Difference between revisions of "Documentation/4.1/Modules/PkModeling"

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Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]]<br>
 
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]]<br>
 
Acknowledgments:
 
Acknowledgments:
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This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research.<br>
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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.<br>
 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research.<br>
 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research.<br>
 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}})<br>
 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}})<br>
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PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
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PkModeling (Pharmacokinetics Modeling) calculates quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images. This module performs two operations:  
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* Convert signal intensities to concentration values
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# Converts signal intensities to concentration values. The concentration values are used to calculate quantitative parameters.
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* Calculate quantitative parameters from concentration values
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# Calculates quantitative parameters from concentration values. These parameters include:
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;Ktrans: Volume transfer constant between blood plasma and EES (extracellular-extravascular space) at each voxel
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;Ve: Fractional volume for extracellular space at each voxel
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;MaxSlope: Maximum slope in the time series curve of each voxel
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;AUC: Area under the curve of each voxel, measured from bolus arrival time to the end time of interval, normalized by the AUC of the AIF
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|[[Image:PkModelingUI.png|thumb|340px|Brain mask as contour]]
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|[[Image:PkModelingUI061912.png|thumb|340px|PkModeling]]
 
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* '''IO'''
 
* '''IO'''
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** '''Input:''': 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
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** '''Input:''' 4D DCE-MRI data; 3D mask showing the location of the arterial input function.
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** '''Output''': 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
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** '''Output:''' 4 volumes showing the maps of quantitative parameters: ktrans, ve, maximum slope, and area under the curve (AUC).
 
* '''Parameters'''
 
* '''Parameters'''
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** '''Parameters from 4D data''':
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** '''PkModeling''':  
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*** TRValue: Repetition time,
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*** T1 Blood Value
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*** TEValue: Echo time,
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*** T1 Tissue Value
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*** FAValue: Flip angle,
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*** Relaxivity Value
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*** TimeAxis: Time series.
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*** Hematocrit Value. Volume percentage of red blood cells in blood.
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** '''Parameters from user input''':  
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*** AUC Time Interval Value: Time interval for AUC calculation
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*** Concentration calculation:
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** '''Acquisition''':
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**** T1BloodValue: T1 blood value
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*** TR Value: Repetition time,
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**** T1TissueValue: T1 tissue value
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*** TE Value: Echo time,
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**** RelaxivityValue: Relaxivity value
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*** FA Value: Flip angle,
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**** S0GradValue: Signal gradient threshold value
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*** Time Axis: Time series.
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*** Quantitative parameters calculation:
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**** FTolerance: Function value tolerance
 
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**** GTolerance: Gradient magnitude tolerance
 
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**** XTolerance: Search space tolerance
 
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**** Epsilon: Step
 
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**** MaxIter: Maximum number of iterations
 
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**** Hematocrit
 
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**** AUCTimeInterval: Time interval for AUC calculation
 
 
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
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* [[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolumeExplorer]]
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* [[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolumeImporter]]
  
 
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{{documentation/{{documentation/version}}/module-section|References}}
 
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* Knopp MV, Giesel FL, Marcos H et al: Dynamic contrast-enhanced magnetic resonance imaging in oncology. Top Magn Reson Imaging, 2001; 12:301-308.
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* Rijpkema M, Kaanders JHAM, Joosten FBM et al: Method for quantitative mapping of dynamic MRI contrast agent uptake in human tumors. J Magn Reson Imaging 2001; 14:457-463.
  
 
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Latest revision as of 07:28, 14 June 2013

Home < Documentation < 4.1 < Modules < PkModeling


For the latest Slicer documentation, visit the read-the-docs.



Introduction and Acknowledgements

Extension: PkModeling
Acknowledgments: 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.
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research.
Author: Yingxuan Zhu, Jim Miller (GE)
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email>

GE Global Research  
National Alliance for Medical Image Computing (NA-MIC)  

Module Description

PkModeling (Pharmacokinetics Modeling) calculates quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images. This module performs two operations:

  1. Converts signal intensities to concentration values. The concentration values are used to calculate quantitative parameters.
  2. Calculates quantitative parameters from concentration values. These parameters include:
Ktrans
Volume transfer constant between blood plasma and EES (extracellular-extravascular space) at each voxel
Ve
Fractional volume for extracellular space at each voxel
MaxSlope
Maximum slope in the time series curve of each voxel
AUC
Area under the curve of each voxel, measured from bolus arrival time to the end time of interval, normalized by the AUC of the AIF

Use Cases

Tutorials

Panels and their use

PkModeling
  • IO
    • Input: 4D DCE-MRI data; 3D mask showing the location of the arterial input function.
    • Output: 4 volumes showing the maps of quantitative parameters: ktrans, ve, maximum slope, and area under the curve (AUC).
  • Parameters
    • PkModeling:
      • T1 Blood Value
      • T1 Tissue Value
      • Relaxivity Value
      • Hematocrit Value. Volume percentage of red blood cells in blood.
      • AUC Time Interval Value: Time interval for AUC calculation
    • Acquisition:
      • TR Value: Repetition time,
      • TE Value: Echo time,
      • FA Value: Flip angle,
      • Time Axis: Time series.

Similar Modules

References

  • Knopp MV, Giesel FL, Marcos H et al: Dynamic contrast-enhanced magnetic resonance imaging in oncology. Top Magn Reson Imaging, 2001; 12:301-308.
  • Rijpkema M, Kaanders JHAM, Joosten FBM et al: Method for quantitative mapping of dynamic MRI contrast agent uptake in human tumors. J Magn Reson Imaging 2001; 14:457-463.

Information for Developers

Work in progress
 Section under construction.
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