PurposeSoftware has a substantial impact on quantitative perfusion MRI values. The lack of genera... more PurposeSoftware has a substantial impact on quantitative perfusion MRI values. The lack of generally accepted implementations, code sharing and transparent testing reduces reproducibility, hindering the use of perfusion MRI in clinical trials. To address these issues, the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) aimed to establish a community‐led, centralized repository for sharing open‐source code for processing contrast‐based perfusion imaging, incorporating an open‐source testing framework.MethodsA repository was established on the OSIPI GitHub website. Python was chosen as the target software language. Calls for code contributions were made to OSIPI members, the ISMRM Perfusion Study Group, and publicly via OSIPI websites. An automated unit‐testing framework was implemented to evaluate the output of code contributions, including visual representation of the results.ResultsThe repository hosts 86 implementations of perfusion processing steps contributed by 12 i...
A lack of validated, open-source code reduces the reliability of perfusion MRI, resulting in dupl... more A lack of validated, open-source code reduces the reliability of perfusion MRI, resulting in duplicate development. To address this problem, the Open Science Initiative for Perfusion Imaging (OSIPI) established a taskforce to collect, validate and harmonise such code. To date, 74 code contributions have been collected, with 14 of these tested. Source code and tests are published in an open-access repository. The OSIPI DCE/DSC-MRI code collection constitutes a valuable resource for researchers, and will ultimately be developed into a standardised, community-driven open-source code library.
Diffusion Weighted MRI (DWI) enables identification of tissue with high cellular density such as ... more Diffusion Weighted MRI (DWI) enables identification of tissue with high cellular density such as tumors. This makes DWI a potentially valuable tool in oncology imaging for both diagnostic imaging and monitoring of treatment. Locally advanced cervical cancer is usually treated with brachytherapy using an intracavitary applicator (Figure 1). MRI guided brachytherapy can be performed by imaging with the applicator in
Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The CHIC Project Workshop (IARWISOCI), 2014
Purpose Recently it has been shown that stratifying patients by certain DCE-MRI parameters can di... more Purpose Recently it has been shown that stratifying patients by certain DCE-MRI parameters can distinguish between patients with better and poorer outcome for advanced cervical cancer. The results from Yuh et al. [1] showed the lowest 10 percentile of the RSI (Relative Signal Increase) to be the best stratifyer. Recent results from Halle et al. [2] have shown the 20-30 percentile of ABrix to be the best stratifyer. A number of these derived model parameters are highly correlated [3] and may thus be redundant. If such a correlation can be determined the computationally fastest and most robust approach could be chosen to enhance clinical use of these functional estimates for improving therapy.
Recent progress in the development of microscopic four point probes permits surface-sensitive con... more Recent progress in the development of microscopic four point probes permits surface-sensitive conductivity measurements on semiconductor surfaces. It is, however, not straightforward to extract the actual values for the surface and space-charge layer conductivity. Here we present an approach to data analysis which is based on numerical finite-element simulations. The results of such simulations are compared to the known analytical
ABSTRACT Our recent paper on the surface conductivity of Si(111)(&surd;3 × &surd;... more ABSTRACT Our recent paper on the surface conductivity of Si(111)(&surd;3 × &surd;3)Ag [1] contains an error in the numerical simulation of the space charge layer conductance presented in figure 2(b) of the paper. A new version of the figure is presented here as figure 1. The incorrect version of this figure suggested that the space charge layer conductivity of Si(111)(&surd;3 × &surd;3)Ag is very similar to that of the clean Si(111)(7 × 7) surface but actually this is not the case. The space charge layer for Si(111)(7 × 7) becomes strongly insulating at low temperatures whereas it is rather conductive over the whole temperature range for Si(111)(&surd;3 × &surd;3)Ag. Figure 1 Figure 1. Experimental results (broken lines and markers) together with simulations (solid lines) of the conductance. The simulation in (b) has now been corrected, but the figure is otherwise the same as figure 2 from [1]. The model calculation shows the expected conductance of the bulk and space charge layer in (a) and (b) and for the expected conductance of a 3 ML Ag film with bulk properties in (c). The error in the calculation of the space charge layer conductivity has an impact on the interpretation of the low temperature measurements. Based on the incorrect calculation, it was concluded that the measurements are always surface sensitive, but this is not the case. In fact, the measured conductance in the low temperature regime is now quite similar to the conductance one could expect for the bulk and space charge layer.The interpretation of the data as a switching due to the surface phase transition is still consistent with results, especially since the transition in conductivity is much steeper than one would expect for a mechanism involving the freezing of carriers in the space charge region. However, we would also like to mention an alternative interpretation at this point. The free-electron like surface state on Si(111)(&surd;3 × &surd;3)Ag is unoccupied at zero temperature because the bottom of the band coincides with the Fermi energy [2]. At finite temperature, thermally excited carriers are present in the surface state band. It is therefore conceivable that the strong change in surface conductivity is caused by the thermal emptying of the surface state band as the temperature is lowered. At low temperature, the surface state band is devoid of carriers and only transport through the bulk and space charge layer can be observed. References [1] Wells J W, Kallehauge J F and Hofmann Ph 2007 J. Phys.: Condens. Matter 19 176008 [2] Crain J N, Gallagher M C, McChesney J L, Bissen M and Himpsel F J 2005 Phys. Rev. B 72 045312
European Journal of Nuclear Medicine and Molecular Imaging, 2012
Tumour hypoxia is linked to treatment resistance. Positron emission tomography (PET) using hypoxi... more Tumour hypoxia is linked to treatment resistance. Positron emission tomography (PET) using hypoxia tracers such as fluoroazomycin arabinoside (FAZA) may allow identification of patients with hypoxic tumours and the monitoring of the efficacy of hypoxia-targeting treatment. Since hypoxia PET is characterized by poor image contrast, and tumour hypoxia undergoes spontaneous changes and is affected by therapy, it remains unclear to what extent PET scans are reproducible. Tumour-bearing mice are valuable in the validation of hypoxia PET, but identification of a reliable reference tissue value (blood sample or image-derived muscle value) for repeated scans may be difficult due to the small size of the animal or absence of anatomical information (pure PET). Here tumour hypoxia was monitored over time using repeated PET scans in individual tumour-bearing mice before and during fractionated radiotherapy. Mice bearing human SiHa cervix tumour xenografts underwent a PET scan 3 h following injection of FAZA on two consecutive days before initiation of treatment (baseline) and again following irradiation with four and ten fractions of 2.5 Gy. On the last scan day, mice were given an intraperitoneal injection of pimonidazole (hypoxia marker), tumours were collected and the intratumoral distribution of FAZA (autoradiography) and hypoxia (pimonidazole immunohistology) were determined in cryosections. Tissue section analysis revealed that the intratumoral distribution of FAZA was strongly correlated with the regional density of hypoxic (pimonidazole-positive) cells, even when necrosis was present, suggesting that FAZA PET provides a reliable measure of tumour hypoxia at the time of the scan. PET-based quantification of tumour tracer uptake relative to injected dose showed excellent reproducibility at baseline, whereas normalization using an image-derived nonhypoxic reference tissue (muscle) proved highly unreliable since a valid and reliable reference value could not be determined. The intratumoral distribution of tracer was stable at baseline as shown by a voxel-by-voxel comparison of the two scans (R = 0.82, range 0.72-0.90). During treatment, overall tracer retention changed in individual mice, but there was no evidence of general reoxygenation. Hypoxia PET scans are quantitatively correct and highly reproducible in tumour-bearing mice. Preclinical hypoxia PET is therefore a valuable and reliable tool for the development of strategies that target or modify hypoxia.
Page 1. Department of Physics and Astronomy University of Aarhus, Denmark Measurements of surface... more Page 1. Department of Physics and Astronomy University of Aarhus, Denmark Measurements of surface conductivity using micro four point probes Jesper F. Kallehauge Supervised by Philip Hofmann March, 2007 MASTER'S THESIS Page 2. Page 3. ...
PurposeSoftware has a substantial impact on quantitative perfusion MRI values. The lack of genera... more PurposeSoftware has a substantial impact on quantitative perfusion MRI values. The lack of generally accepted implementations, code sharing and transparent testing reduces reproducibility, hindering the use of perfusion MRI in clinical trials. To address these issues, the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) aimed to establish a community‐led, centralized repository for sharing open‐source code for processing contrast‐based perfusion imaging, incorporating an open‐source testing framework.MethodsA repository was established on the OSIPI GitHub website. Python was chosen as the target software language. Calls for code contributions were made to OSIPI members, the ISMRM Perfusion Study Group, and publicly via OSIPI websites. An automated unit‐testing framework was implemented to evaluate the output of code contributions, including visual representation of the results.ResultsThe repository hosts 86 implementations of perfusion processing steps contributed by 12 i...
A lack of validated, open-source code reduces the reliability of perfusion MRI, resulting in dupl... more A lack of validated, open-source code reduces the reliability of perfusion MRI, resulting in duplicate development. To address this problem, the Open Science Initiative for Perfusion Imaging (OSIPI) established a taskforce to collect, validate and harmonise such code. To date, 74 code contributions have been collected, with 14 of these tested. Source code and tests are published in an open-access repository. The OSIPI DCE/DSC-MRI code collection constitutes a valuable resource for researchers, and will ultimately be developed into a standardised, community-driven open-source code library.
Diffusion Weighted MRI (DWI) enables identification of tissue with high cellular density such as ... more Diffusion Weighted MRI (DWI) enables identification of tissue with high cellular density such as tumors. This makes DWI a potentially valuable tool in oncology imaging for both diagnostic imaging and monitoring of treatment. Locally advanced cervical cancer is usually treated with brachytherapy using an intracavitary applicator (Figure 1). MRI guided brachytherapy can be performed by imaging with the applicator in
Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The CHIC Project Workshop (IARWISOCI), 2014
Purpose Recently it has been shown that stratifying patients by certain DCE-MRI parameters can di... more Purpose Recently it has been shown that stratifying patients by certain DCE-MRI parameters can distinguish between patients with better and poorer outcome for advanced cervical cancer. The results from Yuh et al. [1] showed the lowest 10 percentile of the RSI (Relative Signal Increase) to be the best stratifyer. Recent results from Halle et al. [2] have shown the 20-30 percentile of ABrix to be the best stratifyer. A number of these derived model parameters are highly correlated [3] and may thus be redundant. If such a correlation can be determined the computationally fastest and most robust approach could be chosen to enhance clinical use of these functional estimates for improving therapy.
Recent progress in the development of microscopic four point probes permits surface-sensitive con... more Recent progress in the development of microscopic four point probes permits surface-sensitive conductivity measurements on semiconductor surfaces. It is, however, not straightforward to extract the actual values for the surface and space-charge layer conductivity. Here we present an approach to data analysis which is based on numerical finite-element simulations. The results of such simulations are compared to the known analytical
ABSTRACT Our recent paper on the surface conductivity of Si(111)(&surd;3 × &surd;... more ABSTRACT Our recent paper on the surface conductivity of Si(111)(&surd;3 × &surd;3)Ag [1] contains an error in the numerical simulation of the space charge layer conductance presented in figure 2(b) of the paper. A new version of the figure is presented here as figure 1. The incorrect version of this figure suggested that the space charge layer conductivity of Si(111)(&surd;3 × &surd;3)Ag is very similar to that of the clean Si(111)(7 × 7) surface but actually this is not the case. The space charge layer for Si(111)(7 × 7) becomes strongly insulating at low temperatures whereas it is rather conductive over the whole temperature range for Si(111)(&surd;3 × &surd;3)Ag. Figure 1 Figure 1. Experimental results (broken lines and markers) together with simulations (solid lines) of the conductance. The simulation in (b) has now been corrected, but the figure is otherwise the same as figure 2 from [1]. The model calculation shows the expected conductance of the bulk and space charge layer in (a) and (b) and for the expected conductance of a 3 ML Ag film with bulk properties in (c). The error in the calculation of the space charge layer conductivity has an impact on the interpretation of the low temperature measurements. Based on the incorrect calculation, it was concluded that the measurements are always surface sensitive, but this is not the case. In fact, the measured conductance in the low temperature regime is now quite similar to the conductance one could expect for the bulk and space charge layer.The interpretation of the data as a switching due to the surface phase transition is still consistent with results, especially since the transition in conductivity is much steeper than one would expect for a mechanism involving the freezing of carriers in the space charge region. However, we would also like to mention an alternative interpretation at this point. The free-electron like surface state on Si(111)(&surd;3 × &surd;3)Ag is unoccupied at zero temperature because the bottom of the band coincides with the Fermi energy [2]. At finite temperature, thermally excited carriers are present in the surface state band. It is therefore conceivable that the strong change in surface conductivity is caused by the thermal emptying of the surface state band as the temperature is lowered. At low temperature, the surface state band is devoid of carriers and only transport through the bulk and space charge layer can be observed. References [1] Wells J W, Kallehauge J F and Hofmann Ph 2007 J. Phys.: Condens. Matter 19 176008 [2] Crain J N, Gallagher M C, McChesney J L, Bissen M and Himpsel F J 2005 Phys. Rev. B 72 045312
European Journal of Nuclear Medicine and Molecular Imaging, 2012
Tumour hypoxia is linked to treatment resistance. Positron emission tomography (PET) using hypoxi... more Tumour hypoxia is linked to treatment resistance. Positron emission tomography (PET) using hypoxia tracers such as fluoroazomycin arabinoside (FAZA) may allow identification of patients with hypoxic tumours and the monitoring of the efficacy of hypoxia-targeting treatment. Since hypoxia PET is characterized by poor image contrast, and tumour hypoxia undergoes spontaneous changes and is affected by therapy, it remains unclear to what extent PET scans are reproducible. Tumour-bearing mice are valuable in the validation of hypoxia PET, but identification of a reliable reference tissue value (blood sample or image-derived muscle value) for repeated scans may be difficult due to the small size of the animal or absence of anatomical information (pure PET). Here tumour hypoxia was monitored over time using repeated PET scans in individual tumour-bearing mice before and during fractionated radiotherapy. Mice bearing human SiHa cervix tumour xenografts underwent a PET scan 3 h following injection of FAZA on two consecutive days before initiation of treatment (baseline) and again following irradiation with four and ten fractions of 2.5 Gy. On the last scan day, mice were given an intraperitoneal injection of pimonidazole (hypoxia marker), tumours were collected and the intratumoral distribution of FAZA (autoradiography) and hypoxia (pimonidazole immunohistology) were determined in cryosections. Tissue section analysis revealed that the intratumoral distribution of FAZA was strongly correlated with the regional density of hypoxic (pimonidazole-positive) cells, even when necrosis was present, suggesting that FAZA PET provides a reliable measure of tumour hypoxia at the time of the scan. PET-based quantification of tumour tracer uptake relative to injected dose showed excellent reproducibility at baseline, whereas normalization using an image-derived nonhypoxic reference tissue (muscle) proved highly unreliable since a valid and reliable reference value could not be determined. The intratumoral distribution of tracer was stable at baseline as shown by a voxel-by-voxel comparison of the two scans (R = 0.82, range 0.72-0.90). During treatment, overall tracer retention changed in individual mice, but there was no evidence of general reoxygenation. Hypoxia PET scans are quantitatively correct and highly reproducible in tumour-bearing mice. Preclinical hypoxia PET is therefore a valuable and reliable tool for the development of strategies that target or modify hypoxia.
Page 1. Department of Physics and Astronomy University of Aarhus, Denmark Measurements of surface... more Page 1. Department of Physics and Astronomy University of Aarhus, Denmark Measurements of surface conductivity using micro four point probes Jesper F. Kallehauge Supervised by Philip Hofmann March, 2007 MASTER'S THESIS Page 2. Page 3. ...
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