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

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 (R²>0.8 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.This work was partially supported by the Human Frontier Science Program (Research Grant 2013).Publicad

A Bayesian model for brain tumor classification using clinical-based features

Proceedings of: IEEE International Conference on Image Processing (ICIP 2014). Paris, October 27-30, 2014.This paper tackles the problem of automatic brain tumor classification from Magnetic Resonance Imaging (MRI) where, traditionally, general-purpose texture and shape features extracted from the Region of Interest (tumor) have become the usual parameterization of the problem. Two main contributions are made in this context. First, a novel set of clinical-based features that intend to model intuitions and expert knowledge of physicians is suggested. Second, a system is proposed that is able to fuse multiple individual scores (based on a particular MRI sequence and a pathological indicator present in that sequence) by using a Bayesian model that produces a global system decision. This approximation provides a quite flexible solution able to handle missing data, which becomes a very likely case in a realistic scenario where the number clinical tests varies from one patient to another. Furthermore, the Bayesian model provides extra information concerning the uncertainty of the final decision. Our experimental results prove that the use of clinical-based feature leads to a significant increment of performance in terms of Area Under the Curve (AUC) when compared to a state-of-the art reference. Furthermore, the proposed Bayesian fusion model clearly outperforms other fusion schemes, especially when few diagnostic tests are available.Publicad

Experiencia preliminar en el tratamiento combinado de metástasis vertebrales mediante radiofrecuencia y cifoplastia en sesión única

Objectives: Describe our preliminary experience in the treatment of vertebral metastases by radiofrequency and Kyphoplasty combined in one single session. Material and methods: Four patients with histologically confirmed single spinal metastasis (breast, prostate, lung and myeloma in L1, L5, D12, D12, respectively) were treated. The indication in all cases was pain with a poor response to medical treatment. All patients had pain in the range 6-7 visual analogue scale (VAS). In two cases there was a lytic lesion of the spinal posterior wall. After obtaining informed consent, and under sedation and local anesthetic the procedure took place. The transpedicular approach took place with a 11 G bone puncture system. Two radiofrequency needles were coaxially inserted to carry out an ablation cycle through each pedicle. During the ablation cycle the tip of the ablation neddle stood between the anterior and middle third of the vertebral body, while the second needle was used as thermal sensor with its end to the height of the vertebral posterior wall. The duration of each cycle of ablation was 8 minutes reaching intratumoral temperatures of 70-80 ºC. Transpedicular Kyphoplasty was performed subsequently. Results: No complications were reported during or after the procedure and patients were discharged in the first 24 hours. There was an immediate improvement in pain after the procedure (with a VAS 1-2 intensity pain) in all patients. During follow up, analgesic medication was withdrawn in three patients, and there was no evidence of disease progression or recurrence of pain (pain intensity 1 (VAS) in a follow-up in the range of 8-14 months). Clinical and radiological follow-up after discharge could not be performed on a patient. Conclusion: The use of radio-frequency associated with Kyphoplasty in vertebral metastatic disease can contribute to the management of refractory pain to medical treatment.Objetivos: Describir nuestra experiencia preliminar en el tratamiento de metástasis vertebrales mediante radiofrecuencia y cifoplastia combinadas en sesión única. Material y métodos: Se trataron cuatro pacientes con metástasis vertebral única confirmada histológicamente (mama, próstata, pulmón y mieloma en D12, L1, L5 y D12, respectivamente). La indicación en todos los casos fue el dolor con una mala respuesta al tratamiento médico habitual. Todos los pacientes presentaban dolor en el rango 6-7 de la escala visual analógica (EVA). En dos casos existía lesión lítica del muro posterior. Tras la obtención del consentimiento informado se realizó el procedimiento bajo sedación e infiltración anestésica local. Se efectuó abordaje transpedicular bilateral con sistemas de punción ósea 11G. Se insertaron de forma coaxial dos agujas de radiofrecuencia para efectuar un ciclo de ablación por cada pedículo. Durante el ciclo de ablación la punta del dispositivo correspondiente se situó en la unión del tercio medio con el tercio anterior del cuerpo vertebral, empleando la segunda aguja como sensor térmico, con su extremo a la altura del muro posterior. La duración de cada ciclo de ablación fue de 8 minutos, alcanzando temperaturas intratumorales de 70-80 ºC. A continuación se realizó cifoplastia transpedicular. Resultados: No se registraron complicaciones intra-periprocedimiento, con alta domiciliaria en las 24 horas siguientes. En todos los pacientes hubo una mejoría inmediata del dolor tras el procedimiento (con dolor de intensidad 1-2 de la EVA). En tres pacientes se retiró progresivamente la medicación analgésica, sin evidencia en ninguno de ellos de progresión local de la enfermedad ni recurrencia-aumento del dolor en el seguimiento (dolor de intensidad 1 de la EVA en un seguimiento en el rango de 8-14 meses). En un paciente no se pudo efectuar seguimiento clínico-radiológico posterior al alta. Conclusión: El empleo de radiofrecuencia asociada a cifoplastia en la enfermedad metastásica vertebral puede contribuir al manejo del dolor refractario al tratamiento médico y al control local de la enfermedad

Is the cerebellum the optimal reference region for intensity normalization of perfusion MR studies in early Alzheimer's disease?

The cerebellum is the region most commonly used as a reference when normalizing the intensity of perfusion images acquired using magnetic resonance imaging (MRI) in Alzheimer's disease (AD) studies. In addition, the cerebellum provides unbiased estimations with nuclear medicine techniques. However, no reports confirm the cerebellum as an optimal reference region in MRI studies or evaluate the consequences of using different normalization regions. In this study, we address the effect of using the cerebellum, whole-brain white matter, and whole-brain cortical gray matter in the normalization of cerebral blood flow (CBF) parametric maps by comparing patients with stable mild cognitive impairment (MCI), patients with AD and healthy controls. According to our results, normalization by whole-brain cortical gray matter enables more sensitive detection of perfusion abnormalities in AD patients and reveals a larger number of affected regions than data normalized by the cerebellum or whole-brain white matter. Therefore, the cerebellum is not the most valid reference region in MRI studies for early stages of AD. After normalization by whole-brain cortical gray matter, we found a significant decrease in CBF in both parietal lobes and an increase in CBF in the right medial temporal lobe. We found no differences in perfusion between patients with stable MCI and healthy controls either before or after normalization

Mean volume (cm³) and standard deviation (SD) of the three reference regions for normalization.

<p>Mean volume (cm³) and standard deviation (SD) of the three reference regions for normalization.</p

Mean CBF values and intra-group variability in intensity for the three reference regions.

<p>CV, coefficient of variation (%); SD, standard deviation; CBFcgm, cerebral blood flow of whole-brain cortical gray matter; CBFcer, cerebral blood flow of cerebellum; CBFwm, cerebral blood flow of whole-brain white matter; <i>F</i>, ANOVA <i>F</i> value; <i>p</i>, ANOVA <i>p</i> value; NS, not significant.</p

Reduced variability in intensity values after normalization by the three reference regions (coefficients of variation, %).

<p>CBF, cerebral blood flow; CBF/CBFcgm, CBF values per region of interest normalized by whole-brain cortical gray matter; CBF/CBFcer, CBF values per region of interest normalized by cerebellum; CBF/CBFwm, CBF values per region of interest normalized by whole-brain white matter. Coefficients of variation show bilateral information per lobe in the three groups (controls, MCI and AD).</p

Dunnett’s test <i>p</i> values for differences between patients and controls in gray matter volume for the medial temporal lobes.

<p>(−) non-significant differences.</p

Demographic and clinical data.

<p>ANOVA of group differences (<i>p</i><0.0001). Significant differences were found between the Alzheimer group and the controls, and between the Alzheimer group and the MCI group. MMSE, Mini Mental State Examination; SD, standard deviation.</p

Example of CBF parametric map.

<p>Example of CBF parametric map.</p