Image fusion Courtesy of Attila Tanács

Segmenting Head & Neck MR images 21 Image Registration Tasks • Different modalities of the same patients • Segmented organs of a modality can be transformed to other mobilities • Voxel intensities in the same 3D position help the decision • Manual segmentation • Automatic clustering Courtesy of Attila Tanács

Segmenting Head & Neck MR images 22 Image Registration Tasks • Multiple patients’ data on the same modality • MRI Images • Segmented organs • Transforming them into a common reference space • Statistical atlas • Atlas can be transformed into a new study space Courtesy of Attila Tanács

Segmenting Head & Neck MR images 23 Image Registration Algorithms • Same patient, different modalities • No movement during the acquisition • Rigid body transformation • Deformation can be seen • Non-linear transformation (B-Spline) • Different patients, same modalities • Non-linear transformation is necessary with linear fitting preliminary • Differences between organ shape/size • Different positions of the head and neck in the studies • Varying position of the organs

Segmenting Head & Neck MR images 24 Statistical Atlas • Statistic on organ position • Where is it? Most common • Steps • Selecting reference study • Target area should be covered • No anomalies • Registering other studies to the reference • Scaled rigid body + B-Spline non-linear refinement • Finding the transformation • Mutual information • No anomalies • Transforming the physicians'’ segmentations into reference space as well with the resulting transformation

Segmenting Head & Neck MR images 25 Application of the Atlas • Transforming the statistical atlas into study to be segmented • Finding the transformation Early result between the new study and the reference study • Using the inverse of transformations on the organ atlas information Courtesy of Attila Tanács

Segmenting Head & Neck MR images 26 Application of the Atlas • Fitting the jugular vein atlas • Physician segmentation (white) • Yellow shows the carotid artery Early result • Statistical atlas (purple spot) • Bright area means • Larger probability • Not easy to register Courtesy of Attila Tanács

Segmenting Head & Neck MR images 27 Application of the Atlas Elastix ITK composite Courtesy of Attila Tanács Spinal cord (green), trachea (yellow), Carotid (red), Jugular (blue), Parotid (brown), SCM (cyan)

Segmenting Head & Neck MR images 28 Application of the Atlas Elastix ITK composite Courtesy of Attila Tanács Hard to judge visually → Numerical evaluation is needed