Slicer Wiki - User contributions [en]

File:PkModelingUI061912.png

2012-06-19T15:40:37Z

EmmaZhu:

Documentation/4.1/Modules/PkModeling

2012-06-19T15:39:55Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|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 ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) calculates quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images. This module performs two operations:
# Converts signal intensities to concentration values. The concentration values are used to calculate quantitative parameters.
# 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

|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI061912.png|thumb|340px|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.

|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.1/Modules/MultiVolumeExplorer]]
* [[Documentation/4.1/Modules/MultiVolumeImporter]]


{{documentation/{{documentation/version}}/module-section|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.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

File:PkModelingUI061212.png

2012-06-12T21:57:04Z

EmmaZhu:

Documentation/4.1/Modules/PkModeling

2012-06-12T21:37:06Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
This is to conver signal intensities to concentration values. The concentration values will be used to calcualte quantitattive parameters next.
* Calculate quantitative parameters from concentration values. These parameters include:
Ktrans: volume transfer constant between blood plasma and EES (extracellular-extravascular space)

Ve: fractional volume for extracellular space

MaxSlope: maximum slope in the time series curve of one voxel

AUC: area under the curve, from bolus arrival time to the end time of interval, normalized by AUC of AIF

|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI061212.png|thumb|340px|PkModeling]]
|
* '''IO'''
** '''Input:''' 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output:''' 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''PkModeling''':
**** T1 Blood Value
**** T1 Tissue Value
**** Relaxivity Value
**** Hematocrit Value
**** 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.

|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.1/Modules/MultiVolumeExplorer]]
* [[Documentation/4.1/Modules/MultiVolumeImporter]]


{{documentation/{{documentation/version}}/module-section|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.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-12T19:38:28Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
This is to conver signal intensities to concentration values. The concentration values will be used to calcualte quantitattive parameters next.
* Calculate quantitative parameters from concentration values. These parameters include:
Ktrans: volume transfer constant between blood plasma and EES (extracellular-extravascular space)
Ve: fractional volume for extracellular space
MaxSlope: maximum slope in the time series curve of one voxel
AUC: area under the curve, from bolus arrival time to the end time of interval, normalized by AUC of AIF

|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI061212.png|thumb|340px|PkModeling]]
|
* '''IO'''
** '''Input:''' 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output:''' 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''PkModeling''':
**** T1 Blood Value
**** T1 Tissue Value
**** Relaxivity Value
**** Hematocrit Value
**** 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.

|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.1/Modules/MultiVolumeExplorer]]
* [[Documentation/4.1/Modules/MultiVolumeImporter]]


{{documentation/{{documentation/version}}/module-section|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.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-05T17:27:45Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
This is to conver signal intensities to concentration values. The concentration values will be used to calcualte quantitattive parameters next.
* Calculate quantitative parameters from concentration values. These parameters include:
Ktrans: volume transfer constant between blood plasma and EES (extracellular-extravascular space)
Ve: fractional volume for extracellular space
MaxSlope: maximum slope in the time series curve of one voxel
AUC: area under the curve, from bolus arrival time to the end time of interval, normalized by AUC of AIF

|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI.png|thumb|340px|PkModeling]]
|
* '''IO'''
** '''Input:''': 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output''': 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''PkModeling''':
**** T1 Blood Value
**** T1 Tissue Value
**** Relaxivity Value
**** Hematocrit Value
**** 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.

|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.1/Modules/MultiVolumeExplorer]]
* [[Documentation/4.1/Modules/MultiVolumeImporter]]


{{documentation/{{documentation/version}}/module-section|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.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-05T16:49:42Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
This is to conver signal intensities to concentration values. The concentration values will be used to calcualte quantitattive parameters next.
* Calculate quantitative parameters from concentration values. These parameters include:
Ktrans: volume transfer constant between blood plasma and EES (extracellular-extravascular space)
Ve: fractional volume for extracellular space
MaxSlope: maximum slope in the time series curve of one voxel
AUC: area under the curve, from bolus arrival time to the end time of interval, normalized by AUC of AIF

|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI.png|thumb|340px|PkModeling]]
|
* '''IO'''
** '''Input:''': 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output''': 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''PkModeling''':
*** Concentration calculation:
**** T1 Blood Value
**** T1 Tissue Value
**** Relaxivity Value
**** Signal Gradient Threshold Value
*** Quantitative parameters calculation:
**** F Tolerance: Function value tolerance
**** G Tolerance: Gradient magnitude tolerance
**** X Tolerance: Search space tolerance
**** Epsilon Value: Step
**** MaxIter Value: Maximum number of iterations
**** Hematocrit Value
**** 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.

|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.1/Modules/MultiVolumeExplorer]]
* [[Documentation/4.1/Modules/MultiVolumeImporter]]


{{documentation/{{documentation/version}}/module-section|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.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-05T16:07:59Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
* Calculate quantitative parameters from concentration values
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI.png|thumb|340px|PkModeling]]
|
* '''IO'''
** '''Input:''': 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output''': 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''Parameters from 4D data''':
*** TR Value: Repetition time,
*** TE Value: Echo time,
*** FA Value: Flip angle,
*** Time Axis: Time series.
** '''Parameters from user input''':
*** Concentration calculation:
**** T1 Blood Value: T1 blood value
**** T1 Tissue Value: T1 tissue value
**** Relaxivity Value: Relaxivity value
**** S0 Gradient Value: Signal gradient threshold value
*** Quantitative parameters calculation:
**** F Tolerance: Function value tolerance
**** G Tolerance: Gradient magnitude tolerance
**** X Tolerance: Search space tolerance
**** Epsilon: Step
**** MaxIter: Maximum number of iterations
**** Hematocrit
**** AUCTimeInterval: Time interval for AUC calculation
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-04T17:52:47Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
* Calculate quantitative parameters from concentration values
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI.png|thumb|340px|PkModeling]]
|
* '''IO'''
** '''Input:''': 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output''': 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''Parameters from 4D data''':
*** TRValue: Repetition time,
*** TEValue: Echo time,
*** FAValue: Flip angle,
*** TimeAxis: Time series.
** '''Parameters from user input''':
*** Concentration calculation:
**** T1BloodValue: T1 blood value
**** T1TissueValue: T1 tissue value
**** RelaxivityValue: Relaxivity value
**** S0GradValue: Signal gradient threshold value
*** Quantitative parameters calculation:
**** FTolerance: Function value tolerance
**** GTolerance: Gradient magnitude tolerance
**** XTolerance: Search space tolerance
**** Epsilon: Step
**** MaxIter: Maximum number of iterations
**** Hematocrit
**** AUCTimeInterval: Time interval for AUC calculation
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

File:PkModelingUI.png

2012-06-04T17:52:03Z

EmmaZhu:

Documentation/4.1/Modules/PkModeling

2012-06-04T17:51:30Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
* Calculate quantitative parameters from concentration values
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|[[Image:PkModelingUI.png|thumb|340px|Brain mask as contour]]
|
* '''IO'''
** '''Input:''': 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output''': 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''Parameters from 4D data''':
*** TRValue: Repetition time,
*** TEValue: Echo time,
*** FAValue: Flip angle,
*** TimeAxis: Time series.
** '''Parameters from user input''':
*** Concentration calculation:
**** T1BloodValue: T1 blood value
**** T1TissueValue: T1 tissue value
**** RelaxivityValue: Relaxivity value
**** S0GradValue: Signal gradient threshold value
*** Quantitative parameters calculation:
**** FTolerance: Function value tolerance
**** GTolerance: Gradient magnitude tolerance
**** XTolerance: Search space tolerance
**** Epsilon: Step
**** MaxIter: Maximum number of iterations
**** Hematocrit
**** AUCTimeInterval: Time interval for AUC calculation
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-04T17:36:18Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
* Calculate quantitative parameters from concentration values
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''IO'''
** '''Input:''': 4D DCE-MRI data in nrrd; 3D mask in nrrd, showing the location of arterial input function.
** '''Output''': 4 volumes in nrrd, showing the maps of quantitative parameters. These parameters are ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''Parameters from 4D data''':
*** TRValue: Repetition time,
*** TEValue: Echo time,
*** FAValue: Flip angle,
*** TimeAxis: Time series.
** '''Parameters from user input''':
*** Concentration calculation:
**** T1BloodValue: T1 blood value
**** T1TissueValue: T1 tissue value
**** RelaxivityValue: Relaxivity value
**** S0GradValue: Signal gradient threshold value
*** Quantitative parameters calculation:
**** FTolerance: Function value tolerance
**** GTolerance: Gradient magnitude tolerance
**** XTolerance: Search space tolerance
**** Epsilon: Step
**** MaxIter: Maximum number of iterations
**** Hematocrit
**** AUCTimeInterval: Time interval for AUC calculation
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-04T17:33:08Z

EmmaZhu:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] 
Acknowledgments:
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. 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu, Jim Miller ({{collaborator|name|ge}}) 
Contact: Yingxuan Zhu, <email>zhuyi@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
|
PkModeling (Pharmacokinetics Modeling) is to calculate the quantitative parameters from DCE-MRI images. The two major parts of it are:
* Convert signal intensities to concentration values
* Calculate quantitative parameters from concentration values
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''IO'''
** '''Input:''': 4D DCE-MRI data in nrrd, 3D mask showing the location of arterial input function.
** '''Output''': 4 volumes showing the maps of quantitative parameters. These parameters include ktrans, ve, maximum slope, and area under the curve (AUC).
* '''Parameters'''
** '''Parameters from 4D data''':
*** TRValue: Repetition time,
*** TEValue: Echo time,
*** FAValue: Flip angle,
*** TimeAxis: Time series.
** '''Parameters from user input''':
*** Concentration calculation:
**** T1BloodValue: T1 blood value
**** T1TissueValue: T1 tissue value
**** RelaxivityValue: Relaxivity value
**** S0GradValue: Signal gradient threshold value
*** Quantitative Parameter calculation:
**** FTolerance: Function value tolerance
**** GTolerance: Gradient magnitude tolerance
**** XTolerance: Search space tolerance
**** Epsilon: Step
**** MaxIter: Maximum number of iterations
**** Hematocrit
**** AUCTimeInterval: Time intervall for AUC calculation
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]

Documentation/4.1/Modules/PkModeling

2012-06-04T16:52:57Z

EmmaZhu:

Documentation/4.1/Modules/PkModeling

2012-06-04T16:51:54Z

EmmaZhu: Created page with ' {{documentation/{{documentation/version}}/module-header}}   {{doc…'

Documentation/4.1/Extensions/PkModeling

2012-06-04T16:44:22Z

EmmaZhu: Redirected page to Documentation/4.1/Modules/PkModeling

#REDIRECT [[Documentation/4.1/Modules/PkModeling]]
[[Category:Documentation/{{documentation/version}}/Extensions]]