I am using version 4.11.0-2020-08-09
I have converted some segmentation from numpy format to nrrd, I also converted my CT volume from numpy to nrrd, I am able to load them fine in slicer 3d, but I wanted to convert this to dicom format so that the segmentations as well as the CT can be read by dicom viewers.correct_loading20241113 390 KB
Seems like RTStruct is the only way or are there better ways to do this ?
I tried to convert to dicom RTSTruct by following the steps below
I would recommend to use DICOM Segmentation Object (instead of the archaic and very limited RT structure set). This option shows up after you install Quantitative reporting extension. For future reference, see list of supported DICOM information objects here.
When I try to export to DICOM Segmentation Object using the Quantitative reporting extension I get two errors. I had loaded the segmentation nrrd as label map and the primary CT volume is also an nrrd object.
I had selected the CT volume as the master volume in segment editor
segmenteditor1885558 86.3 KB
Below is the subject hierarchy, is this correct ?
hierarchy1886321 62.3 KB
But when I export this using DICOM seg it gives the same two errors
You can find a script here that fully automates this process (even takes care of assigning DICOM terminologies, in case someone is just converting plain labelmaps and not segmentation nodes): GitHub - lassoan/LabelmapToDICOMSeg: Script for converting labelmap volumes to DICOM segmentation objects
When it comes to medical imaging, DICOM files are the most popular format by a mile. However, various tools offer different functionalities related to how the files are displayed and what you can do with them. Depending on whether you need to visualize regions of interest in 3D or label lesions with segmentation masks, you may be interested in different software. Some solutions also allow you to browse DICOM files online, while others are only for specific operating systems.
DICOM, which stands for Digital Imaging and Communications in Medicine, is a standard used for storing, transmitting, and handling medical imaging information. This format is widely adopted in fields such as radiology, cardiology, and dentistry, among others.
To open a .dcm file, you'll need specialized software known as a DICOM viewer. These viewers are designed to interpret the unique structure of DICOM files, ensuring that medical images and accompanying information are displayed correctly.
DICOM files stand apart in the realm of digital formats, primarily due to their comprehensive metadata. This metadata doesn't just store the medical image but also provides crucial instructions on how the image should be interpreted and displayed. For instance, a CT scan comprises multiple cross-sectional slices. When saved as DICOM files, each slice carries information about its position, orientation, and sequence relative to others.
When these individual slices are grouped, whether in a folder or zipped archive, a DICOM viewer can seamlessly arrange them into a coherent volumetric sequence. This ensures the data is in its intended order. Moreover, the depth of information in these files allows advanced DICOM viewers to turn the slices into multiplanar reconstruction views (MPR) or 3D visualizations, offering a holistic perspective of the scanned region.
Technically speaking, V7 is not primarily a DICOM viewer. It is a training data platform that allows its customers to solve computer vision tasks, such as object detection. While the platform is used across all industries, it's popular for radiology and digital pathology use cases thanks to its industry-specific features - including its DICOM viewer. As a matter of fact, V7 Darwin was the first ML labeling tool to implement DICOM support, and healthcare professionals are the single biggest user segment of the platform.
Thanks to V7's powerful DICOM functionality, you can use .dcm datasets to train AI models in the cloud, design intricate workflows for labeling and diagnostics, assign specific user roles, and transform the way you interact with and analyze DICOM data. Plus, you can seamlessly use V7 as an online DICOM browser without installing anything on your computer. V7 is your ultimate tool for DICOM analysis, unlocking a world of possibilities for healthcare professionals in search of advanced DICOM viewers.
V7's features, such as orthogonal views, image manipulation, and consensus stages, ensure that you get pixel-perfect segmentations. Moreover, the platform's commitment to data security, being FDA compliant and following HIPAA guidelines, ensures that your data remains protected. With its intuitive interface, high-speed performance, and ML features, it is one of the best solutions on the market.
Many users point out how RadiAnt is "super fast and lightweight," making it perfect for tasks that demand speed and efficiency. However, the interface and the app itself is a bit dated compared to some new solutions available.
OsiriX is one of the world's most popular DICOM viewers, boasting an intuitive user interface combined with high-performance capabilities. Developed from over 17 years of dedicated research in digital imaging, OsiriX not only adheres to the DICOM standard but also offers an open platform for the development of medical image processing tools. Its advanced post-processing techniques in both 2D and 3D, coupled with innovative 3D and 4D navigation, make it a standout. Furthermore, it integrates seamlessly with any PACS system.
MicroDicom is a specialized DICOM viewer for Windows that offers a range of features tailored for radiologists. It's designed to provide an intuitive interface, ensuring that users can easily navigate through complex medical images and data. With its advanced processing capabilities, MicroDicom stands out as a reliable tool for medical imaging.
MicroDicom, with its advanced features and flexible pricing, is a valuable tool for medical professionals. Whether you're an individual practitioner or part of a larger institution, MicroDicom offers solutions tailored to your needs. With its commitment to regular updates and a user-friendly interface, it's a reliable choice for DICOM viewing and processing.
PostDICOM is a robust platform that provides a CE certified Diagnostic DICOM Viewer integrated with its Cloud PACS solution. This platform is designed to facilitate medical teams in accessing, viewing, and reporting images and clinical documents with ease.
PostDICOM ensures the utmost security with features like session and data transfer security, AES 256 encryption, a stringent password policy, and support for Two Factor Authentication (2FA). The platform's commitment to security, combined with its comprehensive features, makes it a top choice for radiologists and researchers.
3D Slicer is a powerful, open-source platform dedicated to medical image informatics, image processing, and three-dimensional visualization. It has been widely adopted by professionals in radiology, surgery, and other related disciplines. The platform's versatility is evident in its ability to handle a variety of imaging data, making it a preferred choice for many.
Beyond general functionalities, 3D Slicer offers extensions tailored for specific needs. For instance, the LungCTAnalyzer extension is designed for the segmentation and analysis of lung CT scans, especially in the context of COVID-19 assessment.
3D Slicer stands out not just for its advanced features but also for its commitment to open-source principles. This ensures that the platform remains accessible to all, fostering innovation and collaboration in the medical imaging community.
3D Slicer is a free DICOM tool, ensuring that professionals and researchers can access its features without any financial barriers. However, certain extensions or additional functionalities might come with their own pricing models.
Horos is a renowned DICOM viewer tailored specifically for MacOS users. It stands out as a free and open-source solution, making it accessible to a wide range of medical professionals. Horos is built upon the foundation of OsiriX, a popular DICOM viewer described earlier on our list. It offers a plethora of features that cater to the needs of radiologists and other medical imaging professionals.
Horos stands out as a powerful and free DICOM viewer for MacOS users. Its rich feature set, combined with community support, makes it a top choice for radiology professionals looking for a reliable and comprehensive DICOM viewing solution on MacOS.
3DimViewer, a collaborative product of 3Dim Laboratory and TESCAN, is a free and open-source DICOM viewer tailored for viewing 3D datasets. Designed to be lightweight and user-friendly, it's compatible with both Windows and Mac OS X, making it a versatile choice for medical professionals and researchers.
3DimViewer stands out as a reliable and comprehensive free DICOM app. Their website offers a range of video tutorials, from DICOM data anonymization to creating 3D models for printing. The team behind the application actively encourages user feedback, suggestions, and contributions, ensuring its continuous evolution to meet the needs of the medical imaging community.
Inobitec DICOM Viewer is a versatile software solution tailored for visualizing, archiving, and exporting medical images in the DICOM format. Compatible with a variety of medical equipment manufacturers, it offers two distinct editions: LITE and PRO, each designed to cater to specific user needs.
Inobitec DICOM Viewer's commitment to quality and continuous development makes it a reliable choice for medical professionals. Its range of features, combined with competitive pricing, ensures that users get value for their investment.
Ginkgo CADx is an advanced open-source DICOM viewer and a dicomizer designed to provide a comprehensive solution for medical imaging. With a focus on both professionals and students in the medical field, Ginkgo CADx offers a wide range of features tailored to meet the needs of radiologists, cardiologists, and other specialists.
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