TY - GEN A1 - Beyer, Thomas A1 - Weigert, Markus A1 - Palm, Christoph A1 - Quick, Harald H. A1 - Müller, Stefan P. A1 - Pietrzyk, Uwe A1 - Vogt, Florian A1 - Martinez, M.J. A1 - Bockisch, Andreas T1 - Towards MR-based attenuation correction for whole-body PET/MR imaging T2 - The Journal of Nuclear Medicine KW - Kernspintomografie KW - Positronen-Emissions-Tomografie KW - Bildgebendes Verfahren KW - Schwächung Y1 - 2006 UR - http://jnm.snmjournals.org/content/47/suppl_1/384P.1.abstract VL - 47 IS - Suppl. 1 SP - 384P ER - TY - CHAP A1 - Palm, Christoph A1 - Pietrzyk, Uwe T1 - Time-Dependent Joint Probability Speed Function for Level-Set Segmentation of Rat-Brain Slices T2 - Proceedings of the SPIE Medical Imaging 6914: Image Processing 69143U N2 - The segmentation of rat brain slices suffers from illumination inhomogeneities and staining effects. State-of-the-art level-set methods model slice and background with intensity mixture densities defining the speed function as difference between the respective probabilites. Nevertheless, the overlap of these distributions causes an inaccurate stopping at the slice border. In this work, we propose the characterisation of the border area with intensity pairs for inside and outside estimating joint intensity probabilities. Method - In contrast to global object and background models, we focus on the object border characterised by a joint mixture density. This specifies the probability of the occurance of an inside and an outside value in direct adjacency. These values are not known beforehand, because inside and outside depend on the level-set evolution and change during time. Therefore, the speed function is computed time-dependently at the position of the current zero level-set. Along this zero level-set curve, the inside and outside values are derived as mean along the curvature normal directing inside and outside the object. Advantage of the joint probability distribution is to resolve the distribution overlaps, because these are assumed to be not located at the same border position. Results - The novel time-dependent joint probability based speed function is compared expermimentally with single probability based speed functions. Two rat brains with about 40 slices are segmented and the results analysed using manual segmentations and the Tanimoto overlap measure. Improved results are recognised for both data sets. KW - Image segmentation KW - Brain KW - Visualization KW - Image processing KW - Medical imaging KW - Neuroimaging KW - Beryllium KW - Kernspintomografie KW - Histologie KW - Schnittdarstellung KW - Bildsegmentierung KW - Gehirn Y1 - 2008 U6 - https://doi.org/10.1117/12.770673 IS - 6914 SP - 69143U-1 EP - 69143U-8 ER - TY - GEN A1 - Weigert, Markus A1 - Palm, Christoph A1 - Quick, Harald H. A1 - Müller, Stefan P. A1 - Pietrzyk, Uwe A1 - Beyer, Thomas T1 - Template for MR-based attenuation correction for whole-body PET/MR imaging T2 - Nuklearmedizin KW - Kernspintomografie KW - Positronen-Emissions-Tomografie KW - Bildgebendes Verfahren KW - Schwächung Y1 - 2007 VL - 46 IS - 2 SP - A115 ER - TY - JOUR A1 - Beyer, Thomas A1 - Weigert, Markus A1 - Quick, Harald H. A1 - Pietrzyk, Uwe A1 - Vogt, Florian A1 - Palm, Christoph A1 - Antoch, Gerald A1 - Müller, Stefan P. A1 - Bockisch, Andreas T1 - MR-based attenuation correction for torso-PET/MR imaging BT - pitfalls in mapping MR to CT data JF - European Journal of Nuclear Medicine and Molecular Imaging N2 - Purpose MR-based attenuation correction (AC) will become an integral part of combined PET/MR systems. Here, we propose a toolbox to validate MR-AC of clinical PET/MRI data sets. Methods Torso scans of ten patients were acquired on a combined PET/CT and on a 1.5-T MRI system. MR-based attenuation data were derived from the CT following MR–CT image co-registration and subsequent histogram matching. PET images were reconstructed after CT- (PET/CT) and MR-based AC (PET/MRI). Lesion-to-background (L/B) ratios were estimated on PET/CT and PET/MRI. Results MR–CT histogram matching leads to a mean voxel intensity difference in the CT- and MR-based attenuation images of 12% (max). Mean differences between PET/MRI and PET/CT were 19% (max). L/B ratios were similar except for the lung where local misregistration and intensity transformation leads to a biased PET/MRI. Conclusion Our toolbox can be used to study pitfalls in MR-AC. We found that co-registration accuracy and pixel value transformation determine the accuracy of PET/MRI. KW - PET/MRI KW - PET/CT KW - Attenuation correction KW - Kernspintomografie KW - Positronen-Emissions-Tomografie KW - Schwächung Y1 - 2008 U6 - https://doi.org/10.1007/s00259-008-0734-0 VL - 35 IS - 6 SP - 1142 EP - 1146 ER - TY - GEN A1 - Weigert, Markus A1 - Beyer, Thomas A1 - Quick, Harald H. A1 - Pietrzyk, Uwe A1 - Palm, Christoph A1 - Müller, Stefan P. T1 - Generation of a MRI reference data set for the validation of automatic, non-rigid image co-registration algorithms T2 - Nuklearmedizin KW - Kernspintomografie KW - Referenzdaten KW - Registrierung KW - Algorithmus Y1 - 2007 VL - 46 IS - 2 SP - A116 ER - TY - CHAP A1 - Palm, Christoph T1 - Fusion of Serial 2D Section Images and MRI Reference BT - an Overview T2 - Workshop Innovative Verarbeitung bioelektrischer und biomagnetischer Signale (bbs2014), Berlin, 10.04.2014 N2 - Serial 2D section images with high resolution, resulting from innovative imaging methods become even more valuable, if they are fused with in vivo volumes. Achieving this goal, the 3D context of the sections would be restored, the deformations would be corrected and the artefacts would be eliminated. However, the registration in this field faces big challenges and is not solved in general. On the other hand, several approaches have been introduced dealing at least with some of these difficulties. Here, a brief overview of the topic is given and some of the solutions are presented. It does not constitute the claim to be a complete review, but could be a starting point for those who are interested in this field. KW - Kernspintomografie KW - Optimierung KW - Magnetic Resonance Imaging KW - MRI KW - Literaturbericht Y1 - 2014 U6 - https://doi.org/10.13140/RG.2.1.1358.3449 ER - TY - CHAP A1 - Palm, Christoph A1 - Graeme, Penny P. A1 - Crum, William R. A1 - Schnabel, Julia A. A1 - Pietrzyk, Uwe A1 - Hawkes, David J. T1 - Fusion of Rat Brain Histology and MRI using Weighted Multi-Image Mutual Information T2 - Proceedings of the SPIE Medical Imaging 6914: Image Processing 69140M N2 - Fusion of histology and MRI is frequently demanded in biomedical research to study in vitro tissue properties in an in vivo reference space. Distortions and artifacts caused by cutting and staining of histological slices as well as differences in spatial resolution make even the rigid fusion a difficult task. State-of- the-art methods start with a mono-modal restacking yielding a histological pseudo-3D volume. The 3D information of the MRI reference is considered subsequently. However, consistency of the histology volume and consistency due to the corresponding MRI seem to be diametral goals. Therefore, we propose a novel fusion framework optimizing histology/histology and histology/MRI consistency at the same time finding a balance between both goals. Method - Direct slice-to-slice correspondence even in irregularly-spaced cutting sequences is achieved by registration-based interpolation of the MRI. Introducing a weighted multi-image mutual information metric (WI), adjacent histology and corresponding MRI are taken into account at the same time. Therefore, the reconstruction of the histological volume as well as the fusion with the MRI is done in a single step. Results - Based on two data sets with more than 110 single registrations in all, the results are evaluated quantitatively based on Tanimoto overlap measures and qualitatively showing the fused volumes. In comparison to other multi-image metrics, the reconstruction based on WI is significantly improved. We evaluated different parameter settings with emphasis on the weighting term steering the balance between intra- and inter-modality consistency. KW - Magnetic resonance imaging KW - Image registration KW - Brain KW - 3D image processing KW - Image fusion KW - In vitro testing KW - In vivo imaging KW - Kernspintomografie KW - Histologie KW - Schnittdarstellung KW - Registrierung KW - Datenfusion Y1 - 2008 U6 - https://doi.org/10.1117/12.770605 IS - 6914 SP - 69140M-1 EP - 69140M-9 ER - TY - CHAP A1 - Weber, Joachim A1 - Doenitz, Christian A1 - Brawanski, Alexander A1 - Palm, Christoph T1 - Data-Parallel MRI Brain Segmentation in Clinicial Use BT - Porting FSL-Fastv4 to GPGPUs T2 - Bildverarbeitung für die Medizin 2015; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 15. bis 17. März 2015 in Lübeck N2 - Structural MRI brain analysis and segmentation is a crucial part in the daily routine in neurosurgery for intervention planning. Exemplarily, the free software FSL-FAST (FMRIB’s Segmentation Library – FMRIB’s Automated Segmentation Tool) in version 4 is used for segmentation of brain tissue types. To speed up the segmentation procedure by parallel execution, we transferred FSL-FAST to a General Purpose Graphics Processing Unit (GPGPU) using Open Computing Language (OpenCL) [1]. The necessary steps for parallelization resulted in substantially different and less useful results. Therefore, the underlying methods were revised and adapted yielding computational overhead. Nevertheless, we achieved a speed-up factor of 3.59 from CPU to GPGPU execution, as well providing similar useful or even better results. KW - Brain Segmentation KW - Magnetic Resonance Imaging KW - Parallel Execution KW - Voxel Spacing KW - General Purpose Graphic Processing Unit KW - Kernspintomografie KW - Gehirn KW - Bildsegmentierung KW - Parallelverarbeitung Y1 - 2015 U6 - https://doi.org/10.1007/978-3-662-46224-9_67 SP - 389 EP - 394 PB - Springer CY - Berlin ER - TY - JOUR A1 - Mang, Andreas A1 - Schnabel, Julia A. A1 - Crum, William R. A1 - Modat, Marc A1 - Camara-Rey, Oscar A1 - Palm, Christoph A1 - Caseiras, Gisele Brasil A1 - Jäger, H. Rolf A1 - Ourselin, Sébastien A1 - Buzug, Thorsten M. A1 - Hawkes, David J. T1 - Consistency of parametric registration in serial MRI studies of brain tumor progression JF - International Journal of Computer Assisted Radiology and Surgery N2 - Object The consistency of parametric registration in multi-temporal magnetic resonance (MR) imaging studies was evaluated. Materials and methods Serial MRI scans of adult patients with a brain tumor (glioma) were aligned by parametric registration. The performance of low-order spatial alignment (6/9/12 degrees of freedom) of different 3D serial MR-weighted images is evaluated. A registration protocol for the alignment of all images to one reference coordinate system at baseline is presented. Registration results were evaluated for both, multimodal intra-timepoint and mono-modal multi-temporal registration. The latter case might present a challenge to automatic intensity-based registration algorithms due to ill-defined correspondences. The performance of our algorithm was assessed by testing the inverse registration consistency. Four different similarity measures were evaluated to assess consistency. Results Careful visual inspection suggests that images are well aligned, but their consistency may be imperfect. Sub-voxel inconsistency within the brain was found for allsimilarity measures used for parametric multi-temporal registration. T1-weighted images were most reliable for establishing spatial correspondence between different timepoints. Conclusions The parametric registration algorithm is feasible for use in this application. The sub-voxel resolution mean displacement error of registration transformations demonstrates that the algorithm converges to an almost identical solution for forward and reverse registration. KW - Inverse registration consistency KW - Parametric serial MR image registration KW - Tumor disease progression KW - Kernspintomografie KW - Registrierung KW - Hirntumor Y1 - 2008 U6 - https://doi.org/10.1007/s11548-008-0234-5 VL - 3 IS - 3-4 SP - 201 EP - 211 ER -