UMMPerfusion: an Open Source Software Tool Towards Quantitative MRI Perfusion Analysis in Clinical Routine

Zöllner, Frank G.; Weisser, G; Reich, Marcel; Kaiser, Sven; Schoenberg, Stefan O.; Sourbron, Steven; Schad, Lothar R.

doi:10.1007/s10278-012-9510-6

Cited by 62 publications

(67 citation statements)

References 49 publications

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“…A radiologist (M.S.) with 5 years' experience in prostate MRI post-processed the DCE MRI data using open source software tool towards quantitative MRI perfusion analysis (UMM Perfusion, OsiriX DICOM viewer, Version 3.9.4; The OsiriX Foundation, Geneva, Switzerland) (43). For each patient, nodules with focally altered perfusion parameters in the prostate bed were considered suspicious.…”

Section: Methodsmentioning

confidence: 99%

Detection of Local Recurrence with 3-Tesla MRI After Radical Prostatectomy: A Useful Method for Radiation Treatment Planning?

Buergy

Sertdemir²,

Weidner

et al. 2018

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Abstract. Background Prostate carcinoma is the second most common cancer in males (1) and although mortality rates have decreased in European countries and the United States (US), it still accounts for more than 258,000 deaths worldwide (2). According to the USpopulation-based Surveillance, Epidemiology, and End Results Program database, ~80% of men with newly diagnosed prostate carcinoma had localized disease at the time of diagnosis (3). Most of these patients selected radical prostatectomy or external beam radiotherapy as their primary treatment option (4,5). Recurrence rates after radical prostatectomy differ widely between around 10% of patients and more than 30% within 5 years (6-8), depending on Gleason score and other risk factors (6). In patients with positive surgical margins, it can be estimated that 20-40% of tumors recur (9, 10) and the majority of patients with biochemical relapse are diagnosed as having local recurrence (11). Radiotherapy as salvage treatment has been shown to improve biochemical control in patients with residual disease or biochemical relapse (12, 13). Stephenson et al. estimated that biochemical control can be achieved by radiotherapy in 48% of patients when salvage treatment starts before the prostatespecific antigen (PSA) level reaches 0.5 ng/ml; if administered at a PSA level of 0.5 ng/ml and above, only 26% of patients treated were free from (further) relapse (14). These results have been confirmed by modern series which additionally showed a clinical benefit in terms of distant metastasis-free survival, disease-specific mortality, and all-cause mortality (15). Furthermore, modern series indicated early salvage radiotherapy, initiated at the earliest sign of measurable PSA, to be beneficial in terms of biochemical and clinical endpoints (15, 16). Severe toxicity of salvage radiotherapy is generally reported to be low (17) but even in modern series, there is a residual risk of grade 3/4 bowel or urinary toxicity (18). 125This article is freely accessible online. (28,29). In a comparative study (29), radiotherapy plans contoured according to consensus guidelines failed to meet QUANTEC (30), and RADICALS (31) trial dose constraints in 75%, and 40% of cases, respectively. These inconsistencies indicate that our current approaches to salvage treatment of prostate carcinoma after radical prostatectomy should be reassessed. Improvement of therapeutic efficacy could be achieved by reducing geographical miss and side-effects by accurate detection of residual disease.Detection of residual prostate carcinoma is possible by magnetic resonance imaging (MRI) and positron-emission tomography-computed tomography (PET-CT). Evidence on restaging of biochemically relapsed patients with PET-CT was recently reviewed by Umbehr et al. (32). The authors analyzed 12 studies and found a pooled sensitivity and specificity of 85%, and 88%, respectively (mean PSA=7.9 ng/ml). In patients with early relapse (PSA <1 ng/ml), however, the authors found no convincing evidence for the use of PET-CT.MRI with (...

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Section: Methodsmentioning

confidence: 99%

Detection of Local Recurrence with 3-Tesla MRI After Radical Prostatectomy: A Useful Method for Radiation Treatment Planning?

Buergy

Sertdemir²,

Weidner

et al. 2018

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“…After the 15 th volume, 0.05 ml of contrast agent (Dotarem, Guerbet, France) was manually administered in the femoral vein, followed by a 1.0 ml saline flush. Of the acquired data the parametric maps of the Plasma flow, Plasma Volume and Tubular flow were calculated using an in house certified OsiriX plugin (UMMperfusion 1.5.2)1819.…”

Section: Methodsmentioning

confidence: 99%

Color-coded visualization of magnetic resonance imaging multiparametric maps

Kather

Weidner

Attenberger

et al. 2017

Sci Rep

Self Cite

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Multiparametric magnetic resonance imaging (mpMRI) data are emergingly used in the clinic e.g. for the diagnosis of prostate cancer. In contrast to conventional MR imaging data, multiparametric data typically include functional measurements such as diffusion and perfusion imaging sequences. Conventionally, these measurements are visualized with a one-dimensional color scale, allowing only for one-dimensional information to be encoded. Yet, human perception places visual information in a three-dimensional color space. In theory, each dimension of this space can be utilized to encode visual information. We addressed this issue and developed a new method for tri-variate color-coded visualization of mpMRI data sets. We showed the usefulness of our method in a preclinical and in a clinical setting: In imaging data of a rat model of acute kidney injury, the method yielded characteristic visual patterns. In a clinical data set of N = 13 prostate cancer mpMRI data, we assessed diagnostic performance in a blinded study with N = 5 observers. Compared to conventional radiological evaluation, color-coded visualization was comparable in terms of positive and negative predictive values. Thus, we showed that human observers can successfully make use of the novel method. This method can be broadly applied to visualize different types of multivariate MRI data.

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“…The models that quantify dynamic contrast enhanced MRI studies (DCE MRI, acquired using the T1 field and processed with software such as the one presented in [29]) are quite different from those used here, but in principle it would be possible to modify this tool so that both types of analyses can be performed; the proposed class architecture allows it and it may be included in future lines of work with this software, along with the already mentioned implementation of additional fitting models.…”

Section: Discussionmentioning

confidence: 99%

Development and validation of an open source quantification tool for DSC-MRI studies

Gordaliza

Mateos-Pérez

Montesinos

et al. 2015

Computers in Biology and Medicine

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Abstract:Motivation: This work presents the development of an open source tool for the quantification of dynamic susceptibility weighted contrast enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license. Materials and methods: This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared. Results: Perfusion parameters and the corresponding parametric images were obtained. When no gamma fitting is used, an excellent agreement with the tool used as a gold standard was obtained (R 2 40.8 and values are within 95% CI limits in Bland Altman plots).Conclusion: An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license.

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UMMPerfusion: an Open Source Software Tool Towards Quantitative MRI Perfusion Analysis in Clinical Routine

Cited by 62 publications

References 49 publications

Detection of Local Recurrence with 3-Tesla MRI After Radical Prostatectomy: A Useful Method for Radiation Treatment Planning?

Detection of Local Recurrence with 3-Tesla MRI After Radical Prostatectomy: A Useful Method for Radiation Treatment Planning?

Color-coded visualization of magnetic resonance imaging multiparametric maps

Development and validation of an open source quantification tool for DSC-MRI studies

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