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Why We Need Standardization for Magnetic Resonance Imaging

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Why We Need Standardization for Magnetic Resonance Imaging

3D printing is remarkably new in the medical field. In the early stages of VisMed3D, we were still conducting case studies and trials to understand the benefits of 3D printers and their capabilities. VisMed3D was approached by a well recognized medical device company with Magnetic Resonance Imaging (MRI or MR Imaging) scans of a patient whodied of a heart complication due to a massive aortic dissection. The scans were compiled and a 3D model of the aortic valve was printed. Upon examination of the model, we noticed that two areas of the aortic wall were thinner (see images below) when compared to other locations, indicating weakness of the wall. Similar weaknesses can cause the formation of a hole in the aortic wall and lead to fatal aortic dissection, as seen in this patient’s case. Our work with this client showcases the preventative and predictive health applications of 3D printing.

During a scan, the MRI machine takes cross-sectional images or “slices” of the body’s interior that doctors use to determine the presence of a condition in a patient. Many 2D slices are taken along a chosen portion of the body in order to view tissue, in its entirety, throughout that body part. However, there is a small gap, between 1-5 mm, in the z-axis between each picture. The smaller the gap between the slices, the larger the number of slices will be. This gap, which directly correlates to the frequency of slices taken, is an important aspect of the MRI that is often overlooked. For a person who knows how to read an MRI scan, the human brain can interpret the information presented in a few images. However, valuable information not seen in 2D images can be presented clearly in 3 dimensions. The human brain cannot effectively convert 2D images into a 3D model, but computer softwares have the ability to do so. Had a 3D model of this scan been completed prior to the aortic dissection, doctors could have found the extremely small dip in the aortic walls and saved the patient’s life.

Traditional analysis of MRI scans, prior to onset of the condition, allows for early detection of many health conditions, but finding these anomalies is hard in two dimensions. 3D modeling has the potential to be an impactful tool in preventative medication, but in order for the technology to be effective, standards must be put in place to guarantee cooperation between MRI scans and 3D printing capabilities. Our model was able to capture this minute weakness in the aortic wall due to the high quality of the MR Images given to us. Currently, there are no standards for what constitutes a proper MRI scan, and this lack of standardization makes it harder for companies, like VisMed3D, to convert scans into accurate and reliable 3D models. We successfully created a high resolution replica of the aorta because the MRI scans we received were in the right file type. With DICOM (.dci) files, the frequency of the slices taken during a scan are very high, and the orientation of the scan are favorable. Without meeting these basic requirements, conversion of an MRI scan into an accurate and precise 3D printed model is not possible.

The file type is arguably the most important requirement of an MRI scan. Without the proper file type, .dci, the software cannot interpret the MRI scan and, therefore, cannot convert the scans into a digital 3D model. Although this may seem trivial, the required file type contains necessary metadata, data that gives information about data on pixel spacing and slice thickness, which will be discussed later, for conversion of scans to a 3D model. MRIs are originally taken in DICOM format, but many lab technicians convert files to unusable file formats, such as .png, .jpeg, etc., before sending the scans out to be interpreted. This practice has been adopted in order to save storage space, which, as a result, saves money. However, it is during this file conversion that the resolution of the file and slice thickness are greatly reduced, as all of the metadata stored in the .dci file is lost. Without this data, computer softwares have to fill in the gaps between slices which can lead to unobserved anomalies in a scan. Once the files are converted and stored onto a CD, the imaging center usually deletes the original .dci files. Even if these files were to be converted back to a usable format, there would be no way to recover the lost metadata, rendering the file useless. Thus, if the files are converted to a different file format, it is practically impossible to create a 3D model using the scans. In order to use MRI scans for an innovative form of preventative medicine, there needs to be a standardization of saved file types. MRI files should be saved as .dci files, rather than converted to other formats. There are costs associated with the extra storage space needed to store DICOM files, but the potential health benefits that come from saving the files in .dci format can be life saving.

When a computer software compiles MRI scans, it attempts to bridge the gaps between slices, creating data, based on an algorithm, for the spaces without information. This process works for simple shapes, but in the case of blood vessels and other complex bodily structures, there are many small nuances that are specific to each individual. These nuances, sometimes smaller than 5 mm, may be in the gaps between slices and, therefore, not scanned. In that case, the computer cannot predict nor model them, leaving important features out of the 3D printed model. When computers analyze complete .dci files, these important features are much more likely to be modeled.  In the case of our scan, the weakness in the wall was captured, but due to the orientation of the machine it went unobserved to the human eye. The computer was able to render the anomaly in the 3D printed version of the aorta because it was located within the scope of the scanned images. If the weakness happened to be located in the 5 mm gap between slices, the computer may have fabricated information for that space, completely missing the feature. In order to avoid this problem, the frequency of the images taken by the software must be increased. With more slices, there will be smaller gaps in between images, which means that there will be less unknown information for the computer to generate. With a more comprehensive set of scans, VisMed3D can create a more accurate and precise depiction of the structure, increasing the predictive power of our models.

Lastly, the scan must be oriented to include as much information as possible in the X and Y directions. The Z axis is considered the length of the body, which is merely numerical information. However, the X and Y axes contain the bulk of the usable information for diagnosing a condition. Although the XZ and YZ planes can be scanned, current technology has not made this affordable; thus, scanning in the XY plane is more useful and more cost effective. To describe what a  slice taken in the XY plane of the body looks like,  imagine slicing from the front of the hip to the back of the hip and looking into the body from the top of your head. Multiple shots with this orientation allow doctors to see a full picture of the patient’s organs and tissue along the Z axis. Just like doctors, computer softwares need all of the information in the XY plane to successfully create a model of a body part. With this logic, the MRI scan should be sliced in a way such that the least important features are perpendicular to the Z axis, or, in other words, aligning the Z axis of the scan with the Z axis of the body. This allows for maximum scanning of the XY plane of the body. However, this is not always the case. If the two axes are not perfectly aligned, similar to the missing information in the gap between slices, the computer software needs to generate information for missing portions of the XY plane. The fabrication of this missing information may cause the model to not accurately depict how the tissue appears in the body. The computer may erase an imperfection in the body that could be critical for diagnosis, expunging the preventative medical applications of this technology. Creating a standard for all MRIs to be taken with both Z axes aligned would allow for maximum accuracy of 3D printed replicas of MRI scans. Thus maximizing the predictive abilities of this emerging technology and saving countless lives.

We have established simple, but necessary, standards that need to be put in place in order to ensure compatibility between MRI and 3D printed modeling technologies. The file type must be saved and exported as a DICOM file (.dci), the frequency of slices taken during the MRI scan should be increased, and the orientation of the MRI scan should align the Z axes of both the machine and the body. With these simple, yet essential standards implemented, we can unleash the immense potential of this new technology. All MRI scans of at-risk patients would be easily converted to 3D printed models, making it easier for doctors to visualize and preemptively diagnose a condition. VisMed3D’s work in modeling the patient’s aorta, following the patient’s aortic dissection, showed us that this patient’s life could have been easily saved. Through the use of this technology, we want to ensure that similar losses of life are prevented. However, we cannot do this alone; VisMed3D needs the cooperation of imaging companies by implementing the proposed standards in order to use our technology as a means of preventative medicine.

 

By: Alyna Pradhan

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