Today’s case is an 11 year old male neutered Rhodesian Ridgeback who has been choking and bringing up white foam.

Everyone has been writing great interpretations of these radiographs in the comments section, keep it up!  It’s good practice to come up with findings and differential diagnoses on unknown cases.

For those of you who are hesitant, here’s a survey question for you. Cast your vote!

I became a Mac user a few years ago, so by far the best DICOM software for me is Osirix. The open source, free software has lots of great features, but for users of eFilm (and former PC users) the interface is not always obvious. In addition, the help available on the Wiki and in the forums is limited and frustrating to search though. I did buy the book (Osirix: the pocket guide) which has some better explanations of the tools.

My goal was to be able to create ROI’s on CT images of several patients, and export them into a spreadsheet format for a research project. Here’s a step-by-step guide on how to go about doing it.

Open the series

To open selected series from multiple patients, start with the database screen. Holding the option key, click on the series under each patient that you want to open. Once they are all selected, press the 2D viewer key at the top of the window. Each series will open in a separate window. You can also just open one or a few at a time since series with many images can slow your computer down dramatically.

Create ROI’s

The ROI tools are located in the “mouse button function” area of the standard toolbar. It has many different options, from oval and square regions, to polygons and freehand pencil ROI’s. It’s worth trying them all out to see how they fit your needs. The repulsor tool (yellow circle) allows you to change the shape of several of these ROI’s, or you can click on the drag points to change the outline. To copy an ROI in the same series, you can use the dropdown ROI menu and choose “propagate ROI”. To copy it to a different patient or series, use command/C when the ROI is selected, then command/V on the image you’d like to place it on. The selector tool is at the bottom of the ROI dropdown menu, and you’ll need it to activate any ROI.

Once you have your ROI in place, double click on it to open the ROI info panel. From here you can rename it, which will be useful once you have exported it to a spreadsheet. Single ROI’s can be exported directly from here as an .xml file. It has all the information, but you’ll have to cut and paste to extract it.

Open the ROI images in a series

The best way to export your ROI data is to use the ROI plugin. The ROI plugin comes with the latest version of Osirix, v.3.2. Unfortunately the export ROI plugin only works on ROI’s that are in the same series. So to make it work, you need to open the images with your ROI’s in a series together. First, close all the windows you have open by clicking on the database button. Your ROI’s will be saved automatically. Next, select the patients’ studies that you have created ROI’s in by using command/click. Then, right click with your mouse and select “open ROI images”. All of the images with ROI’s will open together in a single series.

Export the ROI data

Go to the plugin dropdown menu, and select export ROI. You do not need to select or activate the ROI’s before doing this. The plugin allows you to choose the filename and location for the file, and to choose between .xml and .csv. Click on .csv and save the file. Then from you spreadsheet program, choose file/import. Navigate to your .csv file and import the data. Most spreadsheets will recognize comma separated values and organize the data into columns for you.

That’s it! Now you have a spreadsheet that includes the mean, minimum and maximum values of your ROI, number of pixels, and standard deviation.

Medgadget describes a quick way to create a bookmark folder of your favorite websites.

Clinical cases and Images brings you how to use Google Notebook to save content from your web searches and the best keyboard shortcuts. I liked how using 1 and 2 toggles between feed and list-type entries in Google Reader.

Here’s a new website from the Wellcome Trust that provides high quality medical images. There are some animal-related anatomic images and radiographs.

Here’s an interesting new search engine that integrates gene ontology (Go) with PubMed and MESH terms. More of us might be looking into genetic research, so it’s a good resource to know about. I really liked the left sidebar with MESH terms so that you can filter your results. I was able to type in “osteosarcoma” (19,707 citations), then go to the MESH heirarchy and click on organism, and then dog. That brought up 17 recent articles about osteosarcoma in dogs. If you’re not sure of a key word, this is a great way to browse.

References:

Sumer’s Radiology Site

I’ve been using the MIRC (Medical Resource Imaging Center) software to display the cases featured here on the blog. It’s a concept that took me some time to get my head around; there is software to install, but it all works through a web browser. For users, access to the cases is easy, just point and click. All you need is a web browser such as Firefox or Internet Explorer.

Once you are at the main page, you’ll see a search field on the right side. You can simply click on search to see a list of all the cases on the site. If you’d like to search for something specific, like hemangiosarcoma, type it into the box and click on search. You’ll get a list of all the files that contain that word.

For more options, click on “show advanced search options” under the search field. One of the coolest features is the little check box at the bottom that says “display as unknowns”. If you check it, any cases you search for will have the title hidden so that you can test yourself. There is a second box called “case navigator”, that when checked, lets you click to the next case in your search list without going back to the list of cases.

Just under the main search field, there is a drop-down menu on the right side. The list of storage servers here each contain different information. The default is set to Teaching File, which is where all the teaching cases are stored. The other options are the RSNA MIRC site, and Veterinary Radiology Questions and answers. The RSNA MIRC site shows files on how to install the software, presentations on its use etc. If you are thinking of setting up your own site, it’s a great resource. Questions and Answers is my collection of material from the first and second year veterinary students, mostly on abdominal radiology. Select one or all of these for your search.

Next there are some search fields headed by “select query type”. You can really refine your search by choosing basic, document, content, clinical, image and patient. For example, if you click on document across the top, then choose level, primary, you’ll get a result with all the primary level cases.

Once you get to a case, just click on the tabs across the top to get to the different sections. Images are displayed in the panel on the right one at a time. You can scroll through by clicking on the arrows or by clicking on the thumbnail images. If there is a larger version of the image in the file, you’ll see a “original size” button at the top right of the image panel. Clicking on it will open the larger image in a new window so you can scroll around and see all the detail. Enjoy!

If you’re like me, you browse through the table of contents of journals you like when you remember that a new issue might be out. When I was at the University of Georgia, the library would copy the table of contents of my selected journals and put them in my mailbox. It was a great reminder for me, and kept me up to date. In the last few years, most journals have developed an online presence, and offer e-mailed tables of contents. I signed up for many of the journals that I read, and when they hit the inbox, I browse through to see if there are articles I’m interested in.

Emailed Tables of Contents

The problem with the email service is that you need to create an account at each publisher’s website and subcribe. Sometimes I subscribe to a new journal, then decide I’m not really interested in it, but can’t be bothered to figure out which publisher site it came from to unsubscribe. That leads to more junk email cluttering my inbox. There is a better way!

RSS Feeds for Journal Contents

With the rise of regularly updated web content comes the RSS feed, which stands for really simple syndication. It’s a standard format that allows you to subscribe to content of a website through a feed reader. If you’ve never heard of a feed reader, take a look at Matt Wright’s explanation at www.animalinsides.com. There are lots of them out there; I personally use Google Reader. My whole life seems to be becoming Google-centric…

Journal Contents with iGoogle

If you’re not ready to dive into RSS on your own, here’s another option. For those of you with Google accounts, iGoogle aggregates all of your Google services in one place. If you’re in Gmail, look at the top left of the browser window. There are all sorts of services there; click on Web. That should bring you to the home page. You can add lots of widgets to your page, but I’m going to focus on journal feeds.

Create a new tab (add a tab) and name it something descriptive. Then click on “add stuff”. To the right of the search box and “search homepage content” button, there is a small link that says “add by url”. Open a new tab or window in your browser, and search for the veterinary journal you’re interested in. I created a list of links to the ones I check on regularly. Somewhere on the current issue page, most journals have a small, orange RSS button. Right click on it and choose “copy link” or “copy link location”. Switch windows or tabs back to iGoogle, and paste it into the lower search box (erase the http:// first). Click on “add” and see what happens! Some of mine needed several attempts.

Share the Veterinary Radiology Journal Tab

Is all this too technical ? A cool new Google feature is sharing tabs. I’ve created one called “Veterinary Radiology” with feeds to all the journals that offered RSS. If you have a Google account and you want to share my tab, just send me an email through the web form (include your email address) and I’ll invite you to share. One click, and you can scan the current issues all at once!

You can also click directly on this link to share the tab:

Veterinary Radiology Journals Tab

References:

Clinical Cases and Images
Lifehacker

We all use Powerpoint at some time in our careers, whether it’s giving a lecture to veterinary students, a community group or a scientific meeting. Most people have access to Powerpoint through a home edition of Microsoft Office or a work license. There are ways to use and abuse Powerpoint, and I’m going to give you some tips on how to wow your audience. Today we’ll start with choosing the right background.

Background shade

The first thing I used to do when creating my presentation was spend half a day browsing through background templates to design the look of the slides. While some of the pre-installed backgrounds are attractive, most are too busy and detract from your message. You need to know what type of lighting you need or want to present in to choose a background. In dark venues, dark slides with light writing show well. In bright settings, a light background with dark letters is best.

Create a gradient background

I like a gradient of two close colors or shades of a color for an elegant effect. To create a gradient color background, switch to slide master view under view/master. This master slide is the template for all new slides in your presentation. Using the format/slide background/ command, click on the color bar under the thumbnail of the slide. Choose the fill effects option. In the bottom left corner, you can choose to use one or two colors and select them from the palette. Then look in the upper half of the window to choose your gradient effect. Try a few combinations to see what appeals to you.

Choose the font colors

When you are done with the color, highlight the text of the title (still in master view) and select a color that contrasts with the background using the format/font/color menu. Do the same with the body text. It’s nice to have these as slightly different colors to make the title stand out.

Save as a template

If you like your template creation, it’s worth saving it as a Powerpoint template. Click on file/save as, and choose design template from the drop down menu. Now if you want to use it in the future, you can click on file/project gallery/my templates, and choose it from the list.

I’m sure most of you out there have a collection of articles gathered from many journals, and neatly (or not) filed away in your office. Reading and indexing information from the literature used to mean trips to the library with the photocopy card and sitting down with the highlighter to read them.

Starting in the late 90′s, many journals started posting abstracts and full text articles online. Pubmed also became a huge resource for searching the most recent literature for citations. All of these electronic references need to be stored somewhere, and paperless filing is becoming a much more viable option. Hard drives have almost limitless memory, and interfaces for saving references electronically have become much more user friendly. Now you need to decide how to choose bibliographic software, and how you will use it.

Endnote

The market leader in reference software is Endnote. It’s been around for many years, and is flexible and fairly easy to use. It is a proprietary program, though an educational discount through a college or university makes it much more affordable. UC Davis actually bought a campus-wide license last year. They tend to upgrade to a new version once every year or two, which means you have to spend another $100.00. It’s a disadvantage, though the upgrades have all been good. I actually played ultimate frisbee with a couple of the programmers for Endnote in Philadelphia, and they assured me the new code was a good thing. One caveat is that Thomson Corporation owns the top three reference manager programs; Endnote, Reference Manager and Procite. There are more options on the market now, so the prices may start to come down in the future.

How do you use it?

Endnote is a great program. I created one big library for my references so that I can search for anything. If you break it up into small libraries on different subjects, you might end up doing multiple searches. Endnote has good import filters since it’s the most popular program. If you are at a journal’s website and want to save a reference, most have a link that says “Download to reference software”. Regardless of which one you are using, just click and choose your program. The file should show up in your library; if not you just need to import it from where it was saved. Endnote allows browsing several databases from within the program as well. It’s a little less flexible, but the reference imports are easy and very fast.

Once you have your reference, you might want to organize your information by putting important points in the abstract in bold font, adding keywords to the keyword field, or adding your own notes or summary under the research notes field. All of these are searchable in the library, when you can’t remember what article you read it in. I use this method to organize my literature collection. Another fun feature is being able to save a PDF of the article, and placing a link in the reference file. If your notes aren’t enough, just click and read the original.

Reference manager software also makes life easier when writing articles. There is an interface with Microsoft Word that allows you to place chosen references from your library straight into the document. There are many output styles that conform to journal guidlines, including many from veterinary medicine. Just choose the right one to get an instant bibliography.

Web based reference software

For those who want a library that is accessible to multiple users or available online, there are many more options available now. I’ve tried CiteULike, which has a good interface and the ability to create user groups. VetRadiology is the group where I have been collecting the recent imaging literature. Other free options are Connotea from Nature publishing, and Zotero which is a Firefox extension. (Using Firefox as a browser is a subject for another post!) A popular proprietary web-based manager is RefWorks, which has a yearly fee.

More information

Depending on your needs, some of these will be better options for you than others. There is a great article on Wikipedia that compares the different reference manager software in terms of operating system, cost, options etc. If you are not using this type of software, you should! You’ll save time and be more productive after investing some time in learning more about it.

Many of you, whether you are presenting a case for grand rounds, or for a meeting or more informal lecture, will be using images in your Powerpoint (or Keynote) presentations. It’s hard to know what size, resolution and format to choose to end up with a quality image that is not so big that your computer freezes. We all want to show the audience what to look for in the most clear and efficient way possible. Here are the things I do to optimize my images.

File types

Although most people with digital imaging systems will have images that are in DICOM format, they are not readable by most slide presentation software. You need to select the images you like, and export them in a more generic format such as .jpg or .tif. Tif files preserve the original image size and quality, while .jpgs compress the image to a more reasonable size. I like to save my images as .tif format, then crop and resize to .jpg. That way I still have the original size file in case I ever want to zoom in on a particular lesion. If you save .jpg files several times, they get successively more compressed with loss of detail, and you can end up with a file that is pixellated or too small. Keep the .tif original if you can.

Exporting Images

Depending on what image viewing software you have, you will need to save or export the image to a .tif or .jpg. Before you do, make sure you have adjusted the window and level so that the image looks as good as possible. Also, turn off the patient information that is displayed on the screen. In eFilm, you can do this by clicking on the capital “A” button, and in Osirix go to 2D viewer/Annotations/none. Then save your image to a specified location. If you are photographing with a digital camera, use high resolution and a tripod to hold the camera steady.

Grayscale

Many people have some version of Photoshop for adjusting their images. It has features that are very helpful for adjusting images for presentations, though I am sure other software can do the same job. The first thing is to adjust your image mode to grayscale. Both Osirix and eFilm sometimes save a file in RGB mode, even though it is only shades of gray. Digital cameras also typically operate in color mode. The color channels make your image larger without adding data, and can also make the overall tone a green or purple color. Change them to grayscale right away, unless you have an image with color in it such as Doppler ultrasound.

Crop

The next thing to do is crop your image to the right size. Include enough anatomy that your reader can orient themselves to where they are looking, but eliminate extra dead space. For example, in a lateral radiograph of an abdomen that includes most of the thorax, crop to just cranial to the diaphragm. The important parts of your image will be displayed larger and with more pixels. Cropping too small, for an extreme closeup, can be difficult for the reader to orient to.

Image resolution

Depending on how you exported the image, your radiograph could be set at 1 pixel per inch, or 300 pixels per inch. For displaying on a screen 120 pixels per inch is fine. 72 is a common setting, and may not be enough especially if you compress it as a .jpg. In Photoshop, go to Image/Image size and change the resolution first.

Actual size

The other thing you can change under Image Size is the actual width and height of the image. I usually make the width 7 inches for a radiograph. The standard Powerpoint slide is 8.5×11 inches, so that’s enough width so everything looks good. 7 inches works well for a lateral radiograph, and 4 inches in width is good for a v/d projection.

Save a copy

Once I am happy with the cropping, contrast, size and resolution, I save the file as a .jpg. I admit this is partially through laziness, because then I don’t have to rename the file. It saves as a default the same file name in the same place, but smaller size and with a .jpg extension.

Automate this sequence with Actions

The best thing I learned recently was that you can save this sequence of commands in Photoshop using the Actions palette. Cropping is user defined, so you have to do that yourself, but the grayscale, resolution, size and save actions can all be done automatically. Look under “Actions” in Photoshop help for detailed instructions. All you need to do is find the Actions palette, click “new action”, and record the series of steps we discussed. You can then save it, and use it over and over by “playing” the action, or assigning it to a function key. I just learned about this feature, and can’t believe the time it’s going to save me! Thanks to John Doval for clarifying many of these points today.

Optimizing radiographs for Powerpoint with Photoshop: