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R T Clarke - One of the best experts on this subject based on the ideXlab platform.
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estimating confidence of european wfd ecological status class and wiser bioassessment uncertainty Guidance Software wiserbugs
Hydrobiologia, 2013Co-Authors: R T ClarkeAbstract:The Water Framework Directive (WFD) requires estimates of the confidence and precision associated with any scheme for assessing and monitoring the ecological status class of any European rivers, lakes, transitional or coastal waters. This is a complex important issue, especially for waterbody assessments based on multiple metrics and/or two or more taxonomic groups. This paper aims to contribute towards improving understanding and providing practical approaches to assessing confidence of class by (i) discussing the various sources and causes of uncertainty, (ii) using UK rivers macroinvertebrate datasets to illustrate the estimation of replicate, temporal and spatial variance components and the implications for water body metric precision, confidence of class and optimal sampling design, (iii) introducing new freely available general Software WISER Bioassessment Uncertainty Guidance Software (WISERBUGS) which uses prior sampling uncertainty estimates with user-specified metrics, class limits and metric combination rules to simulate the joint sampling uncertainty in metric EQR values and provide estimates of confidence of class based on individual metrics, (optionally weighted) multi-metric indices and/or multi-metric classification rules (worst case, mean or median class) based on one or more WFD biological quality elements.
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WISER Deliverable D6.1-3: WISERBUGS (WISER Bioassessment Uncertainty Guidance Software) tool for assessing confidence of WFD ecological status classUser Manual and Software: Release 1.1 (Sept 2010)
2010Co-Authors: R T ClarkeAbstract:The aim of the Software program WISERBUGS is to assist in quantifying uncertainty in the assessment of the ecological status of lakes, rivers, transitional (estuarine) and coastal waters. WISERBUGS (WISER Bioassessment Uncertainty Guidance Software) is a product of the WISER (Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery) research project (Grant 226273 - WISER) supported by the European Commission under the Seventh Framework Programme (http://www.wiser.eu/). The WISER project aim was to assist in developing methods for calibrating different biological survey results for lakes, transitional and coastal waters against ecological quality classifications to be developed for the Water Framework Directive (WFD). The WFD requires Member States to assess, monitor, and where inadequate, improve the ecological status of water bodies (rivers, lakes, transitional and coastal waters). All such water bodies are to be classified to one of five ecological status classes (high, good, moderate, poor and bad) with the aim of eventually achieving or maintaining good or better status for all water bodies. The ecological status (i.e. condition) of a water body is often measured using one or more metrics derived from the taxonomic composition and/or abundance obtained from field samples/surveys and/or habitat surveys. The term metric here usually refers to any biological index or other single-valued measure which is designed to measure some aspect of the biological community and its taxonomic composition at a site or water body. The Articles of the Water Framework Directive (Annex V, section 1.3) require that “Estimates of the level of confidence and precision of the results provided by the monitoring programmes shall be given in the (monitoring) Plan”. Thus, water body monitoring and management organisations need to have some understanding and estimates of the confidence to which an individual water body can be assigned to an ecological status class. In addition the WFD requires that the Ecological Status of surface waters of Member States are maintained or improved. However, because of the uncertainties associated with biological monitoring, waterbodies may appear to change Ecological Status over time when, in reality, this is only an artefact due to the uncertainty resulting from the whole bioassessment process and sampling procedures. A core part of the WISER project was to collect standardised field sample and survey information on phytoplankton, aquatic macrophytes, macroinvertebrates, fish and aquatic habitats at each of a wide range of lake, transitional and coastal water body sites across Europe. One important reason for this was to improve understanding and provide estimates of the sampling uncertainty (replicate, sub-sample, spatial and temporal) associated with specific sampling/surveying methods, individual metrics and multi-metric classification rules. The WISERBUGS Software program has been written to provide a general means of using simulations to assess uncertainty in estimates of ecological status class for water bodies based on either single metrics or a combination of metrics, multi-metric indices (MMIs) and multi-metric rules. The User provides prior estimates of the relevant sampling uncertainty for each metric and metric value to be involved in the water body assessments, together with metric status class limits and the rules for combining metrics into an overall water body assessment. WISERBUGS can also be used just to test the effect of new status class limits and multi-metric rules on site/waterbody status assessments, without any uncertainty assessment (by setting all uncertainty components to zero). Although initially designed for use with river macroinvertebrate data and metrics, program WISERBUGS is designed to be as generic as possible, so that it can be used with a wide range of metrics derived from field site sampling and survey data for any single or combination of biological quality elements (BQEs, namely phytoplankton, aquatic flora, macroinvertebrates and/or fish) and any type of water body (rivers, lakes, transitional or coastal waters). The program requires the User to provide a ‘Metric Specification File’ in EXCEL format, in which they specify which metrics are to be used to determine the site or waterbody bioassessments, the individual metric uncertainty estimates and the multi-metric rules for combining information from individual metrics. The uncertainty in the estimate of the (usually) mean value of a metric for a water body depends on the level of sampling replication on which it was based in terms of replicate sampling, spatial and temporal sampling coverage over the area of the water body to be assessed and the period of time for which the water body assessment is to apply. The estimates of uncertainty in individual metric values can include the sampling standard deviation (SD) due to sampling/sub-sampling variation and (optionally) the SD and bias due to sample sorting and identification. In practice the uncertainty SD estimates for each metric for each water body or site to be assessed within WISERBUGS must be based on best-available information from replicated sampling studies on this or environmentally-similar water bodies. The ecological status class assessment for individual metrics can be based on just the observed (O) values of metrics or on normalised Ecological Quality Ratios (EQRs) involving the ratio of the observed metric values to the Reference Condition values (E1) of the metric.The EQR could be a RIVPACS-type O/E ratio where E1 is set a RIVPACS model-based site-specific expected value and E0 is set to zero When several EQRs are used to create a Multi-Metric Index (MMI) by averaging their values, each EQR is forced into the range 0-1 by setting any EQR values greater than 1 to 1. If EQRs are used, then the User can provide an estimate of the error SD for the Reference Condition values (E1) of each metric for the group of sites or water bodies to be assessed. The same User-specified ‘Metric Specification File’ must also give the ecological status class (‘High’ to ‘Poor’) limits for each metric or EQR. Program WISERBUGS allows the User to specify a wide range of rules for combining individual metrics into multi-metric indices (MMI) or for combining individual metric classes into a metric group class and thus in deriving an overall site/waterbody assessment. For example, it can cope with combining status classes for macro-invertebrate metrics designed to measure one type of stress (e.g. eutrophication, diversity or acidification) and then combine (using the same or a different rule) the classes from these individual stress types into an overall class for macro-invertebrates, and then combine (using the same or a different rule) the overall class for macroinvertebrates with that for one or more other biological quality elements (macrophytes, diatoms or fish). For each set of sites/waterbodies to be assessed, the program reads the observed values of each metric to be used from a User-specified ‘Observed metric values’ EXCEL file. The observed values of the metrics must have been calculated previously, outside of program WISERBUGS. The layout of this input file was designed to provide immediate compatibility with the metric values EXCEL files derived and output from the freshwater macroinvertebrate sample Software known as ‘AQEMrap’ or ‘ASTERICS’ (obtainable from the EU Fifth Framework Programme river classification project STAR Web site at www.eu-star.at). The AQEMrap Software could be used to calculate and export observed metric values for freshwater macroinvertebrate samples for input to the WISERBUGS program. The content and format of the User-specified EXCEL input files are explained in detail in Section 4. WISERBUGS uses the uncertainty estimates for each metric to simulate a large number of other possible observed metric or EQR values which could have been obtained for the site/waterbody. If the sampling SD is considered to be constant on a specified transformed scale, then, in each simulation the observed value (x) is first transformed, then a random sampling error (z) added and the result back-transformed to obtain a simulated observed value. Each simulation leads to a status class based on each individual metric and then groups of metrics in the specified multi-metric rules for site/waterbody bioassessment. From the statistical distribution of simulated values and classes, estimates of the probability of belonging to each status class are obtained. The content and format of the EXCEL output file give the ecological status assessment and the associated uncertainty for each site/waterbody is explained in Section 5 WISERBUGS Software and User Manaual was written and produced by Ralph Clarke of Bournemouth University (BourneU) in the UK.
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Estimates and comparisons of the effects of sampling variation using 'national' macroinvertebrate sampling protocols on the precision of metrics used to assess ecological status
Hydrobiologia, 2006Co-Authors: R T Clarke, John Davy-bowker, Leonard Sandin, Nikolai Friberg, Richard K. Johnson, B. BisAbstract:The Water Framework Directive (WFD) of the European Union requires all member countries to provide information on the level of confidence and precision of results in their river monitoring programmes to assess the ecological status class of river sites. As part of the European Union project STAR, the overall effects of sampling variation for a wide range of commonly used metrics and sampling methods were assessed. Replicate samples were taken in each of two seasons at 2-6 sites of varying ecological status class within each of 18 stream types spread over 12 countries, using both the STAR-AQEM method and a national sampling method or, where unavailable, the RIVPACS sampling protocol. The sampling precision of a combination of sampling method and metric was estimated by expressing the replicate sampling variance as a percentage P samp of the total variance in metric values with a stream type; low values of Psamp indicate high precision. Most metrics had percentage sampling variances less than 20% for all or most stream types and methods. Most national methods including RIVPACS had sampling precisions at least as good as those for the STAR-AQEM method as used in their country at the same sites; the main exceptions were the national methods used in Latvia and Sweden. The national methods used in the Czech Republic, Denmark, France, Poland and the RIVPACS method used in the UK and Austria all had percentage sampling variances of less than 10% for the majority of metrics assessed. In contrast, none of the metrics had percentage sampling variances less than 10% when based on either the Italian (IBE) method, which used bank-side sorting, or the Latvian national method which identifies only a limited set of taxa. P samp was lowest on average for the two stream types sampled in the Czech Republic using either the PERLA national method or the STAR-AQEM method. Averaged over all stream types and methods, the three Saprobicbased metrics had the lowest average percentage sampling variances (3–6%) amongst the 26 metrics assessed. These estimates of sampling standard deviation can be used to help assess the uncertainty in single or multi-metric systems for estimating site ecological status using the general STAR Bioassessment Guidance Software (STARBUGS) developed within the STAR project.
Andrea Alimonti - One of the best experts on this subject based on the ideXlab platform.
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Safety profile of 185 ultrasound-guided intra-articular injections for treatment of rheumatic diseases of the hip
Reumatismo, 2011Co-Authors: A. Migliore, S. Tormenta, C. Valente, U. Massafra, A. Latini, L.s. Martin Martin, Andrea AlimontiAbstract:Objective: We have developed a standardized technique for intra-articular injection of the hip joint with the purpose of extending routine intra-articular injection of hyaluronans and steroids to the hip, as commonly used in the knee. The purpose of this study was to examine the safety of this technique in an extended series of patients. Methods: A 7 MHz linear or 3.5 MHz convex transducer was used with a sterilized biopsy guide attached. Intra-articular (IA) injection was performed by inserting into the biopsy guide a 20 gauge needle with the anterosuperior approach. Then, using biopsy real-time Guidance Software, the needle was advanced into the anterior capsular recess, at the level of the femoral head. Results: The standardised technique was used to inject 97 patients (114 hips) with 185 injections of either steroid/local anaesthetic (10) or hyaluronan (175) over a three-year period. The treatment was well tolerated with few, and exclusively local, side effects. No systemic side effects or joint infections were observed in our study. The colour Doppler vision allowed us to avoid injecting blood vessels. In all cases direct visualization of needle introduction and progression into the articular space was shown by on-screen Guidance. Ultrasound Guidance is more economic and faster in comparison to the TC or fluoroscopic Guidance. Contrary to TC or fluoroscopic techniques ultrasound does not require use of radiations or iodized contrast. Conclusion: Our data suggest that the administration of hyaluronans or steroids with ultrasound-guided intra-articular injection is a safe technique for treatment of rheumatic diseases of the hip.
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Profilo di sicurezza di 185 iniezioni intra-articolari sotto guida ecografica nelle coxopatie Safety profile of 185 ultrasound-guided intra-articular injections for treatment of rheumatic diseases of the hip
2004Co-Authors: A. Migliore, S. Tormenta, C. Valente, U. Massafra, A. Latini, Andrea Alimonti, Lavoro OriginaleAbstract:SUMMARY Objective: We have developed a standardized technique for intra-articular injection of the hip joint with the purpose of extending routine intra-articular injection of hyaluronans and steroids to the hip, as commonly used in the knee. The purpose of this study was to examine the safety of this technique in an extended series of patients. Methods: A 7 MHz linear or 3.5 MHz convex transducer was used with a sterilized biopsy guide attached. Intra-articular (IA) injection was performed by inserting into the biopsy guide a 20 gauge needle with the anterosuperior approach. Then, using biopsy real-time Guidance Software, the needle was advanced into the anterior capsular recess, at the level of the femoral head. Results: The standardised technique was used to inject 97 patients (114 hips) with 185 injections of either steroid/local anaesthetic (10) or hyaluronan (175) over a three-year period. The treatment was well tolerated with few, and exclusively local, side effects. No systemic side effects or joint infections were observed in our study. The colour Doppler vision allowed us to avoid injecting blood vessels. In all cases direct visualization of needle introduction and progression into the articular space was shown by on-screen Guidance. Ultrasound Guidance is more economic and faster in comparison to the TC or fluoroscopic Guidance. Contrary to TC or fluoroscopic techniques ultrasound does not require use of radiations or iodized contrast. Conclusion: Our data suggest that the administration of hyaluronans or steroids with ultrasound-guided intra-articular injection is a safe technique for treatment of rheumatic diseases of the hip.
Gabor Fichtinger - One of the best experts on this subject based on the ideXlab platform.
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Software for mr image overlay guided needle insertions the clinical translation process
Proceedings of SPIE, 2013Co-Authors: Tamas Ungi, Paweena Uthainual, Aaron Flammang, Jan Fritz, John A. Carrino, Iulian Iordachita, Gabor FichtingerAbstract:PURPOSE: Needle Guidance Software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile Software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and Software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable Software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that Software requirements were successfully solved after a limited number of operating room tests.
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Medical Imaging: Image-Guided Procedures - Software for MR image overlay guided needle insertions: the clinical translation process
Proceedings of SPIE, 2013Co-Authors: Tamas Ungi, Aaron Flammang, Jan Fritz, John A. Carrino, Iulian Iordachita, Paweena U-thainual, Gabor FichtingerAbstract:PURPOSE: Needle Guidance Software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile Software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and Software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable Software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that Software requirements were successfully solved after a limited number of operating room tests.
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Perk Station—Percutaneous surgery training and performance measurement platform
Computerized Medical Imaging and Graphics, 2009Co-Authors: Siddharth Vikal, John A. Carrino, Iulian Iordachita, Paweena U-thainual, Gregory S. Fischer, Gabor FichtingerAbstract:Abstract Motivation Image-guided percutaneous (through the skin) needle-based surgery has become part of routine clinical practice in performing procedures such as biopsies, injections and therapeutic implants. A novice physician typically performs needle interventions under the supervision of a senior physician; a slow and inherently subjective training process that lacks objective, quantitative assessment of the surgical skill and performance. Shortening the learning curve and increasing procedural consistency are important factors in assuring high-quality medical care. Methods This paper describes a laboratory validation system, called Perk Station, for standardized training and performance measurement under different assistance techniques for needle-based surgical Guidance systems. The initial goal of the Perk Station is to assess and compare different techniques: 2D image overlay, biplane laser guide, laser protractor and conventional freehand. The main focus of this manuscript is the planning and Guidance Software system developed on the 3D Slicer platform, a free, open source Software package designed for visualization and analysis of medical image data. Results The prototype Perk Station has been successfully developed, the associated needle insertion phantoms were built, and the graphical user interface was fully implemented. The system was inaugurated in undergraduate teaching and a wide array of outreach activities. Initial results, experiences, ongoing activities and future plans are reported.
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ROBIO - The Perk Station: Systems design for percutaneous intervention training suite
2008 IEEE International Conference on Robotics and Biomimetics, 2009Co-Authors: Paweena U-thainual, Iulian Iordachita, Siddharth Vikal, Gregory S. Fischer, Gabor FichtingerAbstract:Image-guided percutaneous needle-based surgery has become part of routine clinical practice in performing procedures such as biopsies, injections and therapeutic implants. A novice physician typically performs needle interventions under the supervision of a senior physician; a slow and inherently subjective training process that lacks objective, quantitative assessment of the surgical skill and performance. Current evaluations of needle-based surgery are also rather simplistic: usually only needle tip accuracy and procedure time are recorded, the latter being used as an indicator of economical feasibility. Shortening the learning curve and increasing procedural consistency are critically important factors in assuring high-quality medical care for all segments of society. This paper describes the design and development of a laboratory validation system for measuring operator performance under different assistance techniques for needle-based surgical Guidance systems - The Perk Station. The initial focus of the Perk Station is to assess and compare three different techniques: the image overlay, bi-plane laser guide, and conventional freehand. The integrated system comprises of a flat display with semi-transparent mirror (image overlay), bi-plane laser guide, a magnetic tracking system, a tracked needle, a phantom, and a stand-alone laptop computer running the planning and Guidance Software. The prototype Perk Station has been successfully developed, the associated needle insertion phantoms have been built, and the graphic surgical interface has been implemented.
A. Migliore - One of the best experts on this subject based on the ideXlab platform.
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Safety profile of 185 ultrasound-guided intra-articular injections for treatment of rheumatic diseases of the hip
Reumatismo, 2011Co-Authors: A. Migliore, S. Tormenta, C. Valente, U. Massafra, A. Latini, L.s. Martin Martin, Andrea AlimontiAbstract:Objective: We have developed a standardized technique for intra-articular injection of the hip joint with the purpose of extending routine intra-articular injection of hyaluronans and steroids to the hip, as commonly used in the knee. The purpose of this study was to examine the safety of this technique in an extended series of patients. Methods: A 7 MHz linear or 3.5 MHz convex transducer was used with a sterilized biopsy guide attached. Intra-articular (IA) injection was performed by inserting into the biopsy guide a 20 gauge needle with the anterosuperior approach. Then, using biopsy real-time Guidance Software, the needle was advanced into the anterior capsular recess, at the level of the femoral head. Results: The standardised technique was used to inject 97 patients (114 hips) with 185 injections of either steroid/local anaesthetic (10) or hyaluronan (175) over a three-year period. The treatment was well tolerated with few, and exclusively local, side effects. No systemic side effects or joint infections were observed in our study. The colour Doppler vision allowed us to avoid injecting blood vessels. In all cases direct visualization of needle introduction and progression into the articular space was shown by on-screen Guidance. Ultrasound Guidance is more economic and faster in comparison to the TC or fluoroscopic Guidance. Contrary to TC or fluoroscopic techniques ultrasound does not require use of radiations or iodized contrast. Conclusion: Our data suggest that the administration of hyaluronans or steroids with ultrasound-guided intra-articular injection is a safe technique for treatment of rheumatic diseases of the hip.
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Profilo di sicurezza di 185 iniezioni intra-articolari sotto guida ecografica nelle coxopatie Safety profile of 185 ultrasound-guided intra-articular injections for treatment of rheumatic diseases of the hip
2004Co-Authors: A. Migliore, S. Tormenta, C. Valente, U. Massafra, A. Latini, Andrea Alimonti, Lavoro OriginaleAbstract:SUMMARY Objective: We have developed a standardized technique for intra-articular injection of the hip joint with the purpose of extending routine intra-articular injection of hyaluronans and steroids to the hip, as commonly used in the knee. The purpose of this study was to examine the safety of this technique in an extended series of patients. Methods: A 7 MHz linear or 3.5 MHz convex transducer was used with a sterilized biopsy guide attached. Intra-articular (IA) injection was performed by inserting into the biopsy guide a 20 gauge needle with the anterosuperior approach. Then, using biopsy real-time Guidance Software, the needle was advanced into the anterior capsular recess, at the level of the femoral head. Results: The standardised technique was used to inject 97 patients (114 hips) with 185 injections of either steroid/local anaesthetic (10) or hyaluronan (175) over a three-year period. The treatment was well tolerated with few, and exclusively local, side effects. No systemic side effects or joint infections were observed in our study. The colour Doppler vision allowed us to avoid injecting blood vessels. In all cases direct visualization of needle introduction and progression into the articular space was shown by on-screen Guidance. Ultrasound Guidance is more economic and faster in comparison to the TC or fluoroscopic Guidance. Contrary to TC or fluoroscopic techniques ultrasound does not require use of radiations or iodized contrast. Conclusion: Our data suggest that the administration of hyaluronans or steroids with ultrasound-guided intra-articular injection is a safe technique for treatment of rheumatic diseases of the hip.
Lavoro Originale - One of the best experts on this subject based on the ideXlab platform.
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Profilo di sicurezza di 185 iniezioni intra-articolari sotto guida ecografica nelle coxopatie Safety profile of 185 ultrasound-guided intra-articular injections for treatment of rheumatic diseases of the hip
2004Co-Authors: A. Migliore, S. Tormenta, C. Valente, U. Massafra, A. Latini, Andrea Alimonti, Lavoro OriginaleAbstract:SUMMARY Objective: We have developed a standardized technique for intra-articular injection of the hip joint with the purpose of extending routine intra-articular injection of hyaluronans and steroids to the hip, as commonly used in the knee. The purpose of this study was to examine the safety of this technique in an extended series of patients. Methods: A 7 MHz linear or 3.5 MHz convex transducer was used with a sterilized biopsy guide attached. Intra-articular (IA) injection was performed by inserting into the biopsy guide a 20 gauge needle with the anterosuperior approach. Then, using biopsy real-time Guidance Software, the needle was advanced into the anterior capsular recess, at the level of the femoral head. Results: The standardised technique was used to inject 97 patients (114 hips) with 185 injections of either steroid/local anaesthetic (10) or hyaluronan (175) over a three-year period. The treatment was well tolerated with few, and exclusively local, side effects. No systemic side effects or joint infections were observed in our study. The colour Doppler vision allowed us to avoid injecting blood vessels. In all cases direct visualization of needle introduction and progression into the articular space was shown by on-screen Guidance. Ultrasound Guidance is more economic and faster in comparison to the TC or fluoroscopic Guidance. Contrary to TC or fluoroscopic techniques ultrasound does not require use of radiations or iodized contrast. Conclusion: Our data suggest that the administration of hyaluronans or steroids with ultrasound-guided intra-articular injection is a safe technique for treatment of rheumatic diseases of the hip.