Slides presented at the Steiner Unit, Hammersmith Hospital, 08/06/2012

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Information about Slides presented at the Steiner Unit, Hammersmith Hospital, 08/06/2012
Health & Medicine

Published on March 4, 2014

Author: kevinkeraudren

Source: slideshare.net

Description

These slides present my work during my first year of PhD. The Steiner Unit used to be the MRI Research unit before the whole team moved to St Thomas (King's College).

Organ localisation in Fetal MRI PhD started in October 2011 Kevin Keraudren Steiner Unit, Hammersmith Hospital June 8th , 2012

Introduction What about fetuses? 1 What about fetuses? 3 Own research 2D detector for fetal heads Eye detection 4 Future plans Introduction 2 Own research Future plans K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 2 / 31

Introduction What about fetuses? 1 What about fetuses? 3 Own research 4 Future plans Introduction 2 Own research Future plans K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 3 / 31

Introduction What about fetuses? Own research Future plans Organ localisation What? Automatic detection of organs: center, bounding box or rough segmentation. Why? Segmentation, measurements, optimised or standardised visualisations, browsable body (keyword queries), tagging... How? Machine Learning methods, trained on relevant Training Data. K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 4 / 31

Introduction What about fetuses? Own research Future plans Adults? 2 main groups on this subject: Microsoft (A. Criminisi) Siemens (D. Comaniciu) Main focus on CT data from adults: Modality Subject CT on adult intensities directly related to tissues lay still, can hold breath, aligned with the scanner K. Keraudren (ICL) MRI on fetus relative values and field inhomogeneities movement, random orientation and position of the limbs, bending of the spine Organ localisation in Fetal MRI June 8th , 2012 5 / 31

Introduction What about fetuses? Own research Future plans Siemens: “Hierarchical Parsing and Semantic Navigation of Full Body CT Data”, Seifert et al. (2009) Slice detection K. Keraudren (ICL) Landmark detection Organ localisation in Fetal MRI Object detection + shape refinement June 8th , 2012 6 / 31

Introduction What about fetuses? Own research Future plans Microsoft: “Regression Forests for Efficient Anatomy Detection and Localization in CT Studies”, Criminisi et al. (2011) Automatic organ detection, repositioning of the 3D camera and selection of the best colour transfer function K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 7 / 31

Introduction What about fetuses? 1 What about fetuses? 3 Own research 4 Future plans Introduction 2 Own research Future plans K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 8 / 31

Introduction What about fetuses? Own research Future plans “Automatic Segmentation of Head Structures on Fetal MRI”, Anquez et al. (2009) [FEMONUM] Modeling the eyes for template matching: real eye, model and template 24 MRI volumes, 30-35 gestational weeks, 0.94 × 0.94 × 4 mm3 no motion K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 9 / 31

Introduction What about fetuses? Own research Future plans “Automatic Segmentation of Head Structures on Fetal MRI”, Anquez et al. (2009) [FEMONUM] Graph-cut segmentation of the brain, with rotated template around eyes center 24 MRI volumes, 30-35 gestational weeks, 0.94 × 0.94 × 4 mm3 no motion K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 10 / 31

Introduction What about fetuses? Own research Future plans “Segmentation of the Fetal Envelope on Ante-Natal MRI”, Anquez et al. (2010) Semi-automated registration of a simplified skeleton K. Keraudren (ICL) Mean shape, graphcut initialisation and resulting segmentation Organ localisation in Fetal MRI June 8th , 2012 11 / 31

Introduction What about fetuses? Own research Future plans “Detection of Fetal Anatomies from Ultrasound Images using a Constrained Probabilistic Boosting Tree”, Carneiro et al. (2008) From an annotated database, learn to detect organs Head and whole body K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 12 / 31

Introduction What about fetuses? 1 What about fetuses? 3 Own research 2D detector for fetal heads Eye detection 4 Future plans Introduction 2 Own research Future plans K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 13 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Sagittal head detector Training data (Thanks Vanessa!) Average image 303 tightly cropped images K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 14 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Sagittal head detector Viola&Jones detector from OpenCV Local Binary Pattern (LBP) features Exhaustive search by rotating/mirroring new image K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 15 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads LBP features 1 2 5 4 6 3 7 8 black if ∑ Neighbour < ∑ Middle else white K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 16 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads LBP features First tests of the detection process K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 17 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Detection result 5min for a 1◦ rotation step, less than 1min if 8◦ rotation step. K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 18 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Coronal head detector Training data Average image 666 tightly cropped images K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 19 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Transverse head detector Training data Average image 246 tightly cropped images + mirrored K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 20 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Neck region darker than the brain Influence of background K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 21 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Detection result In volumes, multiple detections increase confidence Movie as example of true and false detection K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 22 / 31

Introduction What about fetuses? Own research Future plans 2D detector for fetal heads Room for improvement Specific task, specific training data: no universal detector Need for more testing, better separation of training and testing data Confidence score, and combining 3 detectors into a classifier Combine with other detectors (eyes?) to increase confidence and orientation K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 23 / 31

Introduction What about fetuses? Own research Future plans Eye detection Eye detection pipeline 1 Slice by slice: 1 2 2 Canny edge detection + template matching Intensity filtering For the whole volume: 1 2 3 4 Grouping candidate circles Forming candidate pairs (25 mm ≤ d ≤ 39 mm) Chan&Vese Level Sets segmentation + shape checking Grouping candidate pairs K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 24 / 31

Introduction What about fetuses? Own research Future plans Eye detection K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 25 / 31

Introduction What about fetuses? Own research Future plans Eye detection Problem of motion (here 1.3mm spacing) Several results returned, ranked by number of detection Is it worth having a more complex pipeline than FEMONUM? K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 26 / 31

Introduction What about fetuses? 1 What about fetuses? 3 Own research 4 Future plans Introduction 2 Own research Future plans K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 27 / 31

Introduction What about fetuses? Own research Future plans Future plans Validate and integrate current detectors Target other organs: dataset of 50 fetuses with lungs, heart, kidneys, liver and whole body (Damodaram et al., 2012) Regression Forests, multi-organs detection Long-term goals: Improve visualisation of fetal MRI data (Semi-)Automatic building of catalogues of organs K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 28 / 31

Introduction What about fetuses? Own research Future plans Thanks! K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 29 / 31

Introduction What about fetuses? Own research Future plans Questions? K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 30 / 31

Introduction What about fetuses? Own research Future plans Manual segmentation with OpenCV Grabcut 20min for 30 slices K. Keraudren (ICL) Organ localisation in Fetal MRI June 8th , 2012 31 / 31

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