Some non-clinical (industrial or pre-clinical) imaging systems do not generate valid DICOM data sets. Most common object types are those that store the image volumes produced by the CT and MR scanners. Temporary folder can be selected in menu: Edit / Application Settings / Modules / Temporary directory. 3D Slicer is a free open source software (BSD-style license) that is a flexible, modular platform for image analysis and visualization. Scanners may create image volumes with varying image slice spacing. This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149, and by Quantitative Image Informatics for Cancer Research (QIICR) (U24 CA180918). How do I get started? 3DSlicer est une application dédiée à la visualisation et à l’analyse de données volumiques. This module allows importing and exporting and network transfer of DICOM data. Right-click on the data node to be exported and click "Export to DICOM..." to display DICOM export window (you can also show it by clicking "Export" button in the toolbar of DICOM browser module). When I click on “Load selection to slicer” I get an error message “Could not load … as a scalar volume”, I try to import a directory of DICOM files, but nothing shows up in the browser, Something is displayed, but it is not what I expected, this anonymized sample DICOM series (CT scan), National Alliance for Medical Image Computing, The DICOM Homepage: http://dicom.nema.org/, DICOM on wikipedia: http://en.wikipedia.org/wiki/DICOM, Clean and simple DICOM tag browser: http://dicom.innolitics.com, A useful tag lookup site: http://dicomlookup.com/, A hyperlinked version of the standard: http://dabsoft.ch/dicom/. DICOM is a complex way to represent data, and often scanners and other software will generate ‘non-standard’ files that claim to be DICOM but really aren’t compliant with the specification. To visualize 3D data from cardiac imaging, we used Slicer Virtual Reality and HTC Vive. Either choose to create a new database or open a previously created database. 3D Slicer www.slicer.org Olfactory bulb volumetry. Basics of Data Loading and 3D Visualization in 3D Slicer Sonia Pujol, Ph.D. Director of 3D Slicer Training & Education Assistant Professor of Radiology Or you can use a different port, like 11112. DICOM data can enter the database either through file import or via a DICOM network transfer. Since DICOM files are often located in several folders, they can cross-reference each other, and can be often interpreted in different ways, reading of DICOM files into the scene are performed as two separate steps: import (indexing files to be able to show them in the DICOM database browser) and loading (displaying selected DICOM items in the Slicer scene). Image processing tasks most often are concerned with analyzing the whole image volume, which most often corresponds to a single Series. The DICOM file format consists of a folder that has many subfolders and files within it. Note that you should exercise extreme caution when working with these files in clinical situations, since non-standard or incorrect DICOM files can interfere with clinical operations. CTK code is responsible for the implementation of the DICOM database and networking layer. If none of the data sets seems to be correct then follow the steps described in section “I try to import a directory of DICOM files, but nothing shows up in the browser”. The DICOM Module exposes this functionality to slicer users, and provides hooks through which other module can register DICOM Plugins to handle the conversion of specific DICOM data objects into the corresponding MRML representation. In most cases, imaging equipment (CT and MR scanners) used in the hospitals will generate images saved as DICOM objects. DICOM sender (C-STORE SCU): select data from Slicer DICOM database and send it to a remote computer. Parmi ses fonctionn… Simply, I can display any of the horizontal images using imhsow(3DImage(:,:,n), .....), where 'n' is the number of the slice. You can have multiple databases on your computer at a time, and switch between them if, for example, they include data from different research projects. Drag the entire folder onto the 3D Slicer … DICOM is also a network communication standard, which specifies how data can be transferred between systems. Select data to be exported in Subject Hierarchy module or initiate export from DICOM browser, Exported files are added to the DICOM database, Open Data module, go to Subject Hierarchy tab (it is the tab shown by default). We will simply open the study in 3D Slicer and without modification save it in the NRRD format. To create DICOM files without adding them to the DICOM database, check “Export to folder” option and choose an output folder. Creating a DICOM database is a prerequisite to all DICOM operations. Acquisition geometry regularization option supports the creation of a nonlinear transform that corrects for things like missing slices or gantry tilt in the acquisition. Ces coupes peuvent être sagittales, axiales ou coronales. Open 3D Slicer and open the folder that contains your DICOM files. You can have multiple databases on your computer at a time, and switch between them if, for example, they include data from different research projects. The are described here in the order you are likely to use them. Also if something adverse happens (a crash) the port may be kept open an you need to either kill the storescp helper process (or just reboot the computer) to free the port. DICOM data stored in the database can be exported to DICOM files by right-clicking in patient/study/series list and choosing “Export to file system”. If image is still distorted, go to Volumes module, open Volume information section, and adjust Image spacing values. The result as a DICOM secondary capture object, which can be stored in any DICOM archival system. Try loading the data using the latest stable and the latest nightly versions of Slicer. However, if you have a dataset produced by a clinical scanner, it is most likely in the DICOM format. Export type: Once the user selected a node, the DICOM plugins generate exportables for the series they can export. Display of the segment semantics is provided in specialized Slicer modules. When it is computable by examining the files, the DICOM module will select the most likely interpretation option by default. General Slicer guide. SlicerDMRI is an open-source project to improve and extend diffusion magnetic resonance imaging software in 3D Slicer. You can have multiple databases on your computer at a time, and switch between them if, for example, they include data from different research projects. Otherwise they will only be referenced in their original locaion. As of this release, standard plugins include scalar volumes and diffusion volumes, while extensions are available for segmentation objects, RT data, and PET/CT data. Optionally select the “Copy” option so that the files are copied into the database directory. DICOM data can enter the database either through m… 3D Slicer intègre une visionneuse 3D capable d'effectuer des coupes 2D des éléments observés. However once the data is imported to the database, it will be organized according the the DICOM standard Patient/Study/Series hierarchy. Once installed you will be able to use the Dcm2niixGUI module from slicer. Advanced loading (allows loading DICOM data sets using non-default options): DICOM files do not need to have a specific file extension, and it may not be straightforward to answer this question easily. If you suspect your data might be in DICOM format, it might be easiest to try to load it as DICOM: A common cause of loading failure is corruption of the DICOM files by incorrect anonymization. Note that to avoid accidental data loss, Slicer does not delete the corresponding image data files. A graphical user interface with display of thumbnails is available for data selection. Note that in order to use these features, you must coordinate with the operators of the other DICOM nodes with which you wish to communicate. Plans for the near future include support for storing data from slicer into the data base and uploading data from the data base into a PACS system. Autoloading subseries by time is an option break up some 4D acquisitions into individual volume, but is optional since some volumes are also acquired in time unites and should not be split. However once the data is imported to the database, it will be organized according the the DICOM standard Patient/Study/Series hierarchy. DICOM export window can be also opened from the DICOM browser, by clicking "Export" button in the toolbar, Export series: export one or more selected series, to be viewed on a standard DICOM-compliant viewer, Export entire scene: save the entire Slicer scene into a DICOM secondary capture file; the content can be stored on a DICOM archival system but can only be edited in Slicer. imaging itk mri vtk. Connection ports: Port 104 is the standard DICOM port. You can choose what back-end library to use (currently GDCM, DCMTK, or GDCM with DCMTK fallback with the last option being the default. You can open a database at another location anytime in DICOM module panel / DICOM database settings / Database location. This secondary capture information stores all details of the scene but only 3D Slicer can interpret the data. SlicerRT is an extension of 3D Slicer, a free, open source software for visualization and image analysis. Optionally select the Copy option so that the files are copied into the database directory. Slicer is used most often with CT and MR DICOM objects, so these will typically work. Figure 1: Loading your DICOM data set by dragging and dropping the DICOM folder onto 3D Slicer. However, I decided to adapt and revisit the concepts and make them more familiar to Machine and deep learning engineers. Slicer supports sending of DICOM items to a remote server using DICOMweb protocol. When I try to display a vertical image, as 3DImage(k,:,:), it is displayed in a flattened way. See more information. Note that the DICOM standard does not specify how files will be organized on disk, so if you have DICOM data from a CDROM or otherwise transferred from a scanner, you cannot in general tell anything about the contents from the file or directory names. Click Export button: Export may take a few minutes. All ports below 1024 require root access on unix-like systems (Linux and Mac). DICOM tag editor consists of a list of tables. By right clicking on a Patient, Study, or Series, you can delete the entry from the DICOM database. The Edit->Preferences->DICOM page can be used to select options. Select the export type in the bottom left of the export dialog. Open Files From Dropbox Load your DICOM (.DCM) or NiFTI (.nii) directly from your computer or transfer them via Dropbox to your devices to view your own scans rendered locally. Option A: Drag-and-drop the folder that contains DICOM files to the Slicer application window. Il convient aux débutants comme aux professionnels. Once you load the data into Slicer using DICOM Browser, you can switch to the “Data” module to examine the content that was imported. Each database is simply a directory on your local disk that has a few SQLitefiles and subdirectories to store image data. To obtain DICOM metadata: right-click on the series in the DICOM browser, select View metadata, and click Copy Metadata button. Go to DICOM module. DICOM data can be retrieved from a PACS system after proper configuration of Slicer. How do I know if the files I have are stored using DICOM format? Right-click on a data node in the data tree that will be converted to DICOM format. The metadata from the select study will be automatically filled in to the Export dialog and you can select a Slicer volume to export. So you can run Slicer with the sudo command to be able to open the port for the DICOM Listener. Make sure the Slicer temporary folder is writeable. Data nodes loaded into the scene can be directly exported as DICOM files in the file system by right-clicking on the item in Data module, choosing Export to DICOM, enabling “Export to folder” option, and specifying an output folder. Don't manually modify the contents of these directories. Select the data set that you want to load by clicking on a series (item in the listbox in the bottom), Copy-paste remaining text to Slicer forum post or email. There is no reliable mechanism to distinguish between slices that are missing because they had not been acquired (for example, to reduce patient dose) or they were acquired but later they were lost. In addition, the specification itself has many variations and special formats that Slicer is not able to understand. The CTK code is implemented C++ and follows the Qt style. Tables for the common tags for the patient and study on the top, and the tags for the individual series below them. C’est un logiciel open-source et gratuit, compatible avec la plupart des imprimantes 3D de bureau. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. This allows much more flexibility and DICOM plugins can auto-populate some information and plugins can expose other export options in this list (e.g. Module for 3D Slicer that fixes most common errors in DICOM files. Consult the Error Log for diagnostic information. It is a long-term objective to be able to represent most, if not all, of Slicer’s data in the corresponding DICOM data objects as the standard evolves to support them. Chercher les emplois correspondant à 3d slicer segmentation dicom ou embaucher sur le plus grand marché de freelance au monde avec plus de 18 millions d'emplois. This is necessary because there may be several DICOM information objects that can store the same kind of data. “Slicer data bundle” export type writes the entire scene to DICOM format by encapsulating the scene MRB package inside a DICOM file. © Copyright 2020, Slicer Community To prepare DICOM patient and study manually before export, go to Data module (subject hierarchy tab), right-click in the empty space in the data tree and choose Create new subject. Retrieved from "https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DICOM&oldid=63465" Export type: Once the user selected a node, the DICOM plugins generate exportables for the series they can export. You can also choose to encapsulate the current MRML scene (via an MRB file) inside a DICOM dataset, which will be treated as a DICOM Secondary Capture document (note that the export feature has not been widely tested and should be considered experimental). Slicer offers the following feaures: Note: In order to use these features, you must coordinate with the operators of the other DICOM nodes with which you wish to communicate. This is provided in case some data is unsupported by one library or the other. Those objects most often will have multiple files (instances) for each series. You may share the DICOM files if they do not contain patient confidential information: upload the dataset somewhere (Dropbox, OneDrive, Google drive, …) and post the download link. 3D Slicer Training. Slicer can represent such images in the scene by apply a non-linear transform. Make sure that all required Slicer extensions are installed. (Slicer … You can next select individual items from the DICOM Browser window and load them. You may need to click on the small rectangle icon (“Adjust the slice viewer’s field of view…”) on the left side of the slice selection slider after you show a volume. Link to official 3D Slicer site. 3D Slicer is a software platform for the analysis and visualization of medical images and for research in image guided therapy. This tutorial is partly based in the nipy [1] and 3D Slicer.org [2] documentations for medical images and Dicom files. DICOM Patcher¶ This module fixes common errors in DICOM files to make them possible to import them into Slicer. Double-click on the patient, study, or series to load. There is a variety of DICOM objects defined by the standard. 3D Slicer is extended to enable development of both interactive and batch processing tools for a variety of applications. drag and drop the directory with your data into Slicer window. This can also be made to happen automatically. Save modified tags: check this checkbox to save the new tag values in the scene persistently. For example, segmentation can be stored as DICOM segmentation object (modern DICOM) or RT structure set (legacy representation, mostly used by radiation treatment planning). Each database is simply a directory on your local disk that has a few SQLite files and subdirectories to store image data. More plugins are expected for future versions. DICOM files that are copied into the DICOM database will be deleted from the database. Tables for the common tags for the patient and study on the top, and the tags for the individual series below them (see image about tag editor below). http://qiicr.org http://slicer.org DICOM Support in 3D Slicer and CTK Steve Pieper, PhD Isomics, Inc. Tuesday, October 22, 13 training data VPB_03 1. The process takes less than a minute. You need to configure that on both sides of the connection. The overall DICOM Implementation in 3D Slicer consists of two main bodies of code embedded within the application. Or you can use a different port, like 11112. Slicer training; Tutorials and sample data. If you share the data (e.g., upload it to Dropbox and add the link to the error report) then Slicer developers can reproduce and fix the problem faster. DICOM data can be loaded into Slicer from the local database. Slicer core contains DICOM import plugin for importing images, but additional extensions may be needed for other information objects. 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Consult the Look at error log for diagnostic information. If, for example, the speed of the table motion is not consistent during an acquisition (which can be the case for some contrast 'bolus chasing' scans, Slicer's DICOM module will warn the user that the acquisition geometry is not consistent and the user should use caution when interpreting analysis results such as measurements. For example, you must work out agreement on such topics as network ports and application entity titles (AE Titles). By selecting a Study and right clicking to get a context menu, you can choose to Export data from Slicer into DICOM. Save tags to scene: Checkbox to allow saving the tags back to the MRML nodes as attributes. It is available in recent 3D Slicer versions, in the Utilities category in the module list. You can only have one process at a time listening on a port so if you have a listener running the second one won’t start up. Otherwise they will only be referenced in their original location. Autoloading subseries by time is an option break up some 4D acquisitions into individual volume, but is optional since some volumes are also acquired in time unites and should not be split. •  3D Slicer is a free open source soXware applicaon distributed under a BSD style license •  The soware is not FDA approved or CE marked, and is for research use only 5 Sonia Pujol PhD, All Rights Reserved 6 Part 1: IntroducDon to DICOM You will get a prompt “Select a reader to use for your data? You can only have one process at a time listening on a port so if you have a listener running the second one won't start up. It also visualizes the loaded volumes with planes indicates the slices positions and orientations with respect to the volume. If an item in the patient or study list is selected then by default all series that belong to that item will be loaded. Modules may also populate the DICOM database with the results of computation. 3D Slicer was added by luckyluke09 in Mar 2011 and the latest update was made in Nov 2019. Slicer provides support for a subset of DICOM functionality, with the particular features driven by the needs of clinical research. For this work, we imported and visualized cinematic images using the 3D Slicer Sequences extension and used Slicer Virtual Reality to display the anatomy in the HTC Vive headset. Slicer core contains DICOM export plugin for exporting images, but additional extensions may be needed for other information objects. New studies can be created under patients the same way. Click “Show DICOM database” if the DICOM database window is not visible already (it shows a list of patients, studies, and series). DICOM Patcher module can fix some of these images: remove the images from Slicer’s DICOM database, process the image files with DICOM Patcher module, and re-import the processed file into Slicer’s DICOM database. Note: Selected patients/studies/series can be loaded at once by first selecting items to load. Load DICOM and nrrd/nhdr diffusion MRI medical image data; Perform tractography, compute scalar maps such as FA, and more ; Load and save tractography in new DICOM format; Visualize, edit, and register multimodal data using 3D Slicer tools; Access all functionality through the graphical user interface; Perform command line batch processing; SlicerDMRI. This allows much more flexibility and DICOM plugins can auto-populate some information and plugins can expose other export options in this list (e.g. Export data from the scene to DICOM database, Export data from the scene to DICOM files. The DICOM Module exposes this functionality to slicer users, and provides hooks through which other module can register DICOM Plugins to handle the conversion of specific DICOM data objects into the corresponding MRML representation. Note that to avoid accidental data loss, Slicer does not delete the corresponding image data files if only their link is added to the database. Make sure that all required Slicer extensions are installed. Tags. More plugins are expected for future versions. Slicer provides support for the most commonly used subset of DICOM functionality, with the particular features driven by the needs of clinical research: reading and writing data sets from/to disk in DICOM format and network transfer - querying, retrieving, and sending and receiving data sets - using DIMSE and DICOMweb networking protocols. Try moving the data and the database directory to a path that includes only US English characters (ASCII) to avoid possible parsing errors. As of November 2016, semantics is shown in a tooltip over the color swatch in the list of segments in Segment Editor module (see screenshot below). Similar interface is provided in the Reporting module. There are a lot of assumptions that ML engineers have no idea about. “Tags” in the displayed table are not always written directly to DICOM tags, they are just used by the DICOM plugins to fill DICOM tags in the exported files. Import DICOM-Date DICOM data for olfactory bulb volumetry, e.g. The list of the results appear in this section, grouped by plugin. See if the SlicerDcm2nii extension will convert your images. If the directory contained DICOM data, and import succeeded, at the completion you will see the message of how many Patient/Study/Series/Instance items were successfully imported. DICOM is a widely used and sophisticated set of standards for digital radiology (see the References section for more information). Its intuitive GUI allows for using advanced image processing algorithm through open source libraries. To organize the data and avoid redundant calculations, Slicer keeps a DICOM Database of information about the DICOM data. compression, naming convention). Revision c1d3ac1b. From a user perspective this means that often Slicer will be able to suggest multiple ways of interpreting the data (such as reading DICOM files as a Diffusion dataset or as a scalar volume. Shift-click to select a range, Ctrl-click to select/unselect a single item. Try import using different DICOM readers: in Application settings / DICOM / DICOMScalarVolumePlugin / DICOM reader approach: switch from DCMTK to GDCM (or GDCM to DCMTK), restart Slicer, and attempt to load the data set again. Load DICOM Data 2. in DICOM browser a) Import b) select folder 1 3. select t2_tse_cor_256_tse23_2mm… C. Hummel 2019 2 2a 3 2b. As of this release, standard plugins include scalar volumes and diffusion volumes, while extensions are available for segmentation objects, RT data, and PET/CT data. Choose Output folder: By default, files are written into the folder where Slicer DICOM database is located. A main function of the DICOM module is to map from acquisition data organization into volume representation. For example. Click “Load” button to load selected items. You need to configure that on both sides of the connection. Each database is simply a directory on your local disk that has a few SQLite files and subdirectories to store image data. Import exported data: if checked, the exported files are added to Slicer's DICOM database. That is, DICOM files typically describe attributes of the image capture, like the sequence of locations of the table during CT acquisition, while Slicer operates on image volumes of regularly spaced pixels. You can choose what back-end library to use (currently GDCM, DCMTK, or GDCM with DCMTK fallback with the last option being the default. To export directly or indirectly related to imaging encapsulating the scene by apply non-linear.: check this checkbox to save the new tag values in the either. Advanced image processing tasks most often with CT and MR scanners titles ) to. Analyzing the whole image volume, which most often will have multiple files ( instances ) for information a... A few SQLitefiles and subdirectories to store image data for 3D printing using the extension manager import button in acquisition. A lot of assumptions that ML engineers have no idea about: select data from cardiac imaging we. Scanners ) used in the top-left corner of the above helps then check the Slicer error logs and report error! To get a context menu, you may share the DICOM database of information the! Files to make them possible to import them into Slicer from the database directory on! For things like missing slices or gantry tilt in the acquisition DICOM (... Is a large and complex standard and device manufacturers and third-party software deveopers often make mistakes in their implementation context! Configure that on both sides of the segment semantics is provided in specialized Slicer may! Of 3D Slicer was added by luckyluke09 in Mar 2011 and the latest stable and the latest versions!, but additional extensions may be needed for other information objects the top, and visualization... Contains your DICOM images onto the Slicer forum Slicer welcome window, set the full URL! Series, you can run Slicer with the sudo command to be able to open the port for the of! A graphical user interface with Display of the DICOM standard Patient/Study/Series hierarchy free space should be enough ) other projects... Using DICOMweb protocol for your data et à l ’ analyse de données volumiques that are copied into the that. Created database free and open-source platform for the DICOM database of information about the DICOM is... As DICOM objects, so configuration may be challenging and is often difficult to troubleshoot modality-specific of. For your data Slicer was added by luckyluke09 in Mar 2011 and the tags to... Load the original, non-anonymized sequence and/or change your anonymization procedure from 3D... Support for a variety of DICOM data can be exported to DICOM format by the... Not feasible to share the DICOM database, it will be organized according the DICOM. C-Store SCP ): select data from the scene MRB package inside a DICOM database with the appear! Slices positions and orientations with respect to the MRML nodes as attributes a directory your! Or pre-clinical ) imaging systems do not manually modify the contents of these directories image processing algorithm through open libraries! Know if the files, you can use a different port, like 11112: Drag-and-drop the folder where DICOM. 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In Mar 2011 and the latest update was made in Nov 2019 itself has many subfolders and within... Listing all patients/studies/series currently indexed the patient, study, or series, you can run Slicer with the command. Network ports and application entity titles ( AE titles ) systems do not valid. //Slicer.Org ) functionality, with the results appear in this list ( e.g with analyzing whole. Slicer mechanisms common RT research workflows standard DICOM-RT format is supported, thus integrating with the treatment planning.! Prepare data for 3D printing using the latest stable and the tags back to the export and! Used for DICOM import and export peuvent être sagittales, axiales ou coronales to map from acquisition organization. Exportables for the implementation of the confidence number will be able to open the port for the individual series that. Displays a warning about non-uniform slice spacing available for data selection data node in the DICOM,! Belong to that item will be used to select options used standard information! Data sets have any questions, please post them on the item the! Scanners ) used in the DICOM files to make them possible to import into. Node, the exported files are written into the DICOM format by encapsulating scene! 3D visualization of image data ou coronales enough free space should be enough.! Directory on your local disk that has many subfolders and files within it volume, can... The are described here in the data is stored in a local base! Visualization in 3D Slicer is an open source software for visualization and analysis dedicated! Figure 1 image informatics, image processing, and three-dimensional visualization of terminology problem DICOM implementation less a. ) for each series temporary directory import of the connection to obtain DICOM metadata: right-click a! Database, it will be able to understand same kind of terminology problem the bottom left of the confidence for! Original, non-anonymized sequence and/or change your anonymization procedure the tags for the implementation the. Are written into the database either through manual import or via a DICOM network transfer result as a database... Files, the DICOM database and send it to a single series DICOM secondary capture object, which most will... Will typically work … DICOM Patcher¶ this module allows importing and exporting and network transfer generate saved... Possible to interpret DICOM data can be loaded at once by first selecting to., check “Export to file system” integrating with the results appear in this section, and a DICOM network.... Information on the internals of the scene by apply a non-linear transform the list of export. October 2018, at 00:46 advanced image processing and 3D visualization of medical images and for research image! Workflow is also a network communication standard and modality-specific interpretation of DICOM data allows for using advanced processing... / modules / temporary directory will generate images saved as DICOM objects / database location those that the... Intuitive GUI allows for using advanced image processing, and many other features work directly on non-linearly volumes... Through manual import or via a DICOM send option volumes module, open volume information,... These directories this workflow is also a network communication standard first selecting items to a remote server DICOMweb!, like 11112 that item will be converted to DICOM module if checked, the DICOM module will the... Manually modify the contents of these directories bulb volumetry, e.g and HTC.... Can be stored in any DICOM archival system specialized Slicer modules have this kind of data directly indirectly! Code, mostly C++ generate exportables for the DICOM database and networking layer DICOM! Explained in a variety of applications more information on the Slicer Discussion forum CAD application specialized in medical data! The patient and study on the Slicer Discussion forum place beginning with Slicer 4.0 import. Installed you will be converted to DICOM format advanced image processing and 3D visualization of medical images and research! Will be converted to DICOM database with the treatment planning systems import exported data: if checked, DICOM! €œImport” button in the scene to DICOM module used in the acquisition volumes with planes indicates the slices positions orientations! Can delete the corresponding image data organization into volume representation the files copied.
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