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1.  Integrating digital teaching-file systems with off-the-shelf presentation software to facilitate speaker-led conferences 
Journal of Digital Imaging  2001;14(Suppl 1):98-101.
Objective: Develop methods for automated transfer of images and associated text from a teaching-file repository into presentation material for speaker-led conferences.erials/Methods:Our institution uses a Microsoft Windows (Microsoft Corp, Redmond, WA) software application to maintain a digital teaching-file database that can store and retrieve content in a case-centric fashion. Virtually any number of images can be stored with any given case. Cases and their associated images can be retrieved via a module that supports searches by American College of Radiology (ACR) code and by free-text Boolean queries on the history, findings, diagnosis, and discussion components of a case. In addition to the software system serving directly as an interactive teaching tool, the digital teaching file itself serves as an image repository and resource for attending radiologists who create their own presentations and lectures. To better support this use, software modules were developed for interprocess communication and automated creation of Powerpoint slides. These modules are fully integrated with the teaching-file software application. A single image or a set of selected images can be automatically made into individual slides with two mouse clicks. Images are automatically centered and optimally sized. A slide title is automatically rendered from the user’s preference of the case history or diagnosis (stored with the case), or via the entry of freeform text. We describe the programming techniques that are used, as well as how several features of the operating system and Powerpoint itself can be integrated with a customized software application to facilitate this objective.Results: The creation of presentation-ready Powerpoint slides is fully automated from within our teaching-file application, and the time required to create a presentation compared to the conventional method of manually seeking and inserting files from within Powerpoint itself, on a per-slide basis, is drastically reduced. The benefits are magnified by having all imagery stored within an organized and searchable database system so that desired images can be easily located.Conclusion: A digital teaching-file system can serve as a useful image repository for purposes ancillary to direct computerized instruction. Software that supports these uses, such as the automated creation of presentation material for speaker-led conferences, facilitates the radiologist’s role as an educator.
PMCID: PMC3452723  PMID: 11442134
2.  General Consumer Communication Tools for Improved Image Management and Communication in Medicine 
Journal of Digital Imaging  2005;18(4):270-279.
We elected to explore new technologies emerging on the general consumer market that can improve and facilitate image and data communication in medical and clinical environment. These new technologies developed for communication and storage of data can improve the user convenience and facilitate the communication and transport of images and related data beyond the usual limits and restrictions of a traditional picture archiving and communication systems (PACS) network. We specifically tested and implemented three new technologies provided on Apple computer platforms. (1) We adopted the iPod, a MP3 portable player with a hard disk storage, to easily and quickly move large number of DICOM images. (2) We adopted iChat, a videoconference and instant-messaging software, to transmit DICOM images in real time to a distant computer for conferencing teleradiology. (3) Finally, we developed a direct secure interface to use the iDisk service, a file-sharing service based on the WebDAV technology, to send and share DICOM files between distant computers. These three technologies were integrated in a new open-source image navigation and display software called OsiriX allowing for manipulation and communication of multimodality and multidimensional DICOM image data sets. This software is freely available as an open-source project at Our experience showed that the implementation of these technologies allowed us to significantly enhance the existing PACS with valuable new features without any additional investment or the need for complex extensions of our infrastructure. The added features such as teleradiology, secure and convenient image and data communication, and the use of external data storage services open the gate to a much broader extension of our imaging infrastructure to the outside world.
PMCID: PMC3046724  PMID: 15988626
PACS; teleradiology; iPod; webcam; ASP
3.  Prospective Volumetric Assessment of the Liver on a Personal Computer by Nonradiologists Prior to Partial Hepatectomy 
World Journal of Surgery  2010;35(2):386-392.
A small remnant liver volume is an important risk factor for posthepatectomy liver failure. ImageJ and OsiriX® are both free, open-source image processing software packages. The aim of the present study was to compare ImageJ and OsiriX® in performing prospective computed tomography (CT) volumetric analysis of the liver on a personal computer (PC) in patients undergoing major liver resection.
Patients scheduled for a right hemihepatectomy were eligible for inclusion. Two surgeons and one surgical trainee measured volumes of total liver, tumor, and future resection specimen prospectively with ImageJ and OsiriX®. A radiologist also measured these volumes with CT scanner-linked Aquarius iNtuition® software. Resection volumes were compared with the actual weights of the liver specimens removed during surgery, and differences between the measured liver volumes were analyzed.
A total of 15 patients (8 men, 7 women) with a median age of 63 years (48–79 years) were included. There was a significant correlation between the measured weights of resection specimens and the volumes calculated prospectively with ImageJ and OsiriX® (r = 0.89; r = 0.83, respectively). There was also a significant correlation between the volumes measured with radiological software iNtuition® and the volumes measured with ImageJ and OsiriX® (r = 0.93; r = 0.95, respectively).
There were no major differences in total liver volumes, resection volumes, or tumour volumes for these three software packages. Prospective hepatic CT volumetry with ImageJ or OsiriX® is reliable and can be accurately used on a PC by nonradiologists. ImageJ and OsiriX® yield results comparable to the radiological software iNtuition®.
PMCID: PMC3017311  PMID: 21136056
4.  Optimization of a low-cost truly preemptive multitasking PC diagnostic workstation 
Journal of Digital Imaging  1997;10(Suppl 1):171-174.
The Windows 95/NT operating systems (Microsoft Corp, Redmond, WA) currently provide the only low-cost truly preemptive multitasking environment and as such become an attractive diagnostic workstation platform. The purpose of this project is to test and optimize display station graphical user interface (GUI) actions previously designed on the pseudomultitasking Macintosh (Apple Computer, Cupertino, CA) platform, and image data transmission using time slicing/dynamic prioritization assignment capabilities of the new Windows platform. A diagnostic workstation in the clinical environment must process two categories of events: user interaction with the GUI through keyboard/mouse input, and transmission of incoming data files. These processes contend for central processing units (CPU) time resulting in GUI “lockout” during image transmission or delay in transmission until GUI “quiet time.” WinSockets and the Transmission Control Protocol/Internet Protocal (TCP/IP) communication protocol software (Microsoft) are implemented using dynamic priority timeslicing to ensure that GUI delays at the time of Digital Imaging and Communications in Medicine (DICOM) file transfer do not exceed 1/10 second. Assignment of thread priority does not translate into an absolute fixed percentage of CPU time. Therefore, the relationship between dynamic priority assignment by the processor, and the GUI and communication application threads will be more fully investigated to optimize CPU resource allocation. These issues will be tested using 10 MB/sec Ethernet and 100 MB/sec fast and wide Ethernet transmission. Preliminary results of typical clinical files (10 to 30 MB) over Ethernet show no visually perceptible interruption of the GUI, suggesting that the new Windows PC platform may be a viable diagnostic workstation option.
PMCID: PMC3452846  PMID: 9268871
preemptive multitasking; diagnostic workstation; optimization; CPU resources
5.  Development and Evaluation of a Low-Cost and High-Capacity DICOM Image Data Storage System for Research 
Journal of Digital Imaging  2010;24(2):190-195.
Thin-slice CT data, useful for clinical diagnosis and research, is now widely available but is typically discarded in many institutions, after a short period of time due to data storage capacity limitations. We designed and built a low-cost high-capacity Digital Imaging and COmmunication in Medicine (DICOM) storage system able to store thin-slice image data for years, using off-the-shelf consumer hardware components, such as a Macintosh computer, a Windows PC, and network-attached storage units. “Ordinary” hierarchical file systems, instead of a centralized data management system such as relational database, were adopted to manage patient DICOM files by arranging them in directories enabling quick and easy access to the DICOM files of each study by following the directory trees with Windows Explorer via study date and patient ID. Software used for this system was open-source OsiriX and additional programs we developed ourselves, both of which were freely available via the Internet. The initial cost of this system was about $3,600 with an incremental storage cost of about $900 per 1 terabyte (TB). This system has been running since 7th Feb 2008 with the data stored increasing at the rate of about 1.3 TB per month. Total data stored was 21.3 TB on 23rd June 2009. The maintenance workload was found to be about 30 to 60 min once every 2 weeks. In conclusion, this newly developed DICOM storage system is useful for research due to its cost-effectiveness, enormous capacity, high scalability, sufficient reliability, and easy data access.
PMCID: PMC3056973  PMID: 20182765
Data storage; archive; computed tomography; PACS; thin-slice CT
6.  Implementation of a filmless mini picture archiving and communication system in ultrasonography: Experience after one year of use 
Journal of Digital Imaging  1997;10(Suppl 1):80-82.
This article details our experience in developing and operating an ultrasound mini-picture archiving and communication system (PACS). Using software developed in-house, low-end MacIntosh computers (Apple Computer Co, Cupertino, CA) equipped with framegrabbers coordinate the entry of patient demographic information, image acquisition, and viewing on each ultrasound scanner. After each exam, the data are transmitted to a central archive server where they can be accessed from anywhere on the network. The archive server also provides web-based access to the data and manages pre-fetch and other requests for data that may no longer be on-line. Archival is fully automatic and is performed on recordable compact disk (CD) without compression. The system has been filmless now for over 18 months. In the meantime, one film processor has been eliminated and the position of one film clerk has been reallocated. Previously, nine ultrasound machines produced approximately 150 sheets of laser film per day (at 14 images per sheet). The same quantity of data are now archived without compression onto a single CD. Start-up costs were recovered within six months, and the project has been extended to include computed tomography (CT) and magnetic resonance imaging (MRI).
PMCID: PMC3452806  PMID: 9268846
Ultrasound; PACS; filmless radiology; recordable CD
7.  CD-based image archival and management on a hybrid radiology intranet 
Journal of Digital Imaging  1997;10(Suppl 1):168-170.
This article describes the design and implementation of a low-cost image archival and management solution on a radiology network consisting of UNIX, IBM personal computer-compatible (IBM, Purchase, NY) and Macintosh (Apple Computer, Cupertino, CA) work-stations. The picture archiving and communications system (PACS) is modular, scaleable and conforms to the Digital Imaging and Communications in Medicine (DICOM) 3.0 standard for image transfer, storage and retrieval. Image data is made available on soft-copy reporting workstations by a work-flow management scheme and on desktop computers through a World Wide Web (WWW) interface. Data archival is based on recordable compact disc (CD) technology and is automated. The project has allowed the radiology department to eliminate the use of film in magnetic resonance (MR) imaging, computed tomography (CT) and ultrasonography.
PMCID: PMC3452834  PMID: 9268870
PACS; recordable CD; image archival; DICOM 3.0; filmless radiology
8.  Virtual Liver Resection and Volumetric Analysis of the Future Liver Remnant using Open Source Image Processing Software 
World Journal of Surgery  2010;34(10):2426-2433.
After extended liver resection, a remnant liver that is too small can lead to postresection liver failure. To reduce this risk, preoperative evaluation of the future liver remnant volume (FLRV) is critical. The open-source OsiriX® PAC software system can be downloaded for free and used by nonradiologists to calculate liver volume using a stand-alone Apple computer. The purpose of this study was to assess the accuracy of OsiriX® CT volumetry for predicting liver resection volume and FLVR in patients undergoing partial hepatectomy.
Preoperative contrast-enhanced liver CT scans of patients who underwent partial hepatectomy were analyzed by three observers. Two surgical trainees measured the total liver volume, resection volume, and tumor volume using OsiriX®, and a radiologist measured these volumes using CT scanner-linked Aquarius iNtuition® software. Resection volume was correlated with prospectively determined resection weight, and differences in the measured liver volumes were analyzed. Interobserver variability was assessed using Bland–Altman plots.
25 patients (M/F ratio: 13/12) with a median age of 61 (range, 34–77) years were included. There were significant correlations between the weight and volume of the resected specimens (Pearson’s correlation coefficient: R2 = 0.95). There were no major differences in total liver volumes, resection volumes, or tumor volumes for observers 1, 2, and 3. Bland–Altman plots showed a small interobserver variability. The mean time to complete liver volumetry for one patient using OsiriX® was 19 ± 3 min.
OsiriX® liver volumetry performed by surgeons is an accurate and time-efficient method for predicting resection volume and FLRV.
PMCID: PMC2936678  PMID: 20652701
9.  MRI-Based Breast Volumetry—Evaluation of Three Different Software Solutions 
Journal of Digital Imaging  2010;23(5):603-610.
As lipofilling of the female breast is becoming more popular in plastic surgery, the use of MRI to assess breast volume has been employed to control postoperative results. Therefore, we sought to evaluate the accuracy of magnetic resonance imaging (MRI)-based breast volumetry software tools by comparing the measurements of silicone implant augmented breasts with the actual implant volume specified by the manufacturer. MRI-based volume analysis was performed in eight bilaterally augmented patients (46 ± 9 years) with three different software programs (Brainlab© I plan 2.6 neuronavigation software; mass analysis, version 5.3, Medis©; and OsiriX© v.3.0.2. 32-bit). The implant volumes analysed by the BrainLab© software had a mean deviation of 2.2 ± 1.7% (r = 0.99) relative to the implanted prosthesis. OsiriX© software analysis resulted in a mean deviation of 2.8 ± 3.0% (r = 0.99) and the Medis© software had a mean deviation of 3.1 ± 3.0% (r = 0.99). Overall, the volumes of all analysed breast implants correlated very well with the real implant volumes. Processing time was 10 min per breast with each system and 30 s (OsiriX©) to 5 min (BrainLab© and Medis©) per silicone implant. MRI-based volumetry is a powerful tool to calculate both native breast and silicone implant volume in situ. All software solutions performed well and the measurements were close to the actual implant sizes. The use of MRI breast volumetry may be helpful in: (1) planning reconstructive and aesthetic surgery of asymmetric breasts, (2) calculating implant size in patients with missing documentation of a previously implanted device and (3) assessing post-operative results objectively.
PMCID: PMC3046681  PMID: 20066465
MRI; volumetry; mamma; breast; lipofilling; silicone implant; BrainLab; OsiriX; Medis
10.  Percutaneous Disc Decompression with Nucleoplasty–Volumetry of the Nucleus Pulposus Using Ultrahigh-Field MRI 
PLoS ONE  2012;7(7):e41497.
To evaluate changes in nucleus pulposus volume as a potential parameter for the effects of disc decompression.
Fifty-two discs (T8 to L1) were extracted from 26 pigs and separated into thoracic (T8 to T11) and thoracolumbar discs (T12 to L1). The discs were imaged using 7.1 Tesla ultrahigh-field magnetic resonance imaging (MRI) with acquisition of axial T2-weighted turbo spin-echo sequences for determination of baseline and postinterventional nucleus pulposus volumes. Volumes were calculated using OsiriX® ( After randomization, one group was treated with nucleoplasty, while the placebo group was treated with an identical procedure but without coblation current. The readers analyzing the MR images were blinded to the kind of procedure performed. Baseline and postinterventional volumes were compared between the nucleoplasty and placebo group.
Average preinterventional nucleus volume was 0.799 (SD: 0.212) ml. Postinterventional volume reduction in the nucleoplasty group was significant at 0.052 (SD: 0.035) ml or 6.30% (p<0.0001) (thoracic discs) and 0.082 (SD: 0.042) ml or 7.25% (p = 0.0078) (thoracolumbar discs). Nucleoplasty achieved volume reductions of 0.114 (SD: 0.054) ml or 14.72% (thoracic) and 0.093 (SD: 0.081) ml or 11.61% (thoracolumbar) compared with the placebo group.
Nucleoplasty significantly reduces thoracic and thoracolumbar nucleus pulposus volumes in porcine discs.
PMCID: PMC3405080  PMID: 22848512
11.  OsiriX: An Open-Source Software for Navigating in Multidimensional DICOM Images 
Journal of Digital Imaging  2004;17(3):205-216.
A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program’s toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at
PMCID: PMC3046608  PMID: 15534753
DICOM viewer; 3D; image fusion; dynamic series; open-source software
12.  The iPad Tablet Computer for Mobile On-Call Radiology Diagnosis? Auditing Discrepancy in CT and MRI Reporting 
Journal of Digital Imaging  2012;25(5):628-634.
Tablet computers such as the iPad, which have a large format, improved graphic display resolution and a touch screen interface, may have an advantage compared to existing mobile devices such as smartphones and laptops for viewing radiological images. We assessed their potential for emergency radiology teleconsultation by reviewing multi-image CT and MRI studies on iPad tablet computers compared to Picture Archival and Communication Systems (PACS) workstations. Annonymised DICOM images of 79 CT and nine MRI studies comprising a range of common on-call conditions, reported on full-featured diagnostic PACS workstation by one Reporting Radiologist, were transferred from PACS to three iPad tablet computers running OsiriX HD v 2.02 DICOM software and viewed independently by three reviewing radiologists. Structured documentation was made of major findings (primary diagnosis or other clinically important findings), minor findings (incidental findings), and user feedback. Two hundred and sixty four readings (88 studies read by three reviewing radiologists) were compared, with 3.4 % (nine of 264) major discrepancies and 5.6 % (15 of 264) minor discrepancies. All reviewing radiologists reported favorable user experience but noted issues with software stability and limitations of image manipulation tools. Our results suggest that emergency conditions commonly encountered on CT and MRI can be diagnosed using tablet computers with good agreement with dedicated PACS workstations. Shortcomings in software and application design should be addressed if the potential of tablet computers for mobile teleradiology is to be fully realized.
PMCID: PMC3447096  PMID: 22562174
iPad; Tablet computer; CT; MRI; Emergency radiology; Teleradiology
13.  A Novel Application of the MIRC Repository in Medical Education 
Journal of Digital Imaging  2005;18(2):85-90.
Medical students on the radiology elective in our institution create electronic presentations to present to each other as part of the requirements for the rotation. Access was given to previous students’ presentations via the web-based system, Medical Imaging Resource Center (MIRC) project, created and supported by the Radiological Society of North America (RSNA). RadPix Power 2 MIRC (Weadock Software, LLC, Ann Arbor, MI) software converted the Microsoft PowerPoint (Redmond, WA) presentations to a MIRC-compatible format. The textual information on each slide is searchable across the entire MIRC database. Future students will be able to benefit from the work of their predecessors.
PMCID: PMC3046707  PMID: 15827829
MIRC; radiology teaching files; PowerPoint; medical education; slides; RadPix; RSNA; education
14.  PowerPoint in the Classroom 
Cell Biology Education  2004;3(3):155-161.
Note from the Editors
Points of View (POV) addresses issues faced within life science education. Cell Biology Education has launched the POV feature to present two or more opinions published in tandem on a common topic. We consider POVs to be “Op-Ed” pieces designed to stimulate thought and dialog on significant educational issues. Each author has the opportunity to revise a POV after reading drafts of the other POVs. In this issue, we ask the question, “Is PowerPoint the best instructional medium to use in your class?” Everyone seems to have an opinion on Microsoft, but the intellectual merits of using PowerPoint (or similar software) is a growing question as states and institutions put more and more money into information technology and distance learning. Four POVs are presented: 1) David Keefe and James Willett provide their case why PowerPoint is an ideal teaching software. Keefe is an educational researcher at the Center for Technology in Learning at SRI International. Willett is a professor at George Mason University in the Departments of Microbial and Molecular Bioscience; as well as Bioinformatics and Computational Biology. 2) Kim McDonald highlights the causes of PowerPointlessness, a term which indicates the frequent use of PowerPoint as a crutch rather than a tool. She is a Bioscience Educator at the Shodor Education Foundation, Inc. 3) Diana Voss asks readers if PowerPoint is really necessary to present the material effectively or not. Voss is a Instructional Computing Support Specialist at SUNY Stony Brook. 4) Cynthia Lanius takes a light-hearted approach to ask whether PowerPoint is a technological improvement or just a change of pace for teacher and student presentations. Lanius is a Technology Integration Specialist in the Sinton (Texas) Independent School District. The authors span the range of teaching experiences and settings from which they bring different points of view to the debate. Readers are encouraged to participate in the online discussion forum hosted by CBE at and/or contact the authors directly.
PMCID: PMC520839  PMID: 15526063
15.  A picture archiving and communications system featuring multiple monitors using Windows98 
Journal of Digital Imaging  1999;12(Suppl 1):106-108.
We present an effective approach to manage, review, and distribute Digital Imaging and Communications in Medicine (DICOM) images with multiple monitors using Windows98 (Microsoft Corp, Redmond, WA) that can be implemented in an office-based setting. Computed tomography (CT), magnetic resonance imaging (MRI), and angiographic DICOM images were collected, compressed, and stored using Medweb (Medweb, Inc, San Francisco, CA) software. The Medweb server used the Linux/UNIX operating system on a Pentium 333-MHz processor with 128 MB of RAM. Short-term storage capacity was about 2 weeks with routine usage of an 11-GB hard drive. Images were presented for reading on a dual-monitor Windows98 Pentium display station with 160 MB of RAM using a Medweb/Netscape (Netscape Communications Corp, Mountain View, CA) viewer. There was no significant discrepancy in diagnosis between electronic and conventional film images. Mean reading time for 32 cases was 118 seconds. The Medweb JAVA plug-in viewer loaded the first image within 30 seconds of selecting the case for review. Full uncompressed 16-bit images allowed different window setting to better assess for pathology. Multiple monitors allowed viewing various hanging protocols. Cine viewing was also possible. Key diagnostic images were electronically transmitted to referring physicians. On-call radiologists were able to access images through the Internet. By combining Medweb, DICOM, and web-browser software using desktop personal computers (PCs), an easily accessible picture archiving and communications system (PACS) is available to radiologists and referring physicians. Multiple monitors are easily configured and managed using Windows98. This system can sustain changes and can be extended to provide variable functions using inexpensive PCs.
PMCID: PMC3452922  PMID: 10342182
16.  Comparison of precision and accuracy of linear measurements performed by two different imaging software programs and obtained from 3D-CBCT images for Le Fort I osteotomy 
Dentomaxillofacial Radiology  2013;42(5):20120178.
The purpose of this study was to compare the precision and accuracy of linear measurements for Le Fort I osteotomy performed by two different imaging software programs and obtained from three-dimensional cone beam CT (3D-CBCT) images.
The study population consisted of 11 dried skulls submitted to CBCT, which generated 3D images. Linear measurements were based on craniometric anatomical landmarks pre-defined by the authors as specifically used for Le Fort I osteotomy and were identified by two radiologists twice each, independently, using Vitrea 3.8.1 (Vital Images Inc., Plymouth, MN) and open-source digital imaging communication in medicine viewer OsiriX 1.2 64-bit (Pixmeo, Geneva, Switzerland). Subsequently, a third examiner made physical measurements using a digital caliper (167 series; Mitutoyo Sul Americana Ltd, Suzano, SP, Brazil).
The results demonstrated a statistically significant difference between OsiriX and the gold standard, especially in the pterygoid process (TPtg L = 0.019, LLpPtg R = 0.016 and LLpPtg L = 0.012). Vitrea showed no statistical difference in comparison with the gold standard, and showed a high level of accuracy in all the measurements performed. The major difference found was 0.42 mm (LLpPtg R). Interexaminer analysis ranged from 0.90 to 0.97 using Vitrea and from 0.8 to 0.97 using OsiriX. Intraexaminer correlation coefficient ranged from 0.90 to 0.98 and from 0.84 to 0.98 for Examiners 1 and 2, respectively, using Vitrea and from 0.93 to 0.99 for Examiner 1 and from 0.64 to 0.96 for Examiner 2 using OsiriX.
Vitrea may be considered as precise and accurate, insofar as it was able to perform all the 3D linear measurements. On the other hand, linear measurements performed using OsiriX were not successful in producing accurate linear measurements for Le Fort I osteotomy.
PMCID: PMC3635772  PMID: 23520394
cone beam computed tomography; 3D imaging; X-ray computed tomography; osteotomy Le Fort
17.  Managing DICOM images: Tips and tricks for the radiologist 
All modalities in radiology practice have become digital, and therefore deal with DICOM images. Image files that are compliant with part 10 of the DICOM standard are generally referred to as “DICOM format files” or simply “DICOM files” and are represented as “.dcm.” DICOM differs from other image formats in that it groups information into data sets. A DICOM file consists of a header and image data sets packed into a single file. The information within the header is organized as a constant and standardized series of tags. By extracting data from these tags one can access important information regarding the patient demographics, study parameters, etc. In the interest of patient confidentiality, all information that can be used to identify the patient should be removed before DICOM images are transmitted over a network for educational or other purposes. In addition to the DICOM format, the radiologist routinely encounters images of several file formats such as JPEG, TIFF, GIF, and PNG. Each format has its own unique advantages and disadvantages, which must be taken into consideration when images are archived, used in teaching files, or submitted for publication. Knowledge about these formats and their attributes, such as image resolution, image compression, and image metadata, helps the radiologist in optimizing the archival, organization, and display of images. This article aims to increase the awareness among radiologists regarding DICOM and other image file formats encountered in clinical practice. It also suggests several tips and tricks that can be used by the radiologist so that the digital potential of these images can be fully utilized for maximization of workflow in the radiology practice.
PMCID: PMC3354356  PMID: 22623808
Compression; DICOM; image file; management; PowerPoint®; resolution
18.  MED42/480: Quick Time Virtual Reality (QTVR) Visualization of 2D and 3D Structures in Medical Education 
QTVR is a movie format, developed by Apple, that enables users to work interactively with 2D and 3D objects in a variety of ways that enhance visualization as compared to still images or linear movie files. This standard has been available for some years but the potentials of its use in medical education has not yet been fully exploited.
Like linear quick time movies, QTVR movies can be readily viewed with an Internet browser (Netscape or Internet Explorer versions 3 or higher) when quick time viewer (available free from Apple) has been installed. Thus the format is well suited for integration into educational web pages. QTVR movies are non-linear movie files that can be manoeuvred by users to:
turn 3D objects
zoom in and out of 2D or 3D objects
pan/scroll objects
activate new QTVR movie files by clicking on hot spots
Each frame in the QTVR movie may itself be a movie. QTVR movies are created with the program QTVR authoring studio on Macintosh computers but resulting files are cross-platform compatible and can be distributed on the Internet or on a CD.
The versatility of the tool enables a large variety of different applications to be made (see: for examples and links to other QTVR resources):
Gross-anatomical visualization of 3D objects can be created by recording a series of images around a real 3D object suspended in a rotating rag.
Panoramic movies can be created by rotating the camera and subsequently stitching images in QTVR authoring studio.
A virtual light- or electron microscope can be created by using a 2D image digitized at high resolution.
Serial sections of i.e. Magnetic Resonance images or CT images can be manoeuvred by the user to reveal anatomical structures for study.
In one example we have placed a sequence of serial MR movies each representing the cardiac cycle. When this movie is moved using the mouse, another plane of the heart is shown, revealing a very dynamic representation of the entire heart.
We plan to further exploit this tool and expect it to be very effective in enhancing interactive learning in topics such as anatomy, cell biology, histology, radiology and cardiology.
PMCID: PMC1761751
Medical Education; Quicktime Virtual Reality; Anatomy; Computer Assisted Learning
19.  Is spinal stenosis assessment dependent on slice orientation? A magnetic resonance imaging study 
European Spine Journal  2011;21(Suppl 6):760-764.
Lumbar spinal stenosis (LSS) treatment is based primarily on the clinical criteria providing that imaging confirms radiological stenosis. The radiological measurement more commonly used is the dural sac cross-sectional area (DSCA). It has been recently shown that grading stenosis based on the morphology of the dural sac as seen on axial T2 MRI images, better reflects severity of stenosis than DSCA and is of prognostic value. This radiological prospective study investigates the variability of surface measurements and morphological grading of stenosis for varying degrees of angulation of the T2 axial images relative to the disc space as observed in clinical practice.
Materials and methods
Lumbar spine TSE T2 three-dimensional (3D) MRI sequences were obtained from 32 consecutive patients presenting with either suspected spinal stenosis or low back pain. Axial reconstructions using the OsiriX software at 0°, 10°, 20° and 30° relative to the disc space orientation were obtained for a total of 97 levels. For each level, DSCA was digitally measured and stenosis was graded according to the 4-point (A–D) morphological grading by two observers.
A good interobserver agreement was found in grade evaluation of stenosis (k = 0.71). DSCA varied significantly as the slice orientation increased from 0° to +10°, +20° and +30° at each level examined (P < 0.0001) (−15 to +32% at 10°, −24 to +143% at 20° and −29 to +231% at 30° of slice orientation). Stenosis definition based on the surface measurements changed in 39 out of the 97 levels studied, whereas the morphology grade was modified only in two levels (P < 0.01).
The need to obtain continuous slices using the classical 2D MRI acquisition technique entails often at least a 10° slice inclination relative to one of the studied discs. Even at this low angulation, we found a significantly statistical difference between surface changes and morphological grading change. In clinical practice, given the above findings, it might therefore not be necessary to align the axial cuts to each individual disc level which could be more time-consuming than obtaining a single series of axial cuts perpendicular to the middle of the lumbar spine or to the most stenotic level. In conclusion, morphological grading seems to offer an alternative means of assessing severity of spinal stenosis that is little affected by image acquisition technique.
PMCID: PMC3535218  PMID: 21656052
Lumbar spinal stenosis (LSS); Imaging; MRI; Lumbar spine; Diagnostic
20.  Catabolic Fate of Streptomyces viridosporus T7A-Produced, Acid-Precipitable Polymeric Lignin upon Incubation with Ligninolytic Streptomyces Species and Phanerochaete chrysosporium† 
Degradation of ground and hot-water-extracted corn stover (Zea mays) lignocellulose by Streptomyces viridosporus T7A generates a water-soluble lignin degradation intermediate termed acid-precipitable polymeric lignin (APPL). The further catabolism of T7A-APPL by S. viridosporus T7A, S. badius 252, and S. setonii 75Vi2 was followed for 3 weeks in aerated shake flask cultures at 37°C in a yeast extract-glucose medium containing 0.05% (wt/vol) T7A-APPL. APPL catabolism by Phanerochaete chrysosporium was followed in stationary cultures in a low-nitrogen medium containing 1% (wt/vol) glucose and 0.05% (wt/vol) T7A-APPL. Metabolism of the APPL was followed by turbidometric assay (600 nm) and by direct measurement of APPL recoverable from the medium. Accumulation and disappearance of soluble low-molecular-weight products of APPL catabolism were followed by gas-liquid chromatography and by high-pressure liquid chromatography, utilizing a diode array detector. Identified and quantified compounds present in culture media included p-coumaric acid, ferulic acid, p-hydroxybenzoic acid, p-hydroxybenzaldehyde, protocatechuic acid, vanillic acid, and vanillin. The further catabolism of these APPL-derived aromatic compounds varied with the culture examined, and only S. setonii and P. chrysosporium completely degraded all of them. Some new intermediates of APPL metabolism also appeared in culture media, but the patterns were culture specific. Additional evidence from high-pressure liquid chromatography analyses indicated that one strain, S. badius, converted a water-soluble fraction evident by high-pressure liquid chromatography (7 to 10 min retention time range) into new products appearing at shorter retention times. Mineralization of a [14C-lignin]APPL was also followed. The percent 14C recovered as 14CO2, 14C-APPL, 14C-labeled water-soluble products, and cell mass-associated radioactivity, were determined for each microorganism after 1 and 3 weeks of incubation in bubbler tube cultures at 37°C. P. chrysosporium evolved the most 14CO2 (10%), and S. viridosporus gave the greatest decrease in recoverable 14C-APPL (23%). The results show that S. badius was not able to significantly degrade the APPL, while the other microorganisms demonstrated various APPL-degrading abilities. The significance of these findings relative to the fate of APPLs in nature was discussed.
PMCID: PMC238835  PMID: 16346967
21.  Development of a Next-Generation Automated DICOM Processing System in a PACS-Less Research Environment 
Journal of Digital Imaging  2012;25(5):670-677.
The use of clinical imaging modalities within the pharmaceutical research space provides value and challenges. Typical clinical settings will utilize a Picture Archive and Communication System (PACS) to transmit and manage Digital Imaging and Communications in Medicine (DICOM) images generated by clinical imaging systems. However, a PACS is complex and provides many features that are not required within a research setting, making it difficult to generate a business case and determine the return on investment. We have developed a next-generation DICOM processing system using open-source software, commodity server hardware such as Apple Xserve®, high-performance network-attached storage (NAS), and in-house-developed preprocessing programs. DICOM-transmitted files are arranged in a flat file folder hierarchy easily accessible via our downstream analysis tools and a standard file browser. This next-generation system had a minimal construction cost due to the reuse of all the components from our first-generation system with the addition of a second server for a few thousand dollars. Performance metrics were gathered and the system was found to be highly scalable, performed significantly better than the first-generation system, is modular, has satisfactory image integrity, and is easier to maintain than the first-generation system. The resulting system is also portable across platforms and utilizes minimal hardware resources, allowing for easier upgrades and migration to smaller form factors at the hardware end-of-life. This system has been in production successfully for 8 months and services five clinical instruments and three pre-clinical instruments. This system has provided us with the necessary DICOM C-Store functionality, eliminating the need for a clinical PACS for day-to-day image processing.
PMCID: PMC3447098  PMID: 22546983
PACS; DCMTK; DICOM; DICOM workflow; DICOM storage
22.  Accuracy and Reliability of Length Measurements on Three-Dimensional Computed Tomography Using Open-Source OsiriX Software 
Journal of Digital Imaging  2012;25(4):486-491.
There is a growing interest in three-dimensional computed tomography (3D-CT) as a research tool for the study of bone, joint anatomy, and kinematics. However, when CT data are processed and handled manually using image processing programs to yield 3D image and coordinate value, systematic and random errors should be validated. We evaluated the accuracy and reliability of length measurement on CT with OsiriX software. 3D-CT scans were made of 14 frozen pig knees with five transosseous holes in the metaphyseal portion of femur. The lengths between tunnel orifices were measured using Mitutoyo Digimatic digital calipers to establish the gold standard, and with the OsiriX program in 3D multi-planar reformatting mode for comparison. All measurements were recorded by a principal (replicate 1, trial 1) and a secondary observer (replicate 2, trial 1) and were repeated once by each observer (trial 2). The mean differences between OsiriX and real measurements were less than 0.1 mm in both replicates, and maximum differences were less than 0.3 mm. There were no significant differences between the replicates and real measurements (p = 0.544 and 0.622 for replicates 1 and 2, respectively). The intraclass correlation coefficients (ICC) were very high between trials and between replicates (ICC = 0.998 and 0.999, respectively). For kinematic analysis of the knees, length measurements on 3D-CT using OsiriX program can be used as alternatives to real measurements with less than 0.3-mm accuracy and very high reliability.
PMCID: PMC3389091  PMID: 22270788
Computed tomography; Accuracy; Reliability; Length; OsiriX
23.  Borderless Teleradiology with CHILI 
Teleradiology is one of the most evolved areas of telemedicine, but one of the basic problems which remains unsolved concerns system compatibility. The DICOM (Digital Imaging and Communications in Medicine) standard is a prerequisite, but it is not sufficient in all aspects. Examples of other currently open issues are security and cooperative work in synchronous teleconferences. Users without a DICOM radiological workstation would benefit from the ability to join a teleradiology network without any special tools. Drawbacks of many teleradiology systems are that they are monolithic in their software design and cannot be adapted to the actual user's environment. Existing radiological systems currently cannot be extended with additional software components. Consequently, every new application usually needs a new workstation with a different look and feel, which must be connected and integrated into the existing infrastructure.
This paper introduces the second generation teleradiology system CHILI. The system has been designed to match both the teleradiology requirements of the American College of Radiology (ACR), and the functionality and usability needs of the users. The experiences of software developers and teleradiology users who participated in the first years of the clinical use of CHILI's predecessor MEDICUS have been integrated into a new design. The system has been designed as a component-based architecture. The most powerful communication protocol for data exchange and teleconferencing is the CHILI protocol, which includes a strong data security concept. The system offers, in addition to its own secure protocol, several different communication methods: DICOM, classic e-mail, Remote Copy functions (RCP), File Transfer Protocol (FTP), the internet protocols HTTP (HyperText Transfer Protocol) and HTTPS (HyperText Transfer Protocol Secure),and CD-ROMs for off-line communication. These transfer methods allow the user to send images to nearly anyone with a computer and a network. The drawbacks of the non-CHILI protocols are that teleconferences are not possible, and that the user must take reasonable precautions for data privacy and security.
The CHILI PlugIn mechanism enables the users or third parties to extend the system capabilities by adding powerful image postprocessing functions or interfaces to other information systems. Suitable PlugIns can be either existing programs, or dedicated applications programmed with interfaces to the CHILI components. The developer may freely choose programming languages and interface toolkits.
The CHILI architecture is a powerful and flexible environment for Picture Archiving and Communications Systems (PACS)and teleradiology. More than 40 systems are currently running in clinical routine in Germany. More than 300,000 images have been distributed among the communication partners in the last two years. Feedback and suggestions from the users influenced the system architecture by a great extent. The proposed and implemented system has been optimized to be as platform independent, open, and secure as possible.
PMCID: PMC1761707  PMID: 11720917
Teleradiology; Telemedicine; Remote Consultation; Diagnostic Imaging; Computer-Assisted Image Interpretation; PACS; Middleware; TLS; Security; Plugin; Visualization
24.  Design and validation of Segment - freely available software for cardiovascular image analysis 
BMC Medical Imaging  2010;10:1.
Commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. We have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. However, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. We believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. Such an initiative might then serve as a bridge between image analysis research and cardiovascular research. The aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (Segment) and to announce its release in a source code format.
Segment can be used for image analysis in magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET). Some of its main features include loading of DICOM images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of MRI flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. Here we present an overview of the validation results and validation procedures for the functionality of the software. We describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. The software has been made freely available for research purposes in a source code format on the project home page
Segment is a well-validated comprehensive software package for cardiovascular image analysis. It is freely available for research purposes provided that relevant original research publications related to the software are cited.
PMCID: PMC2822815  PMID: 20064248
25.  A non-invasive clinical application of wave intensity analysis based on ultrahigh temporal resolution phase-contrast cardiovascular magnetic resonance 
Wave intensity analysis, traditionally derived from pressure and velocity data, can be formulated using velocity and area. Flow-velocity and area can both be derived from high-resolution phase-contrast cardiovascular magnetic resonance (PC-CMR). In this study, very high temporal resolution PC-CMR data is processed using an integrated and semi-automatic technique to derive wave intensity.
Wave intensity was derived in terms of area and velocity changes. These data were directly derived from PC-CMR using a breath-hold spiral sequence accelerated with sensitivity encoding (SENSE). Image processing was integrated in a plug-in for the DICOM viewer OsiriX, including calculations of wave speed and wave intensity. Ascending and descending aortic data from 15 healthy volunteers (30 ± 6 years) data were used to test the method for feasibility, and intra- and inter-observer variability. Ascending aortic data were also compared with results from 15 patients with coronary heart disease (61 ± 13 years) to assess the clinical usefulness of the method.
Rapid image acquisition (11 s breath-hold) and image processing was feasible in all volunteers. Wave speed was physiological (5.8 ± 1.3 m/s ascending aorta, 5.0 ± 0.7 m/s descending aorta) and the wave intensity pattern was consistent with traditionally formulated wave intensity. Wave speed, peak forward compression wave in early systole and peak forward expansion wave in late systole at both locations exhibited overall good intra- and inter-observer variability. Patients with coronary heart disease had higher wave speed (p <0.0001), and lower forward compression wave (p <0.0001) and forward expansion wave (p <0.0005) peaks. This difference is likely related to the older age of the patients’ cohort, indicating stiffer aortas, as well as compromised ventricular function due to their underlying condition.
A non-invasive, semi-automated and reproducible method for performing wave intensity analysis is presented. Its application is facilitated by the use of a very high temporal resolution spiral sequence. A formulation of wave intensity based on area change has also been proposed, involving no assumptions about the cross-sectional shape of the vessel.
PMCID: PMC3472227  PMID: 22876747
Wave intensity analysis; Cardiovascular magnetic resonance; Hemodynamics; Spiral sequence

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