As technology finds its way into every aspect of medicine, great advances have been made in the field of radiology. Radiology once depended on simple two-dimensional images that needed to be manually developed and fixed prior to viewing.
Now, almost all forms of medical imaging have become digitalized and the spectrum of radiology includes not just digital radiographs but also CT scans, MRIs, ultrasound, and nuclear imaging. To maintain standards as well as uniformity across the varied types of medical imaging modalities, the concept of DICOM was introduced. As a medical student or even a full-fledged radiologist, the prospect of dealing with so much technology can seem pretty daunting. It is a standard, internationally accepted format to view, store, retrieve and share medical images.
DICOM conforms to set protocols to maintain accuracy of information relayed through medical images. As a student or practicing radiologist, all medical images that you see are likely to be in the DICOM format. Therefore, it is important to know how to use this format , what are some relevant applications, and how to access the information and features contained within.
The header consists of data that describes the image, the most important being patient data. The header may also give information on image characteristics such as acquisition parameters, pixel intensity, matrix size, and dimensions of the image.
When a file explorer is opened to view DICOM medical imaging data, the header can give patient and image information. The header is usually coded to the image so that the patient to whom the image belongs can easily be identified. Sometimes, you may want to intentionally lose the header data, usually for the purpose of anonymization in research cases.
This can only be done using specific software functions. This depends on the purpose for which you want the files. If you are a patient and have had scans taken, you would probably receive a CD or DVD with images on it. If you are a medical student and want to view DICOM images for learning and study, you can download such images from online resources. If you are a radiologist and need to access files in order to interpret them and identify diagnoses, you will need to use a PACS server.
Online resources: If you are a student and are looking for medical images to learn from, there are several online resources that can help you. This is basically a database in which all medical images are stored. Each hospital usually has its own PACS server.
Any medical image that is taken within a hospital is automatically stored within that PACS server. There are basically two kinds of software for viewing DICOM medical imaging data—proprietary software and third party software. Proprietary software comes along with the hardware for medical imaging and is usually created by the same manufacturer.
Proprietary software allows users to dynamically view sequential images and also allows reconstruction of these images. One major drawback is that these image files can only be viewed in the same location as the hardware. The images can be transferred to portable storage devices or to other computers on the network only by compressing the images described in the section below. After the Pack line around line in trnsyn. Refined the check for an incorrect typecode.
Works for your sample, may not work for others still Thanks Marcel it works. Register yourself now and be a part of our community! Attached the anonymized version. Regards, Robert. Hi, try have to define the offending element as a sequence in dgate. Hi Marcel, i've added to the dgate. Would there be a way to ingest this this into Conquest and fix the file in the process?
Regards, Roni. Hello Roni, With my. RescaleIntercept; But the Y matrix still have the wrong values for the positive pixel values and now zero for the negative ones. Regards, Susana. It shows the values after Modality LUT transformation. The data is unsigned as you can see from Pixel Representation. When you read into matlab you get a matrix X of type uint16 So when you transform it you still have uint16 matrix.
You need to cast it or to create Y as sint16 or better sint32 of the same size as X x and then make the transformation. Once done this way, you will get values identical to Osirix. Appreciate your help. Hi hi AM 16 bits stored signed stored signed pixels is unusual but the pacs should be able to display it. My guess is that you also use lossless jpeg. Transfer syntax. Many implementations of the jpeg lossless, specifically the ones that use cornel university code base and not the jig code have a bug and they fail on 16 bits signed pixel data.
If this is not the case then It's probably something with the reading I 16 bits signed because to cast it to int some applications will make it 17 bits eg dcmtk. I recommend changing your implementation to more common pixels like 16 bit unsigned if you have to use all the 16 bits. It's probably not your bug but it will spare you from explaining that to customers. These bugs were fixed and I might be able to send you a patch for that. Send me an email or fill the contact form on www. I will be working on this issue tomorrow with Agfa rep.
I will let you know the outcome. Thanks for your help. Is there no binary file or sample code which extracts only pixel data as 2D or 3D array?
Hi, i gone through the above code which you updated. But how i need to display the dicom image in vtk? Please can you tell me how you have done the rendering in VTK? Enjoying your blog though. Yes, that's possible. The only example I could fine though is RT Dose and the type is integer, not float.
Why would you want real pixels? Hi Roni, I am a student who is currently doing a project that involves measuring lengths on x-ray images that were exported from the PACS system. I am using the Osirix software to perform the measurements. I found it to be a problem when the measurements were in pix. I need the units to be in centimetres and not pix.
The furthest I managed to get to was a recalibrating option that required me to set a value in cm for the length that was being measured in pix. I do not how to recalibrate it. Alternatively, I thought of just simply using a online conversion calculator to convert from pix to cm.
I am only measuring vertical distance. I was hoping that you could help me out with this issue. I am quite illiterate in this to be honest so if you can please reply in lay man terms. Can I just convert the length measurements just by using an online conversion calculator? Alternatively, if you can teach me how to recalibrate the units from cm to pix on Osirix so that all measurements will be in cm on Osirix, that would be an even better solution. Having that in mind I thought that for huge dcm file it would be wise to extract images out of the dcm consisting of many images, send pure dicom without images and send images sequentially.
Then on the other side upon request I would compose dynamically the dcm file with all the images that were completely sent. However until now I only managed to find dcm file with framed image or one image in the file at most. My question are I kindly ask for the answer : 1. Do you think that what I described seems feasible stripping pixel data, sending pure small dcm without pixel data, and uploading pixel separately?
And do really exist dcm files consisting of many pixel data composed of many images. Or maybe there are dcm files consisting of "in fact" another dcm files or some kind of subset data. So in fact I can have one big dcm, "extract" it into many dcms splitted e. And in that case when considering transmission of big dcm I should split it into number of smaller dcm files and do something with them.
I am a bit lost here. If you could clarify how it works I would appreciate that very much. There are so many solutions out there and some of them are quite good.
First of all, I would like to note that you may not want to transfer the entire DICOM header, specially not over insecure connection.
Instead I recommend transferring only information you need. To your questions: 1 Yes, very reasonable. As I said, there's many way to do this and I recommend that you make a survey of existing solutions. With the evolvement of html5 and javascript, node. The complete content of a Study can span over multiple DICOM Instance and more important can change over time as new Instances are added to the study, for example reports, presentation states, post-processed images and so on.
Within your system boundaries you are free as a bird. Its when you want to communicate with other system that DICOM is your tool, your language to speak to other systems. Hi Roni, Thank you for your answers. I will transfer data over secure connections only, so although I take into account your arguments I am still thinking about transferring full dicom header,.
This is because I am considering only to strip "heavy" part and not to go to deep into dicom data, if possible. Just wanted to confirm that "nested" dicom files exist ie one dcm file can contain many sets of data, specially pixel data which is heavy.
I actually need to do 2 things. Transfer dicom data between some nodes b. Let my app be visible as dicom node, ie let pacs to send data to me and let operator of my app to search for some data to be send on another dicom node. It means that I need to implement a dicom listener and dicom sender be able to issue dicom queries.
Currently as I do it in Java I tried some basics with dcm4chee-toolkit, but I have not decided yet which libraries will be using by the end of the day.
Re: 1. I have to write it myself, however with the help of libraries, I don't want to reinvent the wheel Re: 2. Do you know the place or can offer example Dicom file to download that has some nested data. All I found until now is a singe dcm files or zipped tree of dcm files. If I understand correctly one dcm file can have some nested data and each set of that nested data can contain pixel data space. The idea is to recursively parse that kind of nested dicom exclude pixel data, and then place pixel data back dynamically when image parts are transferred.
I have some doubts however because whatever I saw was rather small dicom files but many. I know I can communicate between my nodes in the way that fits transmission requirements not just DICOM, however as my system must also act as dicom node, I finally have to implement some kind of listener offering buffer to store dicom data and be able to query for the data in another systems acting as dicom node.
Hi Roni, Like Norbert above, I've also been looking for example Dicom files containing multiple images. It would certainly be useful to have some sort of definitive "standards test" data set. Do you know where I could find, or do you have, something like this? Thanks, Rich. There's also many samples in OsiriX web site I try to delete any data that I get and not keep copies of files after I finish the task related to it. Hi Roni, Thanks for the prompt reply!
I was hoping such a data set might already exist for the purpose of covering all real in-use data types and layouts, compression types, etc. But if not, I guess I'll have to continue scavenging. Hi Roni, Thank you for excellent post. There are few specific attributes for this files e. That's why I can't see specific spectroscopic tags I think so. When I open this file with dicom viewer I see set of grayscale squares. I want to extract the spectroscopy data array of intensity from this file using Pixel Data.
It necessary to create spectrum for each voxel. Can I do it or I only need data from attribute Spectroscopy Data ,? Standard says that Spectroscopy Data attribute points to a data stream of intensities that comprise the spectroscopy data.
I look forward to hearing from you. Dear A.
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