DICOM Plugin

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The DICOM plug-in allows to load and visualize DICOM data.

To get more information you can watch these videos:

For Users

Working Area

Description: All DICOM data is represented as a tree in the DICOM Tree Viewer, to facilitate the visualization of patient, study, series and time point data. Using the Space and Time sliders it is possible to navigate through all available slices and timepoints. Click on the “Import” button to add the selected 2D, 3D or 4D (3D + t) images to the Data Tree. In this way they are converted into vtk format and ready to be rendered in other plugins.

Author: Jakub Lyko, Xavi Planes

DICOM Plugin

From the File menu it is possible to load DICOM Files, DICOM Directories, DICOMDIR files. The same operations can be done using the quick access buttons available in the DICOM IO Toolbar.

Dicom IO Toolbar

Browse DICOM Tags

Description: DICOM Browser functionality allows browsing DICOM entries, DICOM entry sequences and management of DICOM time series

Author: Yves Martelli

Browse tags

Browse tags shows all tags in a tree view. When a tag is a sequence, all child items will be appended to the parent item.

In order to facilitate the DICOM tags browsing, the "Browse Tags" window allows to show only the tags that have changed from the previous DICOM slice. This feature can be used to identify the time tag of your DICOM dataset, selecting a DICOM slice from one timepoint, selecting the next slice from another timepoint and check the tags that are changing its value.

PACS Connection

Description: PACS connection tool allows to connect to a PACS server to query/retrieve/send images.

Author: Jakub Lyko

PACS Connection tool

Added possibility to connect to ClearCanvas PACS server that you can install for free here.

CCLogo.png

You can query the database and retrieve a single serie.

Retrieve images from ClearCanvas server

DICOMRT

Is possible to read DICOMRT studies. RTSTRUCT, RTDOSE can be read as images.

  • RTSTRUCT contains the structures defined by the user, like heart of lumb. These structures will be added to GIMIAS as a mask image. This allows to use ROI statistics processing tool to extract statistics from each structure, like volume, maximum dosis and minimum dosis
  • RTDOSE contains the quantity of dosis applied to the patient
DICOMRT

In this image you can see the initial CT image, several structures and the dosis image.

At the right you can see the ROI statistics panel widget. To compute the volume or min/max dose of a structure, you should select the dose image and the desired structure. Setting the check box "Export histogram", is possible to export the histogram inside the structure.

At the bottom you can see the signal viewer with the histograms of heart, left Lumb, tumor bed and tumor bed block. You can see that the dose of heart and lumb is low and the dose of tumor is high.

For developers

DICOM time series (3D+T)

DICOM data sets from different manufacturers have been tested with GIMIAS:

  • GE Medical Systems: CT and MR modalities
  • Philips Medical Systems: CINE MR, PERFUSION MR and US modalities
  • Siemens: CT and MR modalities from the machines Sensation 64, Symphony, TrioTim and Somatom
  • Toshiba: CT modality

Configure your DICOM time tag

You can configure your DICOM time tag that will be used to group the DICOM slices in time points. Using the file DICOMTags.xml that you will find in the resource folder, you can add your own configuration for you own file:

    <tag name="ge_mr" type="class blSmartPointer<class blTagMap>">Unsupported value type
        <tagmap size="4">
            <tag name="condition0" type="std::string">0008,0060:MR</tag>
            <tag name="condition1" type="std::string">0008,0070:ge medical systems</tag>
            <tag name="time_tag" type="std::string">0018,1060:Trigger Time</tag>
            <tag name="in_file" type="bool">1</tag>
        </tagmap>
    </tag>

For each entry, you can define any number of conditions that must be satisfied by the first DICOM file of your dataset. Once all conditions are satisfied, the time tag will be used. The entries are sorted from the major to the minor number of conditions.

To detect the DICOM time tag, you can use the option "Scan Time Tag" in Advanced window and select the tag manually. File:DICOMAdvanced.png

Regular expressions

Added the possibility to provide a regular expression to extract parts of a DICOM time tag value. The regular expressions followsthe ITK (limited) syntax, see [RegularExpression.h] for details. Every modality tag can have an associated regular expression by adding a "%modality%_regex" tag. Some tags are not available at an image level, as for example the Scan Options, in that case, the user needs to specify that the tag needs to be find in the DICOM file with the "%modality%_isinfile" tag. See the following example usage:

<tag name="CT" type="std::string">0018,0022:Scan Options</tag>
<tag name="CT_isinfile" type="bool">1</tag>
<tag name="CT_regex" type="std::string">([0-9]+)</tag>

Another example for truncating an UID to remove its last bit can be:

<tag name="CT" type="std::string">0008,0018:SOP Instance UID</tag>
<tag name="CT_regex" type="std::string">([0-9]+\.)+</tag>

You can also use regular expression for any condition:

<tag name="condition2" type="std::string">0018,1030:.*PERF.*</tag>

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