scholarly journals DCEMRI.jl: A fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis

2014 ◽  
Author(s):  
David S Smith ◽  
Xia Li ◽  
Lori R Arlinghaus ◽  
Thomas E Yankeelov ◽  
E. Brian Welch
Keyword(s):  
Open Source ◽  
Tissue Concentration ◽  
Quantitative Imaging ◽  
Imaging Biomarkers ◽  
Problem Size ◽  
Data Set ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced ◽  
Run Time

We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10-20x speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 x 192 breast image, we achieved run times of < 1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N1.9), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise.

scholarly journals DCEMRI.jl: A fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis

2014 ◽  
Author(s):  
David S Smith ◽  
Xia Li ◽  
Lori R Arlinghaus ◽  
Thomas E Yankeelov ◽  
E. Brian Welch
Keyword(s):  
Open Source ◽  
Tissue Concentration ◽  
Quantitative Imaging ◽  
Imaging Biomarkers ◽  
Problem Size ◽  
Data Set ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced ◽  
Run Time

We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10-20x speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 x 192 breast image, we achieved run times of < 1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N1.9), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise.

scholarly journals Dynamic contrast-enhanced magnetic resonance imaging for monitoring neovascularization during bone regeneration—a randomized in vivo study in rabbits

2021 ◽  
Author(s):  
L. A. R. Righesso ◽  
M. Terekhov ◽  
H. Götz ◽  
M. Ackermann ◽  
T. Emrich ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Bone Regeneration ◽  
Blood Perfusion ◽  
Autogenous Bone ◽  
Resonance Imaging ◽  
Dce Mri ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced

Abstract Objectives Micro-computed tomography (μ-CT) and histology, the current gold standard methods for assessing the formation of new bone and blood vessels, are invasive and/or destructive. With that in mind, a more conservative tool, dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), was tested for its accuracy and reproducibility in monitoring neovascularization during bone regeneration. Additionally, the suitability of blood perfusion as a surrogate of the efficacy of osteoplastic materials was evaluated. Materials and methods Sixteen rabbits were used and equally divided into four groups, according to the time of euthanasia (2, 3, 4, and 6 weeks after surgery). The animals were submitted to two 8-mm craniotomies that were filled with blood or autogenous bone. Neovascularization was assessed in vivo through DCE-MRI, and bone regeneration, ex vivo, through μ-CT and histology. Results The defects could be consistently identified, and their blood perfusion measured through DCE-MRI, there being statistically significant differences within the blood clot group between 3 and 6 weeks (p = 0.029), and between the former and autogenous bone at six weeks (p = 0.017). Nonetheless, no significant correlations between DCE-MRI findings on neovascularization and μ-CT (r =−0.101, 95% CI [−0.445; 0.268]) or histology (r = 0.305, 95% CI [−0.133; 0.644]) findings on bone regeneration were observed. Conclusions These results support the hypothesis that DCE-MRI can be used to monitor neovascularization but contradict the premise that it could predict bone regeneration as well.

scholarly journals Microarray Gene Expression Analysis of Murine Tumor Heterogeneity Defined by Dynamic Contrast-Enhanced MRI

2002 ◽  
Vol 1 (3) ◽  
pp. 153535002002021
Author(s):  
Nick G. Costouros ◽  
Dominique Lorang ◽  
Yantian Zhang ◽  
Marshall S. Miller ◽  
Felix E. Diehn ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Tumor Heterogeneity ◽  
Protein Translation ◽  
Pharmacokinetic Parameters ◽  
Transcriptional Level ◽  
Target Tissue ◽  
Dce Mri ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced

Current methods of studying angiogenesis are limited in their ability to serially evaluate in vivo function throughout a target tissue. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and pharmacokinetic modeling provide a useful method for evaluating tissue vasculature based on contrast accumulation and washout. While it is often assumed that areas of high contrast enhancement and washout comprise areas of increased angiogenesis and tumor activity, the actual molecular pathways that are active in such areas are poorly understood. Using DCE-MRI in a murine subcutaneous tumor model, we were able to perform pharmacokinetic functional analysis of a tumor, coregistration of MRI images with histological cross-sections, immunohistochemistry, laser capture microdissection, and genetic profiling of tumor heterogeneity based on pharmacokinetic parameters. Using imaging as a template for biologic investigation, we have not found evidence of increased expression of proangiogenic modulators at the transcriptional level in either distinct pharmacokinetic region. Furthermore, these regions show no difference on histology and CD31 immunohistochemistry. However, the expression of ribosomal proteins was greatly increased in high enhancement and washout regions, implying increased protein translation and consequent increased cellular activity. Together, these findings point to the potential importance of posttranscriptional regulation in angiogenesis and the need for the development of angiogenesis-specific contrast agents to evaluate in vivo angiogenesis at a molecular level.

scholarly journals Permeability of the windows of the brain: feasibility of dynamic contrast-enhanced MRI of the circumventricular organs

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Inge C. M. Verheggen ◽  
Joost J. A. de Jong ◽  
Martin P. J. van Boxtel ◽  
Alida A. Postma ◽  
Frans R. J. Verhey ◽  
...  
Keyword(s):  
Blood Brain Barrier ◽  
Gray Matter ◽  
Circumventricular Organs ◽  
Brain Barrier ◽  
Dce Mri ◽  
Dynamic Contrast Enhanced ◽  
Blood Brain ◽  
Contrast Enhanced ◽  
The Brain

Abstract Background Circumventricular organs (CVOs) are small structures without a blood–brain barrier surrounding the brain ventricles that serve homeostasic functions and facilitate communication between the blood, cerebrospinal fluid and brain. Secretory CVOs release peptides and sensory CVOs regulate signal transmission. However, pathogens may enter the brain through the CVOs and trigger neuroinflammation and neurodegeneration. We investigated the feasibility of dynamic contrast-enhanced (DCE) MRI to assess the CVO permeability characteristics in vivo, and expected significant contrast uptake in these regions, due to blood–brain barrier absence. Methods Twenty healthy, middle-aged to older males underwent brain DCE MRI. Pharmacokinetic modeling was applied to contrast concentration time-courses of CVOs, and in reference to white and gray matter. We investigated whether a significant and positive transfer from blood to brain could be measured in the CVOs, and whether this differed between secretory and sensory CVOs or from normal-appearing brain matter. Results In both the secretory and sensory CVOs, the transfer constants were significantly positive, and all secretory CVOs had significantly higher transfer than each sensory CVO. The transfer constants in both the secretory and sensory CVOs were higher than in the white and gray matter. Conclusions Current measurements confirm the often-held assumption of highly permeable CVOs, of which the secretory types have the strongest blood-to-brain transfer. The current study suggests that DCE MRI could be a promising technique to further assess the function of the CVOs and how pathogens can potentially enter the brain via these structures. Trial registration: Netherlands Trial Register number: NL6358, date of registration: 2017-03-24

Two-color in vivo dynamic contrast-enhanced pharmacokinetic imaging

2007 ◽  
Vol 12 (3) ◽  
pp. 034016 ◽  
Author(s):  
Yukihiro Hama ◽  
Yoshinori Koyama ◽  
Peter L. Choyke ◽  
Hisataka Kobayashi
Keyword(s):  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced ◽  
Pharmacokinetic Imaging

scholarly journals In Vivo Assessment of Ductal Carcinoma in Situ Grade: A Model Incorporating Dynamic Contrast-enhanced and Diffusion-weighted Breast MR Imaging Parameters

Radiology ◽  
2012 ◽  
Vol 263 (2) ◽  
pp. 374-382 ◽  
Author(s):  
Habib Rahbar ◽  
Savannah C. Partridge ◽  
Wendy B. DeMartini ◽  
Robert L. Gutierrez ◽  
Kimberly H. Allison ◽  
...  
Keyword(s):  
Carcinoma In Situ ◽  
Ductal Carcinoma ◽  
Imaging Parameters ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced ◽  
Breast Mr ◽  
And Diffusion ◽  
In Vivo Assessment

Dynamic contrast-enhanced CT (DCE-CT) as an early biomarker of response in metastatic renal cell carcinoma (mRCC) under anti-angiogenic treatment

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 14003-14003 ◽  
Author(s):  
L. Fournier ◽  
R. Thiam ◽  
C. Cuenod ◽  
J. Medioni ◽  
L. Trinquart ◽  
...  
Keyword(s):  
Treatment Response ◽  
Biological Effect ◽  
Mean Transit Time ◽  
Phase Iii ◽  
Imaging Biomarkers ◽  
Tumor Vascularity ◽  
Dynamic Contrast Enhanced ◽  
Iodinated Contrast ◽  
Contrast Enhanced Ct ◽  
Contrast Enhanced

14003 Background: Evaluation of treatment response for cancer relies on application of criteria based on size such RECIST. However, changes in size are often delayed and small. An accurate and early evaluation of tumor vascular characteristics would allow selection of patients (pts) who would most likely benefit of these therapies and early detection of treatment response to tailor therapy on an individual basis. Changes in tumor vascular parameters were quantified using dynamic contrast-enhanced computed tomography (DCE-CT) as a biomarker for tumor angiogenesis. Methods: A total of 44 mRCC pts were enrolled in an imaging study corollary of two phase III trials evaluating efficacy of anti-angiogenic drugs: sorafenib (N=9) vs. placebo (N=13), or sunitinib (N=17) vs. interferon (N=5). Perfusion CT acquisitions after injection of 80 ml of iodinated contrast agent were performed on a single “functional metastatic target” before treatment and every 6 weeks for follow-up. Microvascular parameters of the functional target were calculated using a dedicated software based on compartmental models: tumor blood flow (TBF) (ml/min/100g), tumor blood volume (TBV) (%), vascular permeability (VP) (ml/min/100g) and mean transit time (MTT) (s). These parameters were correlated to the best treatment response as evaluated by the size variation of the RECIST targets. Results: Among the 26 treated pts, there was a statistically significant drop in TBF and TBV as early as the first cycle of treatment (respectively -50%, p=0.03 and -51%, p<0.01) compared to pre-treatment, showing the biological effect of the drug on tumor vascularity. There was a significantly higher drop in TBF and TBV in pts who would be later classified as responders (N=16) vs. non-responders (N=10) after the first cycle of treatment (-66% vs. -6%, p=0.02; -60% vs. -26.5%, p=0.04). The changes in MTT and VP were not correlated to the best response. Conclusions: The functional imaging biomarkers TBF and TBV quantified by DCE-CT detect the biological effect of anti-angiogenic drugs on tumor vessels. TBF appears as very early predictor of mRCC response to anti-angiogenic drugs supporting the hypothesis that DCE-CT may constitute a surrogate biomarker of angiogenesis inhibition. No significant financial relationships to disclose.

scholarly journals An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Frank G. Zöllner ◽  
Markus Daab ◽  
Steven P. Sourbron ◽  
Lothar R. Schad ◽  
Stefan O. Schoenberg ◽  
...  
Keyword(s):  
Magnetic Resonance ◽  
Open Source ◽  
Open Source Software ◽  
Magnetic Resonance Images ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced
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