Contents

Inobitec DICOM Viewer

6.11. Saving and Opening Segmentation Projects and DTI Projects

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Functionality is available in a separate module which is activated in the Pro edition for an extra fee
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The DICOM Viewer allows for saving segmentation projects and DTI projects in a ﬁle. One project may contain structures and DTI data from diﬀerent series, as well as source DICOM data. If a project was saved without source DICOM data, it cannot be opened without downloading the corresponding series ﬁrst.

Save segmentation project to ﬁle and Open segmentation project from ﬁle buttons (shown with the red frame in Fig. 6.34) are located on the segmented structures panel.

Figure 6.34: Project management buttons

6.11.1 Saving a Project

To enable/disable the saving of source DICOM data, on the main menu, select Options->Settings...->Modules->3D reconstruction, then choose the Project tab and check/uncheck the Save DICOM data of series box. This option is activated by default.

Figure 6.35: 3D reconstruction settings

The DEFAULTS button restores the checkbox Save DICOM data of series.

Click OK to apply the settings or CANCEL to cancel.

To save a project, click the Save segmentation project to ﬁle button on the segmented structures panel. In the dialog box that pops up, provide the path to the ﬁle and the ﬁle name. Click OK to save or Cancel to cancel. The project ﬁle has (spj) extension.

Orientation and projection data on the model are saved in the project. The orientation and projection of the model is restored when the project is opened.

If the project is opened in the MPR reconstruction tab, the following characteristics are restored:

cutting planes turn and arrangement;

model position;

model scale.

The turn of the model slice in the MPR reconstruction tab is not restored.

If the project is opened in the Volume reconstruction tab or in the 3D view window of the MPR reconstruction tab, the following characteristics are restored:

model turn;

model position;

model scale;

projection type.

If the project was saved in the MPR reconstruction tab and opened in the Volume reconstruction tab, the parameters that can be applied only to the 3D view window are restored.

The markers — Marker, Line marker, or Polygonal line marker — are saved in the project for each layer. The length and angle measurements performed with polygonal marker lines are saved in the project ﬁle. The work with markers is described in Section 5.12.

6.11.2 Saving Projects Automatically

Segmentation projects are saved automatically to prevent loss of data as a result of a program crash caused by a technical failure or the user’s actions. Autosave and data recovery are available in MPR reconstruction and Volume reconstruction tabs.

If the license for the extended segmentation module is active and it is the ﬁrst time the user adds, deletes or edits

a segmented structure or base volume;

a surface for a segmented structure or base volume;

a group of ROI DTI, or individual ROI DTI;

a marker (except for segmented structure markers),

in the MPR reconstruction or Volume reconstruction tab, then a dialog box for segmentation projects autosave activation (Fig. 6.36) will pop up.

Figure 6.36: Dialog box for segmentation projects autosave activation

Click YES to enable segmentation projects autosave or NO to cancel.

To enable/disable segmentation projects autosave, on the main menu, select Options->Settings...->Modules->3D reconstruction, then choose the Project tab (Fig. 6.35) and check/uncheck the Enable autosaving box. By default, segmentation projects autosave is disabled. On the Timeout dropdown list, select autosave frequency. The default value is ﬁve minutes.

Autosave option is available only when the extended segmentation module is activated. If the extended segmentation module is not activated, the Enable autosaving option is automatically disabled.

Segmentation projects are automatically saved in the background mode without blocking the interface. Autosave frequency may be selected on the Timeout dropdown list.

When a segmentation project is saved automatically, a ﬁle with .autospj extension is created in a temporary system folder. This ﬁle contains:

segmentation results;
DICOM data source information.

The DICOM data source may be:

a local storage;
a folder with DCM ﬁles;
a DICOMDIR ﬁle;
an XML ﬁle;
a third-party SPJ ﬁle;
an archive with DCM ﬁles.

The data concerning the changes in the base volume in diﬀerent tabs working with the current segmentation project are saved as separate segmented structures. If the user works with the same segmentation project in several MPR reconstruction or Volume reconstruction tabs, the data are automatically saved in the same ﬁle.

If a segmentation project is saved manually with the help of the Save segmentation project to ﬁle button on the segmented structures panel (see Section 6.11.1), the .autospj ﬁle is deleted automatically.

When the user closes the last tab of a segmentation project with unsaved changes, a dialog box for saving the project changes (Fig. 6.37) will pop up.

Figure 6.37: Dialog box for saving the changes in a segmentation project

Click SAVE to save the changes in the project or DISCARD to close the tab without saving the changes. To resume work on the project, click CANCEL. After the project has been saved or the changes have been discarded, the .autospj ﬁle is deleted automatically.

6.11.3 Resuming Work with Segmentation Projects

If the segmentation projects autosave option is enabled, an .autospj ﬁle is created and saved in a temporary folder.

The name of the .autospj ﬁle is generated as follows: <patient name>_<description of the 1st layer series>_…_<description of the n layer series>_ <project #>_<time and date>.autospj, where <project #> — is the unique number that is automatically assigned to a segmentation project for a series or a fused series,
and <time and date> — is the time and date of the ﬁle creation in hhmmssddMMyyyy format, where "hh" stands for hours, "mm" — for minutes, "ss" — for seconds, "dd" — for the day, "MM" — for the month, and "yyyy" — for the year.
The maximum length of the autospj ﬁle name is 100 characters. If this limit is exceeded, the name will be cropped and a "∼" symbol will be placed before _<project #>_<time and date>.

Figure 6.38: Dialog box with crash recovery settings

In case of the program crash, the project ﬁle is restored automatically when the DICOM Viewer is launched again. If there is an .autospj ﬁle in the temporary folder, it is decided that the project must be restored, and a dialog box for resuming work with the last autosaved version of the segmentation project pops up (Fig. 6.38).

In the Disaster recovery settings dialog box, check the autosaved ﬁles for the projects that have to be restored. If none of the ﬁles has been selected, the OK button is inactive. You can choose the mode in which the restored project will be opened: 3D, MPR or Both. Click OK to open the selected segmentation project in the mode speciﬁed or CANCEL to cancel.

If there are several projects, work with them will be resumed in the order in which .autospj ﬁles are listed in the Disaster recovery settings dialog box. If any of the projects cannot be restored, it does not aﬀect the other projects.

If you click CANCEL, .autospj ﬁles are deleted from the temporary folder.

An .autospj ﬁle contains only the information on the third-party DICOM data source. If this source cannot be accessed, the segmentation project cannot be restored.

If the user cannot resume work with any of the segmentation projects as the DICOM data for the series are unavailable, a dialog box will pop up advising to save the data from the autosave ﬁle to a separate .spj ﬁle on the disk. After the user conﬁrms that the data must be saved, a standard Save As dialog box pops up. The name of the ﬁle and its location are to be speciﬁed by the user.

After the ﬁle is saved or the user chooses not to save it, the .autospj ﬁle is deleted from the temporary folder.

6.11.4 Opening a Project with Source DICOM Data

When a project is opened, the DICOM Viewer shows it in the Volume Reconstruction or Multiplanar Reconstruction tab. To choose a default tab, on the main menu, select Options->Settings...->Modules->3D reconstruction, then choose the Project tab (Fig. 6.35), and choose the 3D, MPR or Both opening mode. The 3D mode is chosen by default.

The DEFAULTS button restores the checkbox Save DICOM data of series.

Click OK to apply the settings or CANCEL to cancel.

Orientation and projection data on the model are saved in the project. The orientation and projection of the model is restored when the project is opened. For more information, see Section 6.11.1.

There are three ways to open a project containing source DICOM data in the default tab:

Choose the Open project... option in the File menu. Select the project ﬁle in the window that pops up. Click Open to open the project or Cancel to cancel.
Double-click with the left mouse button on the project ﬁle in the Explorer window. This function is available by default only on Windows OS. On macOS and Linux, you have to use the system functions to create a link between (spj) format and the DICOM Viewer software.
Drag and drop the project ﬁle to the DICOM Viewer shortcut (this option is only available on Windows and macOS). If you drag and drop several project ﬁles to the DICOM Viewer shortcut, each ﬁle will be opened in a separate tab.

To open a part of the project and specify the tab in which it is to be opened, proceed as follows:

On the main menu, select File->Open project as.... A window will pop up, in which you will have to choose the ﬁle containing the project for this series. Click Open to open the project or Cancel to cancel the action. The dialog box shown in Fig. 6.39 will pop up.
Choose the tab in which you want to open the project (3D, MPR or Both). The selected mode will be set by default.
Select the series in the Series list box that need to be opened. By default, all series of the project are selected. Uncheck the box against the series if you don’t want it to be opened in the project.
The order in which the series are displayed is important for working with the project. By default, the series are displayed in the Series list in the same order as when the segmentation project was saved. To change the series order, highlight a series in the Series list box. Use Move up and Move down buttons (indicated by the red frame in Fig. 6.39) to move the selected series up or down.
Click OK to open the project or CANCEL to cancel the operation.
The ﬁrst series on the Series list is considered to be the basic series.
- The basic series on the MPR tab is displayed as the background layer behind the other layers. The background layer is ﬁxed. The center of the background layer coincides with the center of the window. You can move the layers about the background layer or each other with the help of the tools you see on the Fusion of layers panel. The procedure of merging layers is described in Section 4.3.
- The project opened in the volume reconstruction window is displayed as 3D models created independently of each other. The basic series of the project is displayed as a 3D model ﬁxed at the point of origin which is at the same time the center of the model. The models from other series are located in space with respect to the ﬁrst layer model. The change of the order of the layers at the time of opening the project does not aﬀect the mutual arrangement of the models.

If the project does not contain any source DICOM data, when you attempt to open it, an error notiﬁcation will pop up: Cannot ﬁnd DICOM data in the project ﬁle. The procedure of opening projects without DICOM data is described in Section 6.11.5.

Figure 6.39: Dialog box for selecting the project opening parameters

6.11.5 Opening a Project without Source DICOM Data

To open a project without source DICOM data, you ﬁrst need to open the source data in the Volume Reconstruction or Multiplanar Reconstruction tab.

To open a project that does not contain any source data:

Open the initial series for which the project was saved in the Volume Reconstruction or Multiplanar Reconstruction tab.

Open the segmented structure panel by clicking the button.

Click the Open segmentation project from ﬁle button on the segmented structure panel. A window will pop up, in which you will have to choose the ﬁle containing the project for this series. Click Open to open the project or Cancel to cancel the operation.

Orientation and projection data on the model are saved in the project. The orientation and projection of the model is restored when the project is opened. For more information see Section 6.11.1.

The segmented structures and DTI data for this series contained in the project are added to the segmented structure panel. When the project is opened for the second time, the data are added again without replacing the old data. When the structures are edited on the segmentation panel, the ﬁle contents are not changed. If a project ﬁle contains data for several series, only the data referred to the series that is currently open on the volume or multiplanar reconstruction tab will be added.