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  • 1. Andersson, Malin
    et al.
    Jägervall, Karl
    Eriksson, Per
    Persson, Anders
    Granerus, Göran
    Wang, Chunliang
    Linköping Univ, Sweden.
    Smedby, Örjan
    Linköping Univ, Sweden.
    How to measure renal artery stenosis - a retrospective comparison of morphological measurement approaches in relation to hemodynamic significance2015Ingår i: BMC Medical Imaging, ISSN 1471-2342, E-ISSN 1471-2342, Vol. 15, artikel-id 42Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Although it is well known that renal artery stenosis may cause renovascular hypertension, it is unclear how the degree of stenosis should best be measured in morphological images. The aim of this study was to determine which morphological measures from Computed Tomography Angiography (CTA) and Magnetic Resonance Angiography (MRA) are best in predicting whether a renal artery stenosis is hemodynamically significant or not. Methods: Forty-seven patients with hypertension and a clinical suspicion of renovascular hypertension were examined with CTA, MRA, captopril-enhanced renography (CER) and captopril test (Ctest). CTA and MRA images of the renal arteries were analyzed by two readers using interactive vessel segmentation software. The measures included minimum diameter, minimum area, diameter reduction and area reduction. In addition, two radiologists visually judged the diameter reduction without automated segmentation. The results were then compared using limits of agreement and intra-class correlation, and correlated with the results from CER combined with Ctest (which were used as standard of reference) using receiver operating characteristics (ROC) analysis. Results: A total of 68 kidneys had all three investigations (CTA, MRA and CER + Ctest), where 11 kidneys (16.2 %) got a positive result on the CER + Ctest. The greatest area under ROC curve (AUROC) was found for the area reduction on MRA, with a value of 0.91 (95 % confidence interval 0.82-0.99), excluding accessory renal arteries. As comparison, the AUROC for the radiologists' visual assessments on CTA and MRA were 0.90 (0.82-0.98) and 0.91 (0.83-0.99) respectively. None of the differences were statistically significant. Conclusions: No significant differences were found between the morphological measures in their ability to predict hemodynamically significant stenosis, but a tendency of MRA having higher AUROC than CTA. There was no significant difference between measurements made by the radiologists and measurements made with fuzzy connectedness segmentation. Further studies are required to definitely identify the optimal measurement approach.

  • 2. Andersson, Thord
    et al.
    Romu, Thobias
    Karlsson, Anette
    Norén, Bengt
    Forsgren, Mikael F
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning. Linköping University.
    Kechagias, Stergios
    Almer, Sven
    Lundberg, Peter
    Borga, Magnus
    Leinhard, Olof Dahlqvist
    Consistent intensity inhomogeneity correction in water-fat MRI2015Ingår i: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 42, nr 2Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    PURPOSE: To quantitatively and qualitatively evaluate the water-signal performance of the consistent intensity inhomogeneity correction (CIIC) method to correct for intensity inhomogeneities

    METHODS: Water-fat volumes were acquired using 1.5 Tesla (T) and 3.0T symmetrically sampled 2-point Dixon three-dimensional MRI. Two datasets: (i) 10 muscle tissue regions of interest (ROIs) from 10 subjects acquired with both 1.5T and 3.0T whole-body MRI. (ii) Seven liver tissue ROIs from 36 patients imaged using 1.5T MRI at six time points after Gd-EOB-DTPA injection. The performance of CIIC was evaluated quantitatively by analyzing its impact on the dispersion and bias of the water image ROI intensities, and qualitatively using side-by-side image comparisons.

    RESULTS: CIIC significantly ( P1.5T≤2.3×10-4,P3.0T≤1.0×10-6) decreased the nonphysiological intensity variance while preserving the average intensity levels. The side-by-side comparisons showed improved intensity consistency ( Pint⁡≤10-6) while not introducing artifacts ( Part=0.024) nor changed appearances ( Papp≤10-6).

    CONCLUSION: CIIC improves the spatiotemporal intensity consistency in regions of a homogenous tissue type.

  • 3.
    Astaraki, Mehdi
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Wang, Chunliang
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Buizza, G.
    Toma-Dasu, I.
    Lazzeroni, M.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Early survival prediction in non-small cell lung cancer with PET/CT size aware longitudinal pattern2019Ingår i: Radiotherapy and Oncology, ISSN 0167-8140, E-ISSN 1879-0887, ISSN 0167-8140, Vol. 133, s. S208-S209Artikel i tidskrift (Refereegranskat)
  • 4.
    Astaraki, Mehdi
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning. Karolinska Inst, Dept Oncol Pathol, Karolinska Univ Sjukhuset, SE-17176 Stockholm, Sweden.
    Wang, Chunliang
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Buizza, Giulia
    Politecn Milan, Dept Elect Informat & Bioengn, Piazza Leonardo da Vinci 42, I-20133 Milan, Italy..
    Toma-Dasu, Iuliana
    Karolinska Inst, Dept Oncol Pathol, Karolinska Univ Sjukhuset, SE-17176 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Lazzeroni, Marta
    Karolinska Inst, Dept Oncol Pathol, Karolinska Univ Sjukhuset, SE-17176 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Early survival prediction in non-small cell lung cancer from PET/CT images using an intra-tumor partitioning method2019Ingår i: Physica medica (Testo stampato), ISSN 1120-1797, E-ISSN 1724-191X, Vol. 60, s. 58-65Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Purpose: To explore prognostic and predictive values of a novel quantitative feature set describing intra-tumor heterogeneity in patients with lung cancer treated with concurrent and sequential chemoradiotherapy. Methods: Longitudinal PET-CT images of 30 patients with non-small cell lung cancer were analysed. To describe tumor cell heterogeneity, the tumors were partitioned into one to ten concentric regions depending on their sizes, and, for each region, the change in average intensity between the two scans was calculated for PET and CT images separately to form the proposed feature set. To validate the prognostic value of the proposed method, radiomics analysis was performed and a combination of the proposed novel feature set and the classic radiomic features was evaluated. A feature selection algorithm was utilized to identify the optimal features, and a linear support vector machine was trained for the task of overall survival prediction in terms of area under the receiver operating characteristic curve (AUROC). Results: The proposed novel feature set was found to be prognostic and even outperformed the radiomics approach with a significant difference (AUROC(sALop) = 0.90 vs. AUROC(radiomic) = 0.71) when feature selection was not employed, whereas with feature selection, a combination of the novel feature set and radiomics led to the highest prognostic values. Conclusion: A novel feature set designed for capturing intra-tumor heterogeneity was introduced. Judging by their prognostic power, the proposed features have a promising potential for early survival prediction.

  • 5.
    Batool, Nazre
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Chowdhury, Manish
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Moreno, Rodrigo
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Estimation of trabecular bone thickness in gray scale: a validation study2017Ingår i: International Journal of Computer Assisted Radiology and Surgery, Vol. 12, nr Supplement 1Artikel i tidskrift (Refereegranskat)
  • 6.
    Bendazzoli, Simone
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem.
    Brusini, Irene
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning. Karolinska Inst, Dept Neurobiol Care Sci & Soc, Alfred Nobels Alle 23,D3, S-14152 Huddinge, Sweden..
    Damberg, Peter
    Karolinska Inst, Dept Clin Neurosci, Tomtebodavagen 18A P1 5, S-17177 Stockholm, Sweden..
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Andersson, Leif
    Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab Uppsala, Biomedicinskt Ctr BMC, Husargatan 3, S-75237 Uppsala, Sweden..
    Wang, Chunliang
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Automatic rat brain segmentation from MRI using statistical shape models and random forest2019Ingår i: MEDICAL IMAGING 2019: IMAGE PROCESSING / [ed] Angelini, ED Landman, BA, SPIE-INT SOC OPTICAL ENGINEERING , 2019, artikel-id 1094920Konferensbidrag (Refereegranskat)
    Abstract [en]

    In MRI neuroimaging, the shimming procedure is used before image acquisition to correct for inhomogeneity of the static magnetic field within the brain. To correctly adjust the field, the brain's location and edges must first be identified from quickly-acquired low resolution data. This process is currently carried out manually by an operator, which can be time-consuming and not always accurate. In this work, we implement a quick and automatic technique for brain segmentation to be potentially used during the shimming. Our method is based on two main steps. First, a random forest classifier is used to get a preliminary segmentation from an input MRI image. Subsequently, a statistical shape model of the brain, which was previously generated from ground-truth segmentations, is fitted to the output of the classifier to obtain a model-based segmentation mask. In this way, a-priori knowledge on the brain's shape is included in the segmentation pipeline. The proposed methodology was tested on low resolution images of rat brains and further validated on rabbit brain images of higher resolution. Our results suggest that the present method is promising for the desired purpose in terms of time efficiency, segmentation accuracy and repeatability. Moreover, the use of shape modeling was shown to be particularly useful when handling low-resolution data, which could lead to erroneous classifications when using only machine learning-based methods.

  • 7. Bernard, Olivier
    et al.
    Bosch, J G
    Heyde, Brecht
    Alessandrini, Martino
    Barbosa, Daniel
    Camarasu-Pop, S
    Cervenansky, F
    Valette, S
    Mirea, O
    Bernier, M
    Jodoin, P M
    Domingos, J S
    Stebbing, R V
    Keraudren, K
    Oktay, O
    Caballero, J
    Shi, W
    Rueckert, D
    Milletari, F
    Ahmadi, S A
    Smistad, E
    Lindseth, F
    van Stralen, M
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Donal, E
    Monaghan, M
    Papachristidis, A
    Geleijnse, M L
    Galli, E
    Dhooge, Jan
    Standardized evaluation system for left ventricular segmentation algorithms in 3D echocardiography.2015Ingår i: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254XArtikel i tidskrift (Refereegranskat)
    Abstract [en]

    Real-time 3D Echocardiography (RT3DE) has been proven to be an accurate tool for left ventricular (LV) volume assessment. However, identification of the LV endocardium remains a challenging task, mainly because of the low tissue/blood contrast of the images combined with typical artifacts. Several semi and fully automatic algorithms have been proposed for segmenting the endocardium in RT3DE data in order to extract relevant clinical indices, but a systematic and fair comparison between such methods has so far been impossible due to the lack of a publicly available common database. Here, we introduce a standardized evaluation framework to reliably evaluate and compare the performance of the algorithms developed to segment the LV border in RT3DE. A database consisting of 45 multivendor cardiac ultrasound recordings acquired at different centers with corresponding reference measurements from 3 experts are made available. The algorithms from nine research groups were quantitatively evaluated and compared using the proposed online platform. The results showed that the best methods produce promising results with respect to the experts' measurements for the extraction of clinical indices, and that they offer good segmentation precision in terms of mean distance error in the context of the experts' variability range. The platform remains open for new submissions.

  • 8. Blystad, I
    et al.
    Håkansson, I
    Tisell, A
    Ernerudh, J
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University.
    Lundberg, P
    Larsson, E-M
    Quantitative MRI for Analysis of Active Multiple Sclerosis Lesions without Gadolinium-Based Contrast Agent2015Ingår i: American Journal of Neuroradiology, ISSN 0195-6108, E-ISSN 1936-959XArtikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND AND PURPOSE: Contrast-enhancing MS lesions are important markers of active inflammation in the diagnostic work-up of MS and in disease monitoring with MR imaging. Because intravenous contrast agents involve an expense and a potential risk of adverse events, it would be desirable to identify active lesions without using a contrast agent. The purpose of this study was to evaluate whether pre-contrast injection tissue-relaxation rates and proton density of MS lesions, by using a new quantitative MR imaging sequence, can identify active lesions.

    MATERIALS AND METHODS: Forty-four patients with a clinical suspicion of MS were studied. MR imaging with a standard clinical MS protocol and a quantitative MR imaging sequence was performed at inclusion (baseline) and after 1 year. ROIs were placed in MS lesions, classified as nonenhancing or enhancing. Longitudinal and transverse relaxation rates, as well as proton density were obtained from the quantitative MR imaging sequence. Statistical analyses of ROI values were performed by using a mixed linear model, logistic regression, and receiver operating characteristic analysis.

    RESULTS: Enhancing lesions had a significantly (P < .001) higher mean longitudinal relaxation rate (1.22 ± 0.36 versus 0.89 ± 0.24), a higher mean transverse relaxation rate (9.8 ± 2.6 versus 7.4 ± 1.9), and a lower mean proton density (77 ± 11.2 versus 90 ± 8.4) than nonenhancing lesions. An area under the receiver operating characteristic curve value of 0.832 was obtained.

    CONCLUSIONS: Contrast-enhancing MS lesions often have proton density and relaxation times that differ from those in nonenhancing lesions, with lower proton density and shorter relaxation times in enhancing lesions compared with nonenhancing lesions.

  • 9. Blystad, Ida
    et al.
    Warntjes, J. B. Marcel
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University, Sweden.
    Lundberg, Peter
    Larsson, Elna-Marie
    Tisell, Anders
    Quantitative MRI for analysis of peritumoral edema in malignant gliomas2017Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, nr 5, artikel-id e0177135Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background and purpose Damage to the blood-brain barrier with subsequent contrast enhancement is a hallmark of glioblastoma. Non-enhancing tumor invasion into the peritumoral edema is, however, not usually visible on conventional magnetic resonance imaging. New quantitative techniques using relaxometry offer additional information about tissue properties. The aim of this study was to evaluate longitudinal relaxation R-1, transverse relaxation R-2, and proton density in the peritumoral edema in a group of patients with malignant glioma before surgery to assess whether relaxometry can detect changes not visible on conventional images. Methods In a prospective study, 24 patients with suspected malignant glioma were examined before surgery. A standard MRI protocol was used with the addition of a quantitative MR method (MAGIC), which measured R-1, R-2, and proton density. The diagnosis of malignant glioma was confirmed after biopsy/surgery. In 19 patients synthetic MR images were then created from the MAGIC scan, and ROIs were placed in the peritumoral edema to obtain the quantitative values. Dynamic susceptibility contrast perfusion was used to obtain cerebral blood volume (rCBV) data of the peritumoral edema. Voxel-based statistical analysis was performed using a mixed linear model. Results R-1, R-2, and rCBV decrease with increasing distance from the contrast-enhancing part of the tumor. There is a significant increase in R1 gradient after contrast agent injection (P<.0001). There is a heterogeneous pattern of relaxation values in the peritumoral edema adjacent to the contrast-enhancing part of the tumor. Conclusion Quantitative analysis with relaxometry of peritumoral edema in malignant gliomas detects tissue changes not visualized on conventional MR images. The finding of decreasing R-1 and R-2 means shorter relaxation times closer to the tumor, which could reflect tumor invasion into the peritumoral edema. However, these findings need to be validated in the future.

  • 10.
    Brusini, Irene
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Carneiro, Miguel
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet CIBIO, InBIO, P-4485661 Vairao, Portugal.;Univ Porto, Dept Biol, Fac Ciencias, P-4169007 Porto, Portugal..
    Wang, Chunliang
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Rubin, Carl-Johan
    Uppsala Univ, Sci Life Lab Uppsala, Dept Med Biochem & Microbiol, S-75236 Uppsala, Sweden..
    Ring, Henrik
    Uppsala Univ, Dept Neurosci, S-75236 Uppsala, Sweden..
    Afonso, Sandra
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet CIBIO, InBIO, P-4485661 Vairao, Portugal..
    Blanco-Aguiar, Jose A.
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet CIBIO, InBIO, P-4485661 Vairao, Portugal.;CSIC, Inst Invest Recursos Cineget IREC, Ciudad Real 13005, Spain.;UCLM, CSIC, Ciudad Real 13005, Spain..
    Ferrand, Nuno
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet CIBIO, InBIO, P-4485661 Vairao, Portugal.;Univ Porto, Dept Biol, Fac Ciencias, P-4169007 Porto, Portugal.;Univ Johannesburg, Dept Zool, ZA-2006 Auckland Pk, South Africa..
    Rafati, Nima
    Uppsala Univ, Sci Life Lab Uppsala, Dept Med Biochem & Microbiol, S-75236 Uppsala, Sweden..
    Villafuerte, Rafael
    CSIC, IESA, Cordoba 14004, Spain..
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Damberg, Peter
    Karolinska Univ Hosp, Karolinska Expt Res & Imaging Ctr, S-17176 Solna, Sweden..
    Hallbook, Finn
    Uppsala Univ, Dept Neurosci, S-75236 Uppsala, Sweden..
    Fredrikson, Mats
    Uppsala Univ, Dept Psychol, S-75236 Uppsala, Sweden.;Karolinska Inst, Dept Clin Neurosci, S-17177 Stockholm, Sweden..
    Andersson, Leif
    Uppsala Univ, Sci Life Lab Uppsala, Dept Med Biochem & Microbiol, S-75236 Uppsala, Sweden.;Texas A&M Univ, Coll Vet Med & Biomed Sci, Dept Vet Integrat Biosci, College Stn, TX 77843 USA.;Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden..
    Changes in brain architecture are consistent with altered fear processing in domestic rabbits2018Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, nr 28, s. 7380-7385Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The most characteristic feature of domestic animals is their change in behavior associated with selection for tameness. Here we show, using high-resolution brain magnetic resonance imaging in wild and domestic rabbits, that domestication reduced amygdala volume and enlarged medial prefrontal cortex volume, supporting that areas driving fear have lost volume while areas modulating negative affect have gained volume during domestication. In contrast to the localized gray matter alterations, white matter anisotropy was reduced in the corona radiata, corpus callosum, and the subcortical white matter. This suggests a compromised white matter structural integrity in projection and association fibers affecting both afferent and efferent neural flow, consistent with reduced neural processing. We propose that compared with their wild ancestors, domestic rabbits are less fearful and have an attenuated flight response because of these changes in brain architecture.

  • 11.
    Brusini, Irene
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Jörgens, Daniel
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Moreno, Rodrigo
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Dependency of neural tracts'€™ curvature estimations on tractography methods2017Konferensbidrag (Refereegranskat)
  • 12.
    Brusini, Irene
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Jörgens, Daniel
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Moreno, Rodrigo
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Influence of Tractography Algorithms and Settings on Local Curvature Estimations2017Konferensbidrag (Refereegranskat)
  • 13.
    Brusini, Irene
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Jörgens, Daniel
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Moreno, Rodrigo
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Voxel-Wise Clustering of Tractography Data for Building Atlases of Local Fiber Geometry2019Konferensbidrag (Refereegranskat)
    Abstract [en]

    This paper aims at proposing a method to generate atlases of white matter fibers’ geometry that consider local orientation and curvature of fibers extracted from tractography data. Tractography was performed on diffusion magnetic resonance images from a set of healthy subjects and each tract was characterized voxel-wise by its curvature and Frenet–Serret frame, based on which similar tracts could be clustered separately for each voxel and each subject. Finally, the centroids of the clusters identified in all subjects were clustered to create the final atlas. The proposed clustering technique showed promising results in identifying voxel-wise distributions of curvature and orientation. Two tractography algorithms (one deterministic and one probabilistic) were tested for the present work, obtaining two different atlases. A high agreement between the two atlases was found in several brain regions. This suggests that more advanced tractography methods might only be required for some specific regions in the brain. In addition, the probabilistic approach resulted in the identification of a higher number of fiber orientations in various white matter areas, suggesting it to be more adequate for investigating complex fiber configurations in the proposed framework as compared to deterministic tractography.

  • 14.
    Buizza, Giulia
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem. Politecn Milan, CartCasLab, Dept Elect Informat & Bioengn, Piazza Leonardo Da Vinci 42, I-20133 Milan, Italy..
    Toma-Dasu, Iuliana
    Karolinska Univ Sjukhuset, Karolinska Inst, Dept Oncol Pathol, Med Radiat Phys, S-17176 Solna, Sweden..
    Lazzeroni, Marta
    Karolinska Univ Sjukhuset, Karolinska Inst, Dept Oncol Pathol, Med Radiat Phys, S-17176 Solna, Sweden..
    Paganelli, Chiara
    Politecn Milan, CartCasLab, Dept Elect Informat & Bioengn, Piazza Leonardo Da Vinci 42, I-20133 Milan, Italy..
    Riboldi, Marco
    Politecn Milan, CartCasLab, Dept Elect Informat & Bioengn, Piazza Leonardo Da Vinci 42, I-20133 Milan, Italy.;Ludwig Maximilians Univ Munchen, Fac Phys, Coloumbwall 1, D-5748 Garching, Germany..
    Chang, Yong Jun
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Wang, Chunliang
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Early tumor response prediction for lung cancer patients using novel longitudinal pattern features from sequential PET/CT image scans2018Ingår i: Physica medica (Testo stampato), ISSN 1120-1797, E-ISSN 1724-191X, Vol. 54, s. 21-29Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Purpose: A new set of quantitative features that capture intensity changes in PET/CT images over time and space is proposed for assessing the tumor response early during chemoradiotherapy. The hypothesis whether the new features, combined with machine learning, improve outcome prediction is tested. Methods: The proposed method is based on dividing the tumor volume into successive zones depending on the distance to the tumor border. Mean intensity changes are computed within each zone, for CT and PET scans separately, and used as image features for tumor response assessment. Doing so, tumors are described by accounting for temporal and spatial changes at the same time. Using linear support vector machines, the new features were tested on 30 non-small cell lung cancer patients who underwent sequential or concurrent chemoradiotherapy. Prediction of 2-years overall survival was based on two PET-CT scans, acquired before the start and during the first 3 weeks of treatment. The predictive power of the newly proposed longitudinal pattern features was compared to that of previously proposed radiomics features and radiobiological parameters. Results: The highest areas under the receiver operating characteristic curves were 0.98 and 0.93 for patients treated with sequential and concurrent chemoradiotherapy, respectively. Results showed an overall comparable performance with respect to radiomics features and radiobiological parameters. Conclusions: A novel set of quantitative image features, based on underlying tumor physiology, was computed from PET/CT scans and successfully employed to distinguish between early responders and non-responders to chemoradiotherapy.

  • 15.
    Chang, Yongjun
    et al.
    KTH, Skolan för teknik och hälsa (STH).
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Effects of preprocessing in slice-level classification of interstitial lung disease based on deep convolutional networks2018Ingår i: VipIMAGE 2017: Proceedings of the VI ECCOMAS Thematic Conference on Computational Vision and Medical Image Processing Porto, Portugal, October 18-20, 2017, Springer Netherlands, 2018, Vol. 27, s. 624-629Konferensbidrag (Refereegranskat)
    Abstract [en]

    Several preprocessing methods are applied to the automatic classification of interstitial lung disease (ILD). The proposed methods are used for the inputs to an established convolutional neural network in order to investigate the effect of those preprocessing techniques to slice-level classification accuracy. Experimental results demonstrate that the proposed preprocessing methods and a deep learning approach outperformed the case of the original images input to deep learning without preprocessing.

  • 16.
    Chowdhury, Manish
    et al.
    KTH, Skolan för teknik och hälsa (STH).
    Jörgens, Daniel
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Moreno, Rodrigo
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Segmentation of Cortical Bone using Fast Level Sets2017Ingår i: MEDICAL IMAGING 2017: IMAGE PROCESSING / [ed] Styner, MA Angelini, ED, SPIE - International Society for Optical Engineering, 2017, artikel-id UNSP 1013327Konferensbidrag (Refereegranskat)
    Abstract [en]

    Cortical bone plays a big role in the mechanical competence of bone. The analysis of cortical bone requires accurate segmentation methods. Level set methods are usually in the state-of-the-art for segmenting medical images. However, traditional implementations of this method are computationally expensive. This drawback was recently tackled through the so-called coherent propagation extension of the classical algorithm which has decreased computation times dramatically. In this study, we assess the potential of this technique for segmenting cortical bone in interactive time in 3D images acquired through High Resolution peripheral Quantitative Computed Tomography (HR-pQCT). The obtained segmentations are used to estimate cortical thickness and cortical porosity of the investigated images. Cortical thickness and Cortical porosity is computed using sphere fitting and mathematical morphological operations respectively. Qualitative comparison between the segmentations of our proposed algorithm and a previously published approach on six images volumes reveals superior smoothness properties of the level set approach. While the proposed method yields similar results to previous approaches in regions where the boundary between trabecular and cortical bone is well defined, it yields more stable segmentations in challenging regions. This results in more stable estimation of parameters of cortical bone. The proposed technique takes few seconds to compute, which makes it suitable for clinical settings.

  • 17.
    Chowdhury, Manish
    et al.
    KTH, Skolan för teknik och hälsa (STH).
    Klintström, Benjamin
    KTH, Skolan för teknik och hälsa (STH). Linköping University, Sweden.
    Klintström, E.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University, Sweden.
    Moreno, Rodrigo
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Granulometry-based trabecular bone segmentation2017Ingår i: 20th Scandinavian Conference on Image Analysis, SCIA 2017, Springer, 2017, Vol. 10270, s. 100-108Konferensbidrag (Refereegranskat)
    Abstract [en]

    The accuracy of the analyses for studying the three dimensional trabecular bone microstructure rely on the quality of the segmentation between trabecular bone and bone marrow. Such segmentation is challenging for images from computed tomography modalities that can be used in vivo due to their low contrast and resolution. For this purpose, we propose in this paper a granulometry-based segmentation method. In a first step, the trabecular thickness is estimated by using the granulometry in gray scale, which is generated by applying the opening morphological operation with ball-shaped structuring elements of different diameters. This process mimics the traditional sphere-fitting method used for estimating trabecular thickness in segmented images. The residual obtained after computing the granulometry is compared to the original gray scale value in order to obtain a measurement of how likely a voxel belongs to trabecular bone. A threshold is applied to obtain the final segmentation. Six histomorphometric parameters were computed on 14 segmented bone specimens imaged with cone-beam computed tomography (CBCT), considering micro-computed tomography (micro-CT) as the ground truth. Otsu’s thresholding and Automated Region Growing (ARG) segmentation methods were used for comparison. For three parameters (Tb.N, Tb.Th and BV/TV), the proposed segmentation algorithm yielded the highest correlations with micro-CT, while for the remaining three (Tb.Nd, Tb.Tm and Tb.Sp), its performance was comparable to ARG. The method also yielded the strongest average correlation (0.89). When Tb.Th was computed directly from the gray scale images, the correlation was superior to the binary-based methods. The results suggest that the proposed algorithm can be used for studying trabecular bone in vivo through CBCT.

  • 18.
    Chowdhury, Manish
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Rota Bulò, S.
    Moreno, Rodrigo
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Kundu, M.K.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    An Efficient Radiographic Image Retrieval System Using Convolutional Neural Network2016Ingår i: 2016 23rd International Conference on Pattern Recognition (ICPR), Institute of Electrical and Electronics Engineers (IEEE), 2016, s. 3134-3139, artikel-id 7900116Konferensbidrag (Refereegranskat)
    Abstract [en]

    Content-Based Medical Image Retrieval (CBMIR) is an important research field in the context of medical data management. In this paper we propose a novel CBMIR system for the automatic retrieval of radiographic images. Our approach employs a Convolutional Neural Network (CNN) to obtain high- level image representations that enable a coarse retrieval of images that are in correspondence to a query image. The retrieved set of images is refined via a non-parametric estimation of putative classes for the query image, which are used to filter out potential outliers in favour of more relevant images belonging to those classes. The refined set of images is finally re-ranked using Edge Histogram Descriptor, i.e. a low-level edge-based image descriptor that allows to capture finer similarities between the retrieved set of images and the query image. To improve the computational efficiency of the system, we employ dimensionality reduction via Principal Component Analysis (PCA). Experiments were carried out to evaluate the effectiveness of the proposed system on medical data from the “Image Retrieval in Medical Applications” (IRMA) benchmark database. The obtained results show the effectiveness of the proposed CBMIR system in the field of medical image retrieval.

  • 19. Hadimeri, Ursula
    et al.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Fransson, Sven-Göran
    Stegmayr, Bernd
    Hadimeri, Henrik
    Fistula diameter correlates with echocardiographic characteristics in stable hemodialysis patients2015Ingår i: Nephrology@ Point of Care, Vol. 1, nr 1Artikel i tidskrift (Refereegranskat)
  • 20. Holstensson, Maria
    et al.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Poludniowski, Gavin
    Sanches Crespo, Alejandro
    Savitcheva, Irina
    Öberg, Michael
    Grybäck, Per
    Gabrielson, Stefan
    Sandqvist, Patricia
    Bartholdson, Erika
    Axelsson, Rimma
    Comparison of acquisition protocols for ventilation/perfusion SPECT - a Monte Carlo study.2019Ingår i: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    One of the most commonly used imaging techniques for diagnosing pulmonary embolism (PE) is ventilation/perfusion (V/P) scintigraphy. The aim of this study was to evaluate the performance of the currently used imaging protocols for V/P single photon emission computed tomography (V/P SPECT) at two nuclear medicine department sites and to investigate the effect of altering important protocol parameters. &amp;#13; &amp;#13; The Monte Carlo technique was used to simulate 4D digital phantoms with perfusion defects. Six imaging protocols were included in the study and a total of 72 digital patients were simulated. Six dually trained radiologists/nuclear medicine physicians reviewed the images and reported all perfusion mismatch findings. The radiologists also visually graded the image quality. &amp;#13; &amp;#13; No statistically significant differences in diagnostic performance were found between the studied protocols, but visual grading analysis pointed out one protocol as significantly superior to four of the other protocols. Considering the study results, we have decided to harmonize our clinical protocols for imaging patients with suspected PE. The administered Technegas and macro aggregated albumin activities have been altered, a low energy all purpose collimator is used instead of a low energy high resolution collimator and the acquisition times have been lowered.

  • 21.
    Jensen, Kristin
    et al.
    Oslo Univ Hosp, Dept Diagnost Phys, N-0454 Oslo, Norway.;Univ Oslo, Dept Phys, POB 1048 Blindern, N-0316 Oslo, Norway.;Oslo & Akershus Univ Coll Appl Sci, Dept Life Sci & Hlth, POB 4 St Olavs Plass, N-0130 Oslo, Norway..
    Andersen, Hilde Kjernlie
    Oslo Univ Hosp, Dept Diagnost Phys, N-0454 Oslo, Norway..
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Osteras, Bjorn Helge
    Oslo Univ Hosp, Dept Diagnost Phys, N-0454 Oslo, Norway.;Univ Oslo, Inst Clin Med, Oslo, Norway..
    Aarsnes, Anette
    Oslo Univ Hosp, Dept Diagnost Phys, N-0454 Oslo, Norway..
    Tingberg, Anders
    Lund Univ, Dept Med Radiat Phys, Skane Univ Hosp, Malmo, Sweden..
    Fosse, Erik
    Univ Oslo, Inst Clin Med, Oslo, Norway.;Natl Hosp Norway, Intervent Ctr, Oslo, Norway..
    Martinsen, Anne Catrine
    Oslo Univ Hosp, Dept Diagnost Phys, N-0454 Oslo, Norway.;Univ Oslo, Dept Phys, POB 1048 Blindern, N-0316 Oslo, Norway..
    Quantitative Measurements Versus Receiver Operating Characteristics and Visual Grading Regression in CT Images Reconstructed with Iterative Reconstruction: A Phantom Study2018Ingår i: Academic Radiology, ISSN 1076-6332, E-ISSN 1878-4046, Vol. 25, nr 4, s. 509-518Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Rationale and Objectives: This study aimed to evaluate the correlation of quantitative measurements with visual grading regression (VGR) and receiver operating characteristics (ROC) analysis in computed tomography (CT) images reconstructed with iterative reconstruction. Materials and Methods: CT scans on a liver phantom were performed on CT scanners from GE, Philips, and Toshiba at three dose levels. Images were reconstructed with filtered back projection (FBP) and hybrid iterative techniques (ASiR, iDose, and AIDR 3D of different strengths). Images were visually assessed by five readers using a four- and five-grade ordinal scale for liver low contrast lesions and for 10 image quality criteria. The results were analyzed with ROC and VGR. Standard deviation, signal-to-noise ratios, and contrast to-noise ratios were measured in the images. Results: All data were compared to FBP. The results of the quantitative measurements were improved for all algorithms. ROC analysis showed improved lesion detection with ASiR and AIDR and decreased lesion detection with iDose. VGR found improved noise properties for all algorithms, increased sharpness with iDose and AIDR, and decreased artifacts from the spine with AIDR, whereas iDose increased the artifacts from the spine. The contrast in the spine decreased with ASiR and iDose. Conclusions: Improved quantitative measurements in images reconstructed with iterative reconstruction compared to FBP are not equivalent to improved diagnostic image accuracy.

  • 22.
    Jörgens, Daniel
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Moreno, Rodrigo
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Clustering of tensor votes for inference of fibre orientations in DTI data2016Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    mong the various diffusion MRI techniques, diffusion ten-sor imaging (DTI) is still most commonly used in clinicalpractice in order to investigate connectivity and fibre anatomyin the human brain. Besides its apparent advantages of a shortacquisition time and noise robustness compared to other tech-niques, it suffers from its major weakness of assuming a sin-gle fibre model in each voxel. This constitutes a problem forDTI fibre tracking algorithms in regions with crossing fibres.Methods approaching this problem in a postprocessing stepemploy diffusion-like techniques to correct the directional in-formation. We propose an extension of tensor voting in whichinformation from voxels with a single fibre is used to inferorientation distributions in multi fibre voxels. The method isable to resolve multiple fibre orientations by clustering tensorvotes instead of adding them up. Moreover, a new vote cast-ing procedure is proposed which is appropriate even for smallneighbourhoods. To account for the locality of DTI data, weuse a small neighbourhood for distributing information at atime, but apply the algorithm iteratively to close larger gaps.The method shows promising results in both synthetic casesand for processing DTI-data of the human brain.

  • 23.
    Jörgens, Daniel
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Moreno, Rodrigo
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Learning a single step of streamline tractography based on neural networks2018Ingår i: Computational Diffusion MRI, Springer, Cham , 2018, s. 103-116Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 24.
    Jörgens, Daniel
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Moreno, Rodrigo
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Steering second-order tensor voting by vote clustering2016Konferensbidrag (Refereegranskat)
    Abstract [en]

    Among the various diffusion MRI techniques, diffusion tensor imaging (DTI) is still most commonly used in clinical practice in order to investigate connectivity and fibre anatomy in the human brain. Besides its apparent advantages of a short acquisition time and noise robustness compared to other techniques, it suffers from its major weakness of assuming a single fibre model in each voxel. This constitutes a problem for DTI fibre tracking algorithms in regions with crossing fibres. Methods approaching this problem in a postprocessing step employ diffusion-like techniques to correct the directional information. We propose an extension of tensor voting in which information from voxels with a single fibre is used to infer orientation distributions in multi fibre voxels. The method is able to resolve multiple fibre orientations by clustering tensor votes instead of adding them up. Moreover, a new vote casting procedure is proposed which is appropriate even for small neighbourhoods. To account for the locality of DTI data, we use a small neighbourhood for distributing information at a time, but apply the algorithm iteratively to close larger gaps. The method shows promising results in both synthetic cases and for processing DTI-data of the human brain.

  • 25. Karlsson, Anette
    et al.
    Leinhard, Olof Dahlqvist
    Aslund, Ulrika
    West, Janne
    Romu, Thobias
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linkoping Univ, Sweden.
    Zsigmond, Peter
    Peolsson, Anneli
    An Investigation of Fat Infiltration of the Multifidus Muscle in Patients With Severe Neck Symptoms Associated With Chronic Whiplash-Associated Disorder2016Ingår i: Journal of Orthopaedic and Sports Physical Therapy, ISSN 0190-6011, E-ISSN 1938-1344, Vol. 46, nr 10, s. 886-893Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    STUDY DESIGN: Cross-sectional study. BACKGROUND: Findings of fat infiltration in cervical spine multifidus, as a sign of degenerative morphometric changes due to whiplash injury, need to be verified. OBJECTIVES: To develop a method using water/fat magnetic resonance imaging (MRI) to investigate fat infiltration and cross-sectional area of multifidus muscle in individuals with whiplash associated disorders (WADS) compared to healthy controls. METHODS: Fat infiltration and cross-sectional area in the multifidus muscles spanning the C4 to C7 segmental levels were investigated by manual segmentation using water/fat-separated MRI in 31 participants with WAD and 31 controls, matched for age and sex. RESULTS: Based on average values for data spanning C4 to C7, participants with severe disability related to WAD had 38% greater muscular fat infiltration compared to healthy controls (P = .03) and 45% greater fat infiltration compared to those with mild to moderate disability related to WAD (P = .02). There were no significant differences between those with mild to moderate disability and healthy controls. No significant differences between groups were found for multifidus cross-sectional area. Significant differences were observed for both cross-sectional area and fat infiltration between segmental levels. CONCLUSION: Participants with severe disability after a whiplash injury had higher fat infiltration in the multifidus compared to controls and to those with mild/moderate disability secondary to WAD. Earlier reported findings using T1-weighted MRI were reproduced using refined imaging technology. The results of the study also indicate a risk when segmenting single cross-sectional slices, as both cross-sectional area and fat infiltration differ between cervical levels.

  • 26.
    Kataria, Bharti
    et al.
    Linkoping Univ, Dept Radiol, Dept Med & Hlth Sci, Ctr Med Image Sci & Visualizat CMIV, S-58185 Linkoping, Sweden..
    Althen, Jonas Nilsson
    Linkoping Univ, Dept Med & Hlth Sci, Dept Med Phys, Linkoping, Sweden..
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem.
    Persson, Anders
    Linkoping Univ, Dept Radiol, Dept Med & Hlth Sci, Ctr Med Image Sci & Visualizat CMIV, S-58185 Linkoping, Sweden..
    Sokjer, Hannibal
    Linkoping Univ, Dept Med & Hlth Sci, S-58183 Linkoping, Sweden..
    Sandborg, Michael
    Linkoping Univ, Dept Med & Hlth Sci, Dept Med Phys, Linkoping, Sweden..
    Assessment of image quality in abdominal CT: potential dose reduction with model-based iterative reconstruction2018Ingår i: European Radiology, ISSN 0938-7994, E-ISSN 1432-1084, Vol. 28, nr 6, s. 2464-2473Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To estimate potential dose reduction in abdominal CT by visually comparing images reconstructed with filtered back projection (FBP) and strengths of 3 and 5 of a specific MBIR. A dual-source scanner was used to obtain three data sets each for 50 recruited patients with 30, 70 and 100% tube loads (mean CTDIvol 1.9, 3.4 and 6.2 mGy). Six image criteria were assessed independently by five radiologists. Potential dose reduction was estimated with Visual Grading Regression (VGR). Comparing 30 and 70% tube load, improved image quality was observed as a significant strong effect of log tube load and reconstruction method with potential dose reduction relative to FBP of 22-47% for MBIR strength 3 (p < 0.001). For MBIR strength 5 no dose reduction was possible for image criteria 1 (liver parenchyma), but dose reduction between 34 and 74% was achieved for other criteria. Interobserver reliability showed agreement of 71-76% (kappa (w) 0.201-0.286) and intra-observer reliability of 82-96% (kappa (w) 0.525-0.783). MBIR showed improved image quality compared to FBP with positive correlation between MBIR strength and increasing potential dose reduction for all but one image criterion. aEuro cent MBIR's main advantage is its de-noising properties, which facilitates dose reduction. aEuro cent MBIR allows for potential dose reduction in relation to FBP. aEuro cent Visual Grading Regression (VGR) produces direct numerical estimates of potential dose reduction. aEuro cent MBIR strengths 3 and 5 dose reductions were 22-34 and 34-74%. aEuro cent MBIR strength 5 demonstrates inferior performance for liver parenchyma.

  • 27.
    Kataria, Bharti
    et al.
    Linkoping Univ, Dept Radiol, Linkoping, Sweden.;Linkoping Univ, Dept Med & Hlth Sci, Linkoping, Sweden.;Linkoping Univ, Ctr Med Image Sci & Visualizat CMIV, Linkoping, Sweden..
    Althén, Jonas Nilsson
    Linkoping Univ, Dept Med & Hlth Sci, Linkoping, Sweden.;Linkoping Univ, Dept Med Phys, Linkoping, Sweden..
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem.
    Persson, Anders
    Linkoping Univ, Dept Radiol, Linkoping, Sweden.;Linkoping Univ, Dept Med & Hlth Sci, Linkoping, Sweden.;Linkoping Univ, Ctr Med Image Sci & Visualizat CMIV, Linkoping, Sweden..
    Sökjer, Hannibal
    Linkoping Univ, Dept Med & Hlth Sci, Linkoping, Sweden..
    Sandborg, Michael
    Linkoping Univ, Dept Med & Hlth Sci, Linkoping, Sweden.;Linkoping Univ, Ctr Med Image Sci & Visualizat CMIV, Linkoping, Sweden.;Linkoping Univ, Dept Med Phys, Linkoping, Sweden..
    Image quality and pathology assessment in CT Urography: when is the low-dose series sufficient?2019Ingår i: BMC Medical Imaging, ISSN 1471-2342, E-ISSN 1471-2342, Vol. 19, nr 1, artikel-id 64Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background Our aim was to compare CT images from native, nephrographic and excretory phases using image quality criteria as well as the detection of positive pathological findings in CT Urography, to explore if the radiation burden to the younger group of patients or patients with negative outcomes can be reduced. Methods This is a retrospective study of 40 patients who underwent a CT Urography examination on a 192-slice dual source scanner. Image quality was assessed for four specific renal image criteria from the European guidelines, together with pathological assessment in three categories: renal, other abdominal, and incidental findings without clinical significance. Each phase was assessed individually by three radiologists with varying experience using a graded scale. Certainty scores were derived based on the graded assessments. Statistical analysis was performed using visual grading regression (VGR). The limit for significance was set at p = 0.05. Results For visual reproduction of the renal parenchyma and renal arteries, the image quality was judged better for the nephrogram phase (p < 0.001), whereas renal pelvis/calyces and proximal ureters were better reproduced in the excretory phase compared to the native phase (p < 0.001). Similarly, significantly higher certainty scores were obtained in the nephrogram phase for renal parenchyma and renal arteries, but in the excretory phase for renal pelvis/calyxes and proximal ureters. Assessment of pathology in the three categories showed no statistically significant differences between the three phases. Certainty scores for assessment of pathology, however, showed a significantly higher certainty for renal pathology when comparing the native phase to nephrogram and excretory phase and a significantly higher score for nephrographic phase but only for incidental findings. Conclusion Visualisation of renal anatomy was as expected with each post-contrast phase showing favourable scores compared to the native phase. No statistically significant differences in the assessment of pathology were found between the three phases. The low-dose CT (LDCT) seems to be sufficient in differentiating between normal and pathological examinations. To reduce the radiation burden in certain patient groups, the LDCT could be considered a suitable alternative as a first line imaging method. However, radiologists should be aware of its limitations.

  • 28.
    Klintström, Benjamin
    et al.
    KTH, Skolan för teknik och hälsa (STH).
    Klintström, E.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Moreno, Rodrigo
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Feature space clustering for trabecular bone segmentation2017Ingår i: 20th Scandinavian Conference on Image Analysis, SCIA 2017, Springer, 2017, Vol. 10270, s. 65-75Konferensbidrag (Refereegranskat)
    Abstract [en]

    Trabecular bone structure has been shown to impact bone strength and fracture risk. In vitro, this structure can be measured by micro-computed tomography (micro-CT). For clinical use, it would be valuable if multi-slice computed tomography (MSCT) could be used to analyse trabecular bone structure. One important step in the analysis is image volume segmentation. Previous segmentation techniques have either been computer resource intensive or produced sub-optimal results when used on MSCT data. This paper proposes a new segmentation method that tries to balance good results against computational complexity. Material. Fourteen human radius specimens where scanned with MSCT and segmented using the proposed method as well as two segmentation methods previously used to segment trabecular bone (Otsu and Automated Region Growing (ARG)). The proposed method (named FCH) uses a combination of feature space clustering, edge detection and hysteresis thresholding. For evaluation, we computed correlations with the reference method micro-CT for 7 structure parameters and measured segmentation time. Results. Correlations with micro-CT were highest for FCH in 3 cases, highest for ARG in 3 cases, and in general lower for Otsu. Both FCH and ARG had correlations higher than 0.80 for all parameters, except for trabecular thickness and trabecular termini. FCH was 60 times slower than Otsu, but 5 times faster than ARG. Discussion. The high correlations with micro-CT suggest that with a suitable segmentation method it might be possible to analyse trabecular bone structure using MSCT-machines. The proposed segmentation method may represent a useful balance between speed and accuracy.

  • 29. Klintström, Benjamin
    et al.
    Klintström, Eva
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Moreno, Rodrigo
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Feature space clustering for trabecular bone segmentation2017Ingår i: Scandinavian Conference on Image Analysis, 2017, s. 65-75Konferensbidrag (Refereegranskat)
  • 30. Klintström, Eva
    et al.
    Klintström, Benjamin
    Moreno, Rodrigo
    KTH, Skolan för teknik och hälsa (STH).
    Brismar, Torkel B.
    Pahr, Dieter H.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH).
    Predicting Trabecular Bone Stiffness from Clinical Cone-Beam CT and HR-pQCT Data; an In Vitro Study Using Finite Element Analysis2016Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, nr 8, artikel-id e0161101Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Stiffness and shear moduli of human trabecular bone may be analyzed in vivo by finite element (FE) analysis from image data obtained by clinical imaging equipment such as high resolution peripheral quantitative computed tomography (HR-pQCT). In clinical practice today, this is done in the peripheral skeleton like the wrist and heel. In this cadaveric bone study, fourteen bone specimens from the wrist were imaged by two dental cone beam computed tomography (CBCT) devices and one HR-pQCT device as well as by dual energy X-ray absorptiometry (DXA). Histomorphometric measurements from micro-CT data were used as gold standard. The image processing was done with an in-house developed code based on the automated region growing (ARG) algorithm. Evaluation of how well stiffness (Young's modulus E3) and minimum shear modulus from the 12, 13, or 23 could be predicted from the CBCT and HR-pQCT imaging data was studied and compared to FE analysis from the micro-CT imaging data. Strong correlations were found between the clinical machines and micro-CT regarding trabecular bone structure parameters, such as bone volume over total volume, trabecular thickness, trabecular number and trabecular nodes (varying from 0.79 to 0.96). The two CBCT devices as well as the HR-pQCT showed the ability to predict stiffness and shear, with adjusted R-2-values between 0.78 and 0.92, based on data derived through our in-house developed code based on the ARG algorithm. These findings indicate that clinically used CBCT may be a feasible method for clinical studies of bone structure and mechanical properties in future osteoporosis research.

  • 31.
    Klintström, Eva
    et al.
    Linköping Univ, Dept Med & Hlth Sci, Campus US, S-58185 Linköping, Sweden.;Linkoping Univ, Ctr Med Image Sci & Visualizat CMIV, Campus US, S-58185 Linkoping, Sweden..
    Klintström, Benjamin
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH).
    Pahr, Dieter
    Vienna Univ Technol, Inst Lightweight Design & Struct Biomech, Vienna, Austria..
    Brismar, Torkel B.
    Karolinska Univ Hosp, Karolinska Inst, Dept Clin Sci Intervent & Technol, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Radiol, Stockholm, Sweden..
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning. Linköping Univ, Dept Med & Hlth Sci, Linköping, Sweden..
    Moreno, Rodrigo
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Direct estimation of human trabecular bone stiffness using cone beam computed tomography2018Ingår i: Oral surgery, oral medicine, oral pathology and oral radiology, ISSN 2212-4403, E-ISSN 2212-4411, Vol. 126, nr 1, s. 72-82Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Objectives. The aim of this study was to evaluate the possibility of estimating the biomechanical properties of trabecular bone through finite element simulations by using dental cone beam computed tomography data. Study Design. Fourteen human radius specimens were scanned in 3 cone beam computed tomography devices: 3-D Accuitomo 80 (J. Morita MFG., Kyoto, Japan), NewTom 5 G (QR Verona, Verona, Italy), and Verity (Planmed, Helsinki, Finland). The imaging data were segmented by using 2 different methods. Stiffness (Young modulus), shear moduli, and the size and shape of the stiffness tensor were studied. Corresponding evaluations by using micro-CT were regarded as the reference standard. Results. The 3-D Accuitomo 80 (J. Morita MFG., Kyoto, Japan) showed good performance in estimating stiffness and shear moduli but was sensitive to the choice of segmentation method. Newtom 5 G (QR Verona, Verona, Italy) and Verity (Planmed, Helsinki, Finland) yielded good correlations, but they were not as strong as Accuitomo 80 U. Morita MFG., Kyoto, Japan). The cone beam computed tomography devices overestimated both stiffness and shear compared with the micro-CT estimations. Conclusions. Finite element-based calculations of biomechanics from cone beam computed tomography data are feasible, with strong correlations for the Accuitomo 80 scanner a. Morita MFG., Kyoto, Japan) combined with an appropriate segmentation method. Such measurements might be useful for predicting implant survival by in vivo estimations of bone properties.

  • 32. Lidayova, Kristina
    et al.
    Frimmel, Hans
    Bengtsson, Ewert
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Improved centerline tree detection of diseased peripheral arteries with a cascading algorithm for vascular segmentation2017Ingår i: Journal of Medical Imaging, ISSN 2329-4302, E-ISSN 2329-4310, Vol. 4, nr 2, artikel-id 024004Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Vascular segmentation plays an important role in the assessment of peripheral arterial disease. The segmentation is very challenging especially for arteries with severe stenosis or complete occlusion. We present a cascading algorithm for vascular centerline tree detection specializing in detecting centerlines in diseased peripheral arteries. It takes a three-dimensional computed tomography angiography (CTA) volume and returns a vascular centerline tree, which can be used for accelerating and facilitating the vascular segmentation. The algorithm consists of four levels, two of which detect healthy arteries of varying sizes and two that specialize in different types of vascular pathology: severe calcification and occlusion. We perform four main steps at each level: appropriate parameters for each level are selected automatically, a set of centrally located voxels is detected, these voxels are connected together based on the connection criteria, and the resulting centerline tree is corrected from spurious branches. The proposed method was tested on 25 CTA scans of the lower limbs, achieving an average overlap rate of 89% and an average detection rate of 82%. The average execution time using four CPU cores was 70 s, and the technique was successful also in detecting very distal artery branches, e. g., in the foot.

  • 33. Lidayová, K.
    et al.
    Betancur, D. A. G.
    Frimmel, H.
    Hoyos, M. H.
    Orkisz, M.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Airway-tree segmentation in subjects with acute respiratory distress syndrome2017Ingår i: 20th Scandinavian Conference on Image Analysis, SCIA 2017, Springer, 2017, Vol. 10270, s. 76-87Konferensbidrag (Refereegranskat)
    Abstract [en]

    Acute respiratory distress syndrome (ARDS) is associated with a high mortality rate in intensive care units. To lower the number of fatal cases, it is necessary to customize the mechanical ventilator parameters according to the patient’s clinical condition. For this, lung segmentation is required to assess aeration and alveolar recruitment. Airway segmentation may be used to reach a more accurate lung segmentation. In this paper, we seek to improve lung segmentation results by proposing a novel automatic airway-tree segmentation that is able to address the heterogeneity of ARDS pathology by handling various lung intensities differently. The method detects a simplified airway skeleton, thereby obtains a set of seed points together with an approximate radius and intensity range related to each of the points. These seeds are the input for an onion-kernel region-growing segmentation algorithm where knowledge about radius and intensity range restricts the possible leakage in the parenchyma. The method was evaluated qualitatively on 70 thoracic Computed Tomography volumes of subjects with ARDS, acquired at significantly different mechanical ventilation conditions. It found a large proportion of airway branches including tiny poorly-aerated bronchi. Quantitative evaluation was performed indirectly and showed that the resulting airway segmentation provides important anatomic landmarks. Their correspondences are needed to help a registration-based segmentation of the lungs in difficult ARDS cases where the lung boundary contrast is completely missing. The proposed method takes an average time of 43 s to process a thoracic volume which is valuable for the clinical use.

  • 34. Lidayová, K.
    et al.
    Frimmel, H.
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University, Sweden.
    Bengtsson, E.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University, Sweden.
    Fast vascular skeleton extraction algorithm2016Ingår i: Pattern Recognition Letters, ISSN 0167-8655, E-ISSN 1872-7344, Vol. 76, s. 67-75Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Vascular diseases are a common cause of death, particularly in developed countries. Computerized image analysis tools play a potentially important role in diagnosing and quantifying vascular pathologies. Given the size and complexity of modern angiographic data acquisition, fast, automatic and accurate vascular segmentation is a challenging task.In this paper we introduce a fully automatic high-speed vascular skeleton extraction algorithm that is intended as a first step in a complete vascular tree segmentation program. The method takes a 3D unprocessed Computed Tomography Angiography (CTA) scan as input and produces a graph in which the nodes are centrally located artery voxels and the edges represent connections between them. The algorithm works in two passes where the first pass is designed to extract the skeleton of large arteries and the second pass focuses on smaller vascular structures. Each pass consists of three main steps. The first step sets proper parameters automatically using Gaussian curve fitting. In the second step different filters are applied to detect voxels - nodes - that are part of arteries. In the last step the nodes are connected in order to obtain a continuous centerline tree for the entire vasculature. Structures found, that do not belong to the arteries, are removed in a final anatomy-based analysis. The proposed method is computationally efficient with an average execution time of 29s and has been tested on a set of CTA scans of the lower limbs achieving an average overlap rate of 97% and an average detection rate of 71%.

  • 35. Lidayová, K.
    et al.
    Frimmel, H.
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Bengtsson, E.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Skeleton-based fast, fully automated generation of vessel tree structure for clinical evaluation of blood vessel systems2017Ingår i: Skeletonization: Theory, Methods and Applications, Elsevier, 2017, s. 345-382Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    This chapter focuses on skeleton detection for clinical evaluation of blood vessel systems. In clinical evaluation, there is a need for fast and accurate segmentation algorithms that can reliably provide vessel measurements and additional information for clinicians to decide the diagnosis.Since blood vessels have a characteristic tubular shape, their segmentation can be accelerated and facilitated by first identifying the rough vessel centerlines, which can be seen as a special case of an image skeleton extraction algorithm. A segmentation algorithm will finally use the resulting skeleton as a seed region during the segmentation. The proposed method takes an unprocessed 3D computed tomography angiography (CTA) scan as an input and generates a connected graph of centrally located arterial voxels. The method works in two levels, where large arteries are captured in the first level, and small arteries are added in the second one. Experimental results show that the method can achieve high overlap rate and acceptable detection rate accuracies. High computational efficiency of the method opens the possibility for an interactive clinical use.

  • 36. Lidayová, K.
    et al.
    Gupta, A.
    Frimmel, H.
    Sintorn, I. -M
    Bengtsson, E.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Classification of cross-sections for vascular skeleton extraction using convolutional neural networks2017Ingår i: 21st Annual Conference on Medical Image Understanding and Analysis, MIUA 2017, Springer, 2017, Vol. 723, s. 182-194Konferensbidrag (Refereegranskat)
    Abstract [en]

    Recent advances in Computed Tomography Angiography provide high-resolution 3D images of the vessels. However, there is an inevitable requisite for automated and fast methods to process the increased amount of generated data. In this work, we propose a fast method for vascular skeleton extraction which can be combined with a segmentation algorithm to accelerate the vessel delineation. The algorithm detects central voxels - nodes - of potential vessel regions in the orthogonal CT slices and uses a convolutional neural network (CNN) to identify the true vessel nodes. The nodes are gradually linked together to generate an approximate vascular skeleton. The CNN classifier yields a precision of 0.81 and recall of 0.83 for the medium size vessels and produces a qualitatively evaluated enhanced representation of vascular skeletons.

  • 37. Lidayová, Kristína
    et al.
    Lindblad, Joakim
    Sladoje, Nataša
    Frimmel, Hans
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Coverage segmentation of 3D thin structures2015Ingår i: Image Processing Theory, Tools and Applications (IPTA), 2015 International Conference on, IEEE conference proceedings, 2015, s. 23-28Konferensbidrag (Refereegranskat)
    Abstract [en]

    We present a coverage segmentation method for extracting thin structures in three-dimensional images. The proposed method is an improved extension of our coverage segmentation method for 2D thin structures. We suggest implementation that enables low memory consumption and processing time, and by that applicability of the method on real CTA data. The method needs a reliable crisp segmentation as an input and uses information from linear unmixing and the crisp segmentation to create a high-resolution crisp reconstruction of the object, which can then be used as a final result, or down-sampled to a coverage segmentation at the starting image resolution. Performed quantitative and qualitative analysis confirm excellent performance of the proposed method, both on synthetic and on real data, in particular in terms of robustness to noise.

  • 38.
    Mahbod, A.
    et al.
    Romania.
    Ellinger, I.
    Romania.
    Ecker, R.
    Romania.
    Smedby, Örjan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Wang, Chunliang
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Medicinsk avbildning.
    Breast Cancer Histological Image Classification Using Fine-Tuned Deep Network Fusion2018Ingår i: 15th International Conference on Image Analysis and Recognition, ICIAR 2018, Springer, 2018, s. 754-762Konferensbidrag (Refereegranskat)
    Abstract [en]

    Breast cancer is the most common cancer type in women worldwide. Histological evaluation of the breast biopsies is a challenging task even for experienced pathologists. In this paper, we propose a fully automatic method to classify breast cancer histological images to four classes, namely normal, benign, in situ carcinoma and invasive carcinoma. The proposed method takes normalized hematoxylin and eosin stained images as input and gives the final prediction by fusing the output of two residual neural networks (ResNet) of different depth. These ResNets were first pre-trained on ImageNet images, and then fine-tuned on breast histological images. We found that our approach outperformed a previous published method by a large margin when applied on the BioImaging 2015 challenge dataset yielding an accuracy of 97.22%. Moreover, the same approach provided an excellent classification performance with an accuracy of 88.50% when applied on the ICIAR 2018 grand challenge dataset using 5-fold cross validation.

  • 39.
    Mahbod, Amirreza
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Chowdhury, Manish
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Automatic brain segmentation using artificial neural networks with shape context2018Ingår i: Pattern Recognition Letters, ISSN 0167-8655, E-ISSN 1872-7344, Vol. 101, s. 74-79Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Segmenting brain tissue from MR scans is thought to be highly beneficial for brain abnormality diagnosis, prognosis monitoring, and treatment evaluation. Many automatic or semi-automatic methods have been proposed in the literature in order to reduce the requirement of user intervention, but the level of accuracy in most cases is still inferior to that of manual segmentation. We propose a new brain segmentation method that integrates volumetric shape models into a supervised artificial neural network (ANN) framework. This is done by running a preliminary level-set based statistical shape fitting process guided by the image intensity and then passing the signed distance maps of several key structures to the ANN as feature channels, in addition to the conventional spatial-based and intensity-based image features. The so-called shape context information is expected to help the ANN to learn local adaptive classification rules instead of applying universal rules directly on the local appearance features. The proposed method was tested on a public datasets available within the open MICCAI grand challenge (MRBrainS13). The obtained average Dice coefficient were 84.78%, 88.47%, 82.76%, 95.37% and 97.73% for gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), brain (WM + GM) and intracranial volume respectively. Compared with other methods tested on the same dataset, the proposed method achieved competitive results with comparatively shorter training time.

  • 40. Marreiros, Filipe M. M.
    et al.
    Rossitti, Sandro
    Karlsson, Per M.
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Gustafsson, Torbjorn
    Carleberg, Per
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Superficial vessel reconstruction with a multiview camera system2016Ingår i: Journal of Medical Imaging, ISSN 2329-4302, E-ISSN 2329-4310, Vol. 3, nr 1, artikel-id 015001Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We aim at reconstructing superficial vessels of the brain. Ultimately, they will serve to guide the deformation methods to compensate for the brain shift. A pipeline for three-dimensional (3-D) vessel reconstruction using three mono-complementary metal-oxide semiconductor cameras has been developed. Vessel centerlines are manually selected in the images. Using the properties of the Hessian matrix, the centerline points are assigned direction information. For correspondence matching, a combination of methods was used. The process starts with epipolar and spatial coherence constraints (geometrical constraints), followed by relaxation labeling and an iterative filtering where the 3-D points are compared to surfaces obtained using the thin-plate spline with decreasing relaxation parameter. Finally, the points are shifted to their local centroid position. Evaluation in virtual, phantom, and experimental images, including intraoperative data from patient experiments, shows that, with appropriate camera positions, the error estimates (root-mean square error and mean error) are similar to 1 mm.

  • 41. Marreiros, Filipe M. M.
    et al.
    Rossitti, Sandro
    Karlsson, Per M.
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Gustafsson, Torbjorn
    Carleberg, Per
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Superficial vessel reconstruction with a Multiview camera system (vol 3, 015001, 2016)2016Ingår i: Journal of Medical Imaging, ISSN 2329-4302, E-ISSN 2329-4310, Vol. 3, nr 1, artikel-id 019801Artikel i tidskrift (Refereegranskat)
  • 42. Marreiros, Filipe M. M.
    et al.
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping Univ, Sweden.
    Rossitti, Sandro
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping Univ, Sweden.
    Non-rigid point set registration of curves: registration of the superficial vessel centerlines of the brain2016Ingår i: MEDICAL IMAGING 2016: IMAGE-GUIDED PROCEDURES, ROBOTIC INTERVENTIONS, AND MODELING, SPIE - International Society for Optical Engineering, 2016, artikel-id UNSP 978611Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this study we present a non-rigid point set registration for 3D curves (composed by 3D set of points). The method was evaluated in the task of registration of 3D superficial vessels of the brain where it was used to match vessel centerline points. It consists of a combination of the Coherent Point Drift (CPD) and the Thin-Plate Spline (TPS) semilandmarks. The CPD is used to perform the initial matching of centerline 3D points, while the semilandmark method iteratively relaxes/slides the points. For the evaluation, a Magnetic Resonance Angiography (MRA) dataset was used. Deformations were applied to the extracted vessels centerlines to simulate brain bulging and sinking, using a TPS deformation where a few control points were manipulated to obtain the desired transformation (T-1). Once the correspondences are known, the corresponding points are used to define a new TPS deformation(T-2). The errors are measured in the deformed space, by transforming the original points using T-1 and T-2 and measuring the distance between them. To simulate cases where the deformed vessel data is incomplete, parts of the reference vessels were cut and then deformed. Furthermore, anisotropic normally distributed noise was added. The results show that the error estimates (root mean square error and mean error) are below 1 mm, even in the presence of noise and incomplete data.

  • 43. Medrano-Gracia, Pau
    et al.
    Ormiston, John
    Webster, Mark
    Beier, Susann
    Ellis, Chris
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Young, Alistair
    Cowan, Brett
    A Study of Coronary Bifurcation Shape in a Normal Population2017Ingår i: Journal of Cardiovascular Translational Research, ISSN 1937-5387, E-ISSN 1937-5395, Vol. 10, nr 1, s. 82-90Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    During percutaneous coronary intervention, stents are placed in narrowings of the arteries to restore normal blood flow. Despite improvements in stent design, deployment techniques and drug-eluting coatings, restenosis and stent thrombosis remain a significant problem. Population stent design based on statistical shape analysis may improve clinical outcomes. Computed tomographic (CT) coronary angiography scans from 211 patients with a zero calcium score, no stenoses and no intermediate artery, were used to create statistical shape models of 446 major coronary artery bifurcations (left main, first diagonal and obtuse marginal and right coronary crux). Coherent point drift was used for registration. Principal component analysis shape scores were tested against clinical risk factors, quantifying the importance of recognised shape features in intervention including size, angles and curvature. Significant differences were found in (1) vessel size and bifurcation angle between the left main and other bifurcations; (2) inlet and curvature angle between the right coronary crux and other bifurcations; and (3) size and bifurcation angle by sex. Hypertension, smoking history and diabetes did not appear to have an association with shape. Physiological diameter laws were compared, with the Huo-Kassab model having the best fit. Bifurcation coronary anatomy can be partitioned into clinically meaningful modes of variation showing significant shape differences. A computational atlas of normal coronary bifurcation shape, where disease is common, may aid in the design of new stents and deployment techniques, by providing data for bench-top testing and computational modelling of blood flow and vessel wall mechanics.

  • 44. Medrano-Gracia, Pau
    et al.
    Ormiston, John
    Webster, Mark
    Beier, Susann
    Young, Alistair
    Ellis, Chris
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Cowan, Brett
    A computational atlas of normal coronary artery anatomy2016Ingår i: EuroIntervention, ISSN 1774-024X, E-ISSN 1969-6213, Vol. 12, nr 7, s. 845-854Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aims: The aim of this study was to define the shape variations, including diameters and angles, of the major coronary artery bifurcations. Methods and results: Computed tomographic angiograms from 300 adults with a zero calcium score and no stenoses were segmented for centreline and luminal models. A computational atlas was constructed enabling automatic quantification of 3D angles, diameters and lengths of the coronary tree. The diameter (mean +/- SD) of the left main coronary was 3.5 +/- 0.8 mm and the length 10.5 +/- 5.3 mm. The left main bifurcation angle (distal angle or angle B) was 89 +/- 21 degrees for cases with, and 75 +/- 23 degrees for those without an intermediate artery (p<0.001). Analogous measurements of diameter and angle were tabulated for the other major bifurcations (left anterior descending/diagonal, circumflex/obtuse marginal and right coronary crux). Novel 3D angle definitions are proposed and analysed. Conclusions: A computational atlas of normal coronary artery anatomy provides distributions of diameter, lengths and bifurcation angles as well as more complex shape analysis. These data define normal anatomical variation, facilitating stent design, selection and optimal treatment strategy. These population models are necessary for accurate computational flow dynamics, can be 3D printed for bench testing bifurcation stents and deployment strategies, and can aid in the discussion of different approaches to the treatment of coronary bifurcations.

  • 45. Mendrik, AM
    et al.
    Vincken, KL
    Kuijf, HJ
    Breeuwer, M
    Bouvy, W
    de Bresser, J
    Alansary, A
    de Bruijne, M
    Caras, A
    El-Baz, A
    Jogh, A
    Katyal, AR
    Khan, AR
    van der Lijn, F
    Mahmood, Q
    Mukherjee, R
    van Opbroek, A
    Paneri, S
    Pereira, S
    Persson, M
    Rajch, M
    Sarikaya, D
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University.
    Silval, CA
    Vrooman, HA
    Vyas, S
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University.
    Zhao, L
    Biessels, GJ
    Viergever, MA
    MRBrainS Challenge: Online Evaluation Framework for Brain Image Segmentation in 3T MRI Scans2015Ingår i: Computational Intelligence and Neuroscience, ISSN 1687-5265, E-ISSN 1687-5273, Vol. 2015, artikel-id 813696Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Many methods have been proposed for tissue segmentation in brain MRI scans. The multitude of methods proposed complicates the choice of one method above others. We have therefore established the MRBrainS online evaluation framework for evaluating (semi)automatic algorithms that segment gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) on 3T brain MRI scans of elderly subjects (65–80 y). Participants apply their algorithms to the provided data, after which their results are evaluated and ranked. Full manual segmentations of GM, WM, and CSF are available for all scans and used as the reference standard. Five datasets are provided for training and fifteen for testing. The evaluated methods are ranked based on their overall performance to segment GM, WM, and CSF and evaluated using three evaluation metrics (Dice, H95, and AVD) and the results are published on the MRBrainS13 website. We present the results of eleven segmentation algorithms that participated in the MRBrainS13 challenge workshop at MICCAI, where the framework was launched, and three commonly used freeware packages: FreeSurfer, FSL, and SPM. The MRBrainS evaluation framework provides an objective and direct comparison of all evaluated algorithms and can aid in selecting the best performing method for the segmentation goal at hand.

  • 46.
    Moreno, Rodrigo
    et al.
    Linköping University.
    Borga, Magnus
    Klintström, Eva
    Brismar, Torkel
    Smedby, Örjan
    Linköping University.
    Anisotropy Estimation of Trabecular Bone in Gray-Scale: Comparison Between Cone Beam and Micro Computed Tomography Data2015Ingår i: Developments in Medical Image Processing and Computational Vision / [ed] Tavares, Joao Manuel R. S.; Natal Jorge, Renato, Springer, 2015, Vol. 19, s. 207-220Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Measurement of anisotropy of trabecular bone has clinical relevance in osteoporosis. In this study, anisotropy measurements of 15 trabecular bone biopsies from the radius estimated by different fabric tensors on images acquired through cone beam computed tomography (CBCT) and micro computed tomography (micro-CT) were compared. The results show that the generalized mean intercept length (MIL) tensor performs better than the global gray-scale structure tensor, especially when the von Mises-Fisher kernel is applied.  Also, the generalized MIL tensor yields consistent results between the two scanners. These results suggest that this tensor is appropriate for estimating anisotropy in images acquired in vivo through CBCT.

  • 47.
    Moreno, Rodrigo
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University.
    Gradient-Based Enhancement of Tubular Structures in Medical Images2015Ingår i: Medical Image Analysis, ISSN 1361-8415, E-ISSN 1361-8423, Vol. 26, nr 1, s. 19-29Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Vesselness filters aim at enhancing tubular structures in medical images. The most popular vesselness filters are based on eigenanalyses of the Hessian matrix computed at different scales. However, Hessian-based methods have well-known limitations, most of them related to the use of second order derivatives. In this paper, we propose an alternative strategy in which ring-like patterns are sought in the local orientation distribution of the gradient. The method takes advantage of symmetry properties of ring-like patterns in the spherical harmonics domain. For bright vessels, gradients not pointing towards the center are filtered out from every local neighborhood in a first step. The opposite criterion is used for dark vessels. Afterwards, structuredness, evenness and uniformness measurements are computed from the power spectrum in spherical harmonics of both the original and the half-zeroed orientation distribution of the gradient. Finally, the features are combined into a single vesselness measurement. Alternatively, a structure tensor that is suitable for vesselness can be estimated before the analysis in spherical harmonics. The two proposed methods are called Ring Pattern Detector (RPD) and Filtered Structure Tensor (FST) respectively. Experimental results with computed tomography angiography data show that the proposed filters perform better compared to the state-of-the-art.

  • 48.
    Moreno, Rodrigo
    et al.
    KTH, Skolan för teknik och hälsa (STH).
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Vesselness Estimation through Higher-Order Orientation Tensors2016Ingår i: International Symposium on Biomedical Imaging (ISBI), IEEE Computer Society, 2016, s. 1139-1142Konferensbidrag (Refereegranskat)
    Abstract [en]

    We recently proposed a method for estimating vesselness based on detection of ring patterns in the local distribution ofthe gradient. This method has a better performance than other state-of-the-art algorithms. However, the original implementation of the method makes use of the spherical harmonics transform locally, which is time consuming. In this paper we propose an equivalent formulation of the method based on higher-order tensors. A linear mapping between the spherical harmonics transform and higher-order orientation tensors is used in order to reduce the complexity of the method. With the new implementation, the analysis of computed tomography angiography data can be performed 2.6 times faster compared with the original implementation.

  • 49.
    Moreno, Rodrigo
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Pahr, Dieter
    Prediction of Apparent Trabecular Bone Stiffness through Fourth-Order Fabric Tensors2015Ingår i: Biomechanics and Modeling in Mechanobiology, ISSN 1617-7959, E-ISSN 1617-7940Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The apparent stiffness tensor is an important mechanical parameter for characterizing trabecular bone. Previous studies have modeled this parameter as a function of mechanical properties of the tissue, bone density and a second-order fabric tensor, which encodes both anisotropy and orientation of trabecular bone. Although these models yield strong correlations between observed and predicted stiffness tensors, there is still space for reducing accuracy errors.In this paper we propose a model that uses fourth-order instead of second-order fabric tensors. First, the totally symmetric part of the stiffness tensor is assumed proportional to the fourth-order fabric tensor in the logarithmic scale. Second, the asymmetric part of the stiffness tensor is derived from relationships among components of the harmonic tensor decomposition of the stiffness tensor. The mean intercept length (MIL), generalized MIL (GMIL) and global structure tensor fourth-order were computed from images acquired through micro computed tomography of 264 specimens of the femur. The predicted tensors were compared to the stiffness tensors computed by using the micro finite element method (micro-FE), which was considered as the gold standard, yielding strong correlations (R^2 above 0.962). The GMIL tensor yielded the best results among the tested fabric tensors. The Frobenius error, geodesic error and the error of the norm were reduced by applying the proposed model by 3.75%, 0.07% and 3.16%, respectively compared to the model by Zysset and Curnier (1995) with the second-order MIL tensor. From the results, fourth-order fabric tensors are a good alternative to the more expensive micro-FE stiffness predictions.

  • 50. Norén, Bengt
    et al.
    Dahlström, Nils
    Forsgren, Mikael Fredrik
    Leinhard, Olof Dahlqvist
    Kechagias, Stergios
    Almer, Sven
    Wirell, Staffan
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering. Linköping University.
    Lundberg, Peter
    Visual assessment of biliary excretion of Gd-EOB-DTPA in patients with suspected diffuse liver disease–A biopsy-verified prospective study2015Ingår i: European Journal of Radiology Open, ISSN 2352-0477, Vol. 2, s. 19-25Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Objectives: To qualitatively evaluate late dynamic contrast phases, 10, 20 and 30. min, after administration of Gd-EOB-DTPA with regard to biliary excretion in patients presenting with elevated liver enzymes without clinical signs of cirrhosis or hepatic decompensation and to compare the visual assessment of contrast agent excretion with histo-pathological fibrosis stage, contrast uptake parameters and blood tests. Methods: 29 patients were prospectively examined using 1.5T MRI. The visually assessed presence or absence of contrast agent for each of five anatomical regions in randomly reviewed time-series was summarized on a four grade scale for each patient. The scores, including a total visual score, were related to the histo-pathological findings, the quantitative contrast agent uptake parameters, expressed as KHep or LSC_N, and blood tests. Results: No relationship between the fibrosis grade or contrast uptake parameters could be established. A negative correlation between the visual assessment and alkaline phosphatase (ALP) was found. Comparing a sub-group of cholestatic patients with fibrosis score and Gd-EOB-DTPA dynamic parameters did not add any additional significant correlation. Conclusions: No correlation between visually assessed biliary excretion of Gd-EOB-DTPA and histo-pathological or contrast uptake parameters was found. A negative correlation between the visual assessment and alkaline phosphatase (ALP) was found.

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