View source for PET-CT/Documentation/Modules/GuidedInterventionPETCT

= Introduction and Acknowledgements =
Authors: Andinet Enquobahrie [http://www.kitware.com Kitware], Guillaume Sala, [http://www.kitware.com Kitware], Rahul Khare, [http://www.childrensnational.org ChildrensNational], Julien Finet [http://www.kitware.com Kitware], Dženan Zukić [http://www.kitware.com Kitware]<br>
Acknowledgements: This work is supported by NIH grants 2R42CA153488-02A1, R41CA153488-01 and 3R42CA153488-03S1 "Improving liver lesion biopsy in the CT suite through fusion with PET images"<br>
Contact: Andinet Enquobahrie, Dženan Zukić<br>

= Module Description =

The GuidedInterventionPETCT is a workflow-based module that guides the user in a step-by-step interface to realize a guided biopsy after fusing respiratory-compensated PET/CT with images in the interventional CT suite.<br>
In each step of the workflow we prepare the necessary requirements to fulfill the end goal, following a given pipeline: Registration of the different volumes acquired, establishing the connection between the tracking device and Slicer, registration of the coordinate system of the tracking system and the registered volume and live tracking of the needle in Slicer.<br>
This module uses existing modules to accomplish some of the steps:<br>
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/OpenIGTLinkIF OpenIGTLinkIF]
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/Annotations Annotations]
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/FiducialRegistration Fiducial Registration]
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/VolumeResliceDriver Volume Reslice Driver]
*[[PET-CT/Documentation/Modules/Pivot_Calibration | Pivot Calibration]]

= Use Cases =

<gallery widths=300px perrow=3>
Image:GuidedPETCTWorkflowStep1.png|Step1: Load Data
Image:GuidedPETCTWorkflowStep2.png|Step2: Registration PET/CT and interventional CT
Image:GuidedPETCTWorkflowStep3.png|Step3: OpenIGTLinkIF
Image:GuidedPETCTWorkflowStep4.png|Step4: Pivot Calibration
Image:GuidedPETCTWorkflowStep5.png|Step5: Tracker to CT registration
Image:GuidedPETCTWorkflowStep6.png|Step6: Path planner
Image:GuidedPETCTWorkflowStep7.png|Step6: Guidance
</gallery>

= Panels =

== Loading Step ==
{| width="100%"
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The loading step is the first step of the workflow. The user selects the data that is going to be used for the guided biopsy.<br>
Read [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/LoadingData here] the instructions to load data into Slicer.<br>

* '''MC PET Volume''': This combobox allows selecting the motion-compensated PET scans.
* '''MC CT Volume''': This combobox allows selecting the motion-compensated CT scans.
* '''CBCT Volume''': This combobox allows selecting the interventional CT Scan.

The volumes in these comboboxes will be used to compute the image registration, between the pre-operative PET/CT acquisition and the interventional CT. The fused PET and interventional CT images will guide the biopsy procedure.

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|[[File:GuidedPETCTWorkflowStep1Panel.png|thumb|300px|Loading data panel]]
|}

== Volume Registration Step ==
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In this step we compute the image registration of the motion-compensated PET/CT and interventional CT.<br>
The user can tweak initial position and orientation - in case that the automatic registration fail or to make it converge faster.<br>

* '''Sampling percent''': Percentage of voxels which are sampled to calculate registration metric
* '''Precise rigid phase''': Should a higher-resolution rigid registration be conducted in addition to low resolution rigid registration?
* '''BSpline''': Should a BSpline registration be conducted in addition to rigid registration?
* '''Grid Size''': Number of divisions for BSpline registration. Bigger number mean more degrees of freedom, implying slower registration with a potential for higher precision.

* '''Start Registration''': Push Button to start the registration with the volumes selected in the previous step.

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|[[File:GuidedPETCTWorkflowStep2Panel.png|thumb|300px|Volume Registration panel]]
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== OpenIGTLinkIF Step ==
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In this step of the workflow we establish the link between Slicer and the tracking system.<br>
To establish this connection we import the OpenIGTLinkIF module of Slicer.
For more information about the use of this module please see the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/OpenIGTLinkIF OpenIGTLinkIF] documentation.<br>
One method to establish the connection is using IGSTK:<br>
*Run the executable [http://public.kitware.com/IGSTKWIKI/index.php/Using_OpenIGTLink_in_IGSTK#Broadcast_Tracking_data_using_OpenIGTLink OpenIGTLinkTrackerBroadcasting] giving a configuration file for the given tracking system (e.g [[Media:IGSTK_polarisHybridConfiguration.xml|Polaris configuration file]], [[Media:IGSTK_micronConfiguration.xml|Micron configuration file]])

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|[[File:GuidedPETCTWorkflowStep3Panel.png|thumb|300px|OpenIGTLinkIF panel]]
|}

== Pivot Calibration Step ==
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This section allows the user to run a pivot calibration algorithm on the tracker device (whose connection was establish on the previous step). To accomplish this, we import the existing PivotCalibration module.<br>
For more information about the use of this module please see the [[PET-CT/Documentation/Modules/Pivot_Calibration | Pivot Calibration]] documentation.<br>

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|[[File:GuidedPETCTWorkflowStep4Panel.png|thumb|300px|Pivot calibration panel]]
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== Hardware Registration Step ==
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This step allows the user to run a fiducial registration to transform the tracker coordinate system to the registered volume (PET/CT scans with the interventional CT scans) coordinate system.<br>
To run the fiducial registration we need to create two fiducial lists (TrackerMarkers and CTMarkers) containing respective points in the different coordinate system.

For more information about the fiducial registration, please see the documentation [http://www.slicer.org/slicerWiki/index.php/Documentation/4.5/Modules/FiducialRegistration here].<br>

* '''Acquire 1 tracker fiducial''': This button allows the user, by clicking on it, to create a new fiducial at the current position of the tracking device, and adding it to the "TrackerMarkers" list.

* '''Place 1 image fiducial''': The user needs to place the fiducials on the CT volume (in a position corresponding to TrackerMarkers) to be able to run the registration.<br> 
* '''Register''': This button allows the user to call the fiducial registration CLI module with two fiducial lists previously filled.

|[[File:GuidedPETCTWorkflowStep5Panel.png|thumb|300px|Hardware registration panel]]
|}

== Path Planner ==
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In this step the guidance path can be planned. "Place target" and "Place entry point" buttons allow the user to choose those points in the PET/CT fused image using mouse. "Entry from needle tip" allow entry point to be taken from the current needle tip position (usually after the interventional radiologist has placed it on the skin of the patient). Clicking on positions in the "RAS" row jumps all the slices to that position (target or entry point).

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|[[File:GuidedPETCTWorkflowStep6Panel.png|thumb|300px|Path planner panel]]
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== Guidance ==
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This is the last step of the workflow. It displays 4 slice views: axial, sagittal, a slice through the needle, and a slice perpendicular to the needle, all according to the position of the tracker device. The panel allows control over visual properties of the needle, rotation of bottom-right slice and saving of statistical data and screenshots. The data is saved to computer user's home folder (''C:\Users\username'', ''/home/username'', etc depending on the operating system).

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|[[File:GuidedPETCTWorkflowStep7Panel.png|thumb|300px|Guidance panel]]
|}