Please see the 3 T User Information page for policies and procedures related to safety and user training.
BIC introductory and intermediate training sessions are typically held at the beginning of the Fall semester. Even though we get sporadic requests throughout the year it is simply not feasible to hold full sessions for individual users. Instead BIC staff has created a series of videos that showcase a majority of the material covered in the introductory user training session. The only information that is not covered is placement of the phantom in the headcoil and the use of the bed controls, both of which are best understood in person. It is recommended that potential new users watch this series before approaching BIC staff with any and all questions related to scanning. Videos that cover more advanced techniques will be added as needed.
#1 – Patient Registration
Registering the patient is the first step. Along the top of the screen you’ll see all the main menu options. Click on Patient and select Register. There’s a lot of information you can include, but only the BOLD sections are required to start scanning. The Exam option will be greyed out until all the required fields are filled in. With the exception of the Study field, none of the information can be altered later on; so input the correct values before continuing. Once you hit Exam you will be asked to confirm some patient information.
#2 – Browsing Protocols
As mentioned earlier, the Study field can be changed even after registering the patient. You can browse protocol folders and subfolders easily by clicking on the Region, Exams and Programs pull-down menus. Once you find the protocol you wish to use there are several different ways of loading them into the scan queue. You can left click and drag a scan from right to left or you can left click and then tap the
#3 – Loading Whole Protocol
Highlighting the protocol name in the Programs section and clicking
#4 – Localizer
Once a protocol is selected the first scan done is a localizer. It is quick and usually located at the beginning of a protocol. Drag it to the active scan queue, double-click to make it the active scan, and then click Apply to start. The bottom left of the screen displays a countdown for how much time is left until the scan finishes. Once completed the images load into the main three display windows, with each window showing a different slice orientation.
#5 - Contrast and brightness
After selecting an image you can hold down the middle mouse button and hover over it to control the contrast and brightness. Moving up and down controls brightness while moving left to right controls contrast
#6 - Zoom pan
Hovering the mouse over different parts of the image will change the cursor as well as its function. Holding the left mouse button anywhere other than the edges of the yellow slice prescription window (or green saturation bands window) and moving left to right will pan the image, while moving up and down will zoom. Notice how the cursor changes as you move around and hover over different sections.
#7 - MPRAGE after localizer
Typical protocols follow up the localizer with a hi-resolution anatomical scan (MPRAGE). Use the coronal, sagittal and transverse images obtained by the localizer to set up the slice prescription you’d like to use. Highlight the MPRAGE, bring it over to the active scan queue, and double-click. A yellow box will appear over the localizer images in the three viewing windows. Hover over the center circle of one of the boxes to see the mouse cursor change to a weird cross with arrows at its tips. Click and drag the left mouse button when this happens to position the slices. Typically users get whole head MPRAGE images, but your protocol may vary. Once you are happy with the positioning hit Apply and the scan will begin after the magnet finishes shimming and you acknowledge the stimulation warning.
#8 - Neuro 3D avocado
Once you’ve acquired a hi-res anatomical it can be loaded into the Neuro 3D application to be viewed in 3D. Once the images have been reconstructed go to Applications > Neuro 3D to start the app and bring up the Patient Browser and drag the anatomical to any of the four viewing windows. Four different images pop up on the screen; axial, coronal, sagittal and isometric 3D. By manipulating the colored lines in the first three images you can cycle through the slices in all three views. The isometric 3D view, while not as helpful for examining data quality, is really freaking cool. The object can be rotated and manipulated in a variety of ways and is often the go-to choice for researchers when their subjects ask to see some images of their brain. See if you can figure out what object was scanned in the example video. Hint: It’s not an egg.
#9 - Parameter cards for sequence
Although most users will never need to change sequence parameters on the fly, it is possible to cycle through them using the various sub tabs in the bottom right once a scan is selected and loaded up. From here you can view TR, slice thickness, orientation, and all other parameters that are typically determined at the time the protocol is being developed. Familiarize yourself with these tabs to gain a deeper understanding of the scan parameters
#10 - using MPRAGE for setting up slices for subsequent scans
Once the MPRAGE finishes (watch the timer tick down in the bottom left corner!) the square next to the sequence name will fill with a white head outline and a thumbnail of the first image in the series will appear on the film strip above; this tells you that the system has completed reconstructing the images. Grab the filmstrip preview image and drag it to one of the three larger viewing windows to load the MPRAGE. From here you can cycle through all the images via the button in the top right corner. Because you are able to view all the images here in the Exam tab (rather than switching over to the Viewing tab) this feature is quite helpful for placing subsequent slice prescriptions and verifying that the section you are trying to image is always within view. Select and bring over your follow-up scan then double-click on it to bring up the yellow slice prescription window. Now adjust the position of the slices while cycling through them until you are satisfied with their location and orientation.
#11 - FLAIR positioning error and restart
Once you start positioning your slices it can be easy to lose your footing and wind up with the wrong orientation, especially if you hover the mouse cursor over the edge of the box and rotate it. So what happens if you things become royally FUBAR? Don’t worry -- all is not lost! Simply cancel the scan, drag it to the trash and bring over a fresh version from the protocol on the right. This will reset the orientation to the default position so you can start over.
#12 - Inline Display
When acquiring fMRI data it is good practice to use the Inline Display to monitor the images as they are being reconstructed in real-time. That way you can tell almost instantaneously if your subject moves or if you’re getting artifacts or ghosts. The Inline Display can be turned on by clicking the second button in the column on the bottom right of the screen. The box can be re-sized, the zoom/pan, contrast and brightness can also be changed in this view.
#13 - Viewing tab intro
Once the fMRI data has finished reconstructing it does not automatically get loaded into the filmstrip view like the MPRAGE did. This is because fMRI data can only be viewed in detail in the Viewing tab, which is close to the top right corner of the screen. When you click on it the interface will change. Sometimes your images will be loaded in automatically, but if they are not you can do it manually via the Patient Browser. Here you can cycle through all slices that have been acquired.
#14 - Viewing tab multi view layout
Once inside the Viewing tab the display can be changed to show from 1 to 16 different scans on the screen at the same time. 1:1 displays the largest image on the screen. It’s possible to cycle through the series of scans that have been acquired by using the Series Up and Series Down buttons on the keyboard. You can also cycle through the images of individual series by pressing the Image Up and Image Down buttons on the keyboard (located directly below the previous two buttons). Just as in the Exam window, you can adjust the contrast and brightness as well as zoom in and pan the image.
#15 -Viewing tab image tools
The Viewing tab also includes imaging tools that are not commonly used but are worth mentioning. Following along with the video example, there are buttons to zoom, pan and even return the contrast and brightness to the default values (after changing them by holding down the middle mouse button)
#16 - Checking for error messages
Occasionally you’ll run into some error messages that may or may not prevent you from scanning, so it’s important to know where they appear. Sometimes the problem is self explanatory, other times it isn’t. If you encounter such messages relay the information to BIC staff so we can address the issue ASAP. In the video example I attempted to do a scan with the headcoil not plugged in properly. At first the scanner comes up with a pop-up message however, please note that these pop-ups do not always appear. If you look down at the bottom right of the screen you’ll notice a red slash over a waveform. Clicking on that icon will bring up the error messages screen and explain in a bit more detail what is going on.
#17 - Osirix data transfer
Once your scanning session is finished it is time to transfer the data to the recording Mac located in the BIC hallway. Bring up the Patient Browser and select your study. From there go to Transfer > Send To > Osiris and click Send. At the bottom of the screen you’ll see several messages regarding the transfer. First you’ll see Send request accepted followed by Send successfully completed to OSIRIS for patient name: XXXXXX which means the data transfer is complete. If you’d like you can click on the Network Job Status icon on the bottom right that pops-up when you begin a transfer. This lets you monitor the transfer, cancel or restart it.
#18 - Close patient
Closing the patient can be done before or after the data transfer; whenever you are wrapping up in the control room. Simply go to Patient > Close Patient.
#19 - Protecting and deleting data
Putting a protection on a data set is absolutely essential if you are unable to transfer data to the recording Mac for any reason. This protection prevents data from being deleted easily. If someone tries to delete the data a warning appears informing them of the protection. The data cannot be deleted until the protection is removed. Refer to the video for an example
#20 – Scanner shut down
If you are the last scan of the day then you will have to shut down the scanner once you’re finished. To do this click on System > End Session and from here you will have four options: Log Off (not used), Shutdown System (shuts down the whole scanner), Restart System (restarts the scanner) and Restart Application (restarts Syngo MR console). Select Shutdown System and wait for the Windows screen to appear that says "It is now safe to turn off your computer", and then push the System Shutdown button on the wall of the control room. If you experience error messages than BIC staff may suggest restarting the magnet as a solution, so it is good to remember where these menu options are located.
#21 – Editing Resources displayed in Calpendo
Since the BIC adds new facilities for our users to reserve, we have uploaded a quick video to demonstrate how to edit the resources that are displayed when looking at the Calpendo booking calendar. To display all the new resources, go to the Bookmarks menu on the lower left of Calpendo, select "Edit Resources to display" and add all or as many as you want. Each can then be displayed or hidden with a single mouse click on the resource name.