Slicer Wiki - User contributions [en]

Documentation/4.5/Modules/DSC MRI Analysis

2016-01-07T22:23:08Z

Stevedaxiao:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

{|
|
[[Image:DSC logo.png | 100px]]
|
Extension: [[Documentation/{{documentation/version}}/Extensions/DSC_MRI_Analysis|DSC_MRI_Analysis]] 

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, and by National Cancer Institute as part of the Quantitative Imaging Network initiative (U01CA154601) and QIICR (U24CA180918). 

Implementation of the DSC MRI Analysis was contributed by Xiao Da from MGH. 

Author: Xiao Da (MGH), Yangming Ou (MGH), Andriy Fedorov (BWH), Steve Pieper (Isomics), Jayashree Kalpathy-Cramer (MGH) 
Contact: Xiao Da, <email>XDA@mgh.harvard.edu</email> 
|}

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|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
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|{{collaborator|logo|martinos}}|{{collaborator|longname|martinos}}
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{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dynamic Susceptibility Contrast (DSC) MRI imaging is an important functional imaging method that enables quantitative assessment of tissue hemodynamic patterns. Abnormality of blood flow, volume and permeability is frequently observed during tumor growth, and characterization of these perfusion attributes has become clinically important for both diagnosis and therapy planning. In the context of glial neoplasms, perfusion characteristics have been shown to correlate with tumor type and grade and hence influence treatment decisions. 
DSC MRI imaging is based on the principle that flow of a paramagnetic contrast agent through a capillary bed will transiently change the magnetic susceptibility of the given tissue. Decreased signal intensity on spin-echo or gradient-echo images after the first pass of the contrast agent, frequently described as susceptibility-induced T2* shortening, is the result of this temporal change in magnetic susceptibility. This signal time curve is then converted into a concentration time curve, and use of tracer kinetic analysis various hemodynamic variables, such as cerebral blood volume, cerebral blood flow, and mean transit time, as well as metrics that address vessel leakage may be estimated. Combined, these metrics enable microvascular imaging, providing a visual correlate of blood flow, volume, and vessel permeability.




{{documentation/{{documentation/version}}/module-section|Use Cases}}
*Estimation of quantitative parameters(rCBV,rCBF and MTT) from DSC MRI.
*Guide diagnosis, prognosis and therapy planning.
*Brain Tumor, Stroke, Adrenoleukodystrophy and other diseases.
{|
|[[Image:DSC Result.png|thumb|500px|Framework to Estimate DSC Parametric Maps]]
|}


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

{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:DSC GUI V0.png|thumb|400px|DSC MRI Analysis GUI]]
|
* '''PkModeling Parameters''':
** '''CBF/CBV Time Interval Value''': Time interval for CBF/CBV calculation.
** '''Use Population AIF''': A mean AIF is calculated from a functional form instead of from the input using the aifMask or a prescribed AIF.
* '''IO'''
** '''Input 4D image''': 4D DSC MRI Image.
** '''ROI Mask Image''': Mask designating the location for DSC analysis.
** '''AIF Mask Image''': Mask designating the location of the arterial input function (AIF). AIF can either be calculated from the input using the aifMask, prescribed directly in concentration units using the prescribedAIF option, or via a population AIF.
** '''Prescribed AIF''': Prescribed arterial input function (AIF).
** '''Output K2 image''': Leakage map.
** '''Output RCBV image''': Relative Cerebral Blood Volume (rCBV) map.
** '''Output RCBF image''': Relative Cerebral Blood Flow (rCBF) map.
** '''Output MTT image''': Mean Transit Time (MTT) map.
*'''Advanced options'''
** '''BAT Calculation Mode''': PeakGradient(Default) or UseConstantBAT.
** '''Constant BAT''': Constant bolus arrival time value.
** '''Output Bolus Arrival Time Image''': The bolus arrival time calculated at each pixel.
** '''Output Concentration 4D Image''': Delta R2* concentration image.
** '''Output Fitted Data 4D Image''': Fitted Delta R2* concentration image.
|}


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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://www.healthcare.siemens.com/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/groups/public/@global/@imaging/@mri/documents/download/mdaw/mtix/~edisp/brain_perfusion_how_why-00093544.pdf Introduction of DSC MRI from Siemens]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657863/ Equations for conversion of signal to concentration for DSC]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208985/pdf/nihms596683.pdf Other method to investigate DSC MRI]
* [http://www.ncbi.nlm.nih.gov/pubmed/16611779 Leakage correction for DSC MRI]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
* [https://github.com/QIICR/DSC_Analysis Source code for analysis of DSC MRI]


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

Documentation/Nightly/Modules/DSC MRI Analysis

2016-01-07T22:22:08Z

Stevedaxiao:

File:DSC Result.png

2016-01-07T22:16:08Z

Stevedaxiao: Stevedaxiao uploaded a new version of File:DSC Result.png

Documentation/Nightly/Modules/PkModeling

2016-01-04T21:26:29Z

Stevedaxiao:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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, and by National Cancer Institute as part of the Quantitative Imaging Network initiative (U01CA151261) and QIICR (U24CA180918). 
Implementation of the pharmacokinetics modeling was contributed by Yingxuan Zhu and Jim Miller from GE Research. 
Author: Yingxuan Zhu (while at GE), Andrey Fedorov (SPL), John Evans (MGH), Jim Miller ({{collaborator|name|ge}}) 
Contact: Jim Miller, <email>millerjv@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
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|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
}}

{{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 (min^-1)
;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}}
* estimation of quantitative perfusion parameters from DCE MRI
* treatment response evaluation
* breast, prostate, brain DCE MRI analysis
{|
|[[Image:BC1_DCE.png|thumb|340px|Sample frame from a breast DCE MRI dataset (one of the datasets presented in a study by Huang et al. [6]]]
|[[Image:BC1_Ktrans_map_ROI.png|thumb|340px|Ktrans map result of PK modeling using population AIF (Parker et al., [5])]]
|-
|[[Image:QIN-PROSTATE-2_DCE.png|thumb|340px|Sample frame from a prostate DCE MRI dataset (QIN-PROSTATE-002 from TCIA QIN-PROSTATE collection)]]
|[[Image:QIN-PROSTATE-2_Ktrans_map_ROI.png|thumb|340px|Ktrans map result of PK modeling using population AIF (Parker et al., [5])]]
|}


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


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

{|
|[[Image:PkModelingUI061912.png|thumb|340px|PkModeling]]
|
* '''PkModeling Parameters''':
** T1 Blood Value (milliseconds)
** T1 Tissue Value (milliseconds) (default value is the published value for prostate tissue estimated in healthy individuals (see Ref. de Bazelaire et al.)
** r1 Relaxivity Value of the contrast agent, L x mol^(-1) x s^(-1). This value is contrast agent specific. Default setting of 0.0039 corresponds to Gd-DPTA (Magnevist) at 3T, see Ref. Pintaske et al. You will need to adjust this setting based on the magnet signal strength and contrast agent.
** Hematocrit Value. Volume percentage of red blood cells in blood.
** AUC Time Interval Value: Time interval for AUC calculation
** Use Population AIF: A mean AIF is calculated from a functional form instead of from the input using the aifMask or a prescribed AIF. See Ref. Parker et al.
* '''IO'''
** '''Input 4D Image''': 4D DCE-MRI data
** '''T1 Map Image''': T1 Map
** '''AIF Mask Image''': Mask designating the location of the arterial input function (AIF). AIF can either be calculated from the input using the aifMask, prescribed directly in concentration units using the prescribedAIF option, or via a population AIF.
** '''Prescribed AIF''': Prescribed arterial input function (AIF). AIF can either be calculated from the input using the aifMask option, via a population AIF, or can be prescribed directly in concentration units using the prescribedAIF option. An example of how a prescribed AIF can be defined is in [[File:AIF_example.mcsv.zip|this example .mcsv file]] (unzip before importing into Slicer!). Note that the x column corresponds to timestamps in seconds, and the y column is the contrast agent concentration (NOT image signal intensity).
** '''Output Ktrans image''': volume transfer constant between blood plasma and extravascular extracellular space (EES) (min^-1)
** '''Output ve image''': volume of EES per unit volume of tissue
** '''Output fpv image''': (or v_p) blood plasma volume per unit of tissue
** '''Output maximum slope image''': maximum slope of the signal intensity curve between any two consecutive timepoints
** '''Output AUC image''': area under the curve in the first 90 seconds
* '''Advanced options''':
** '''BAT Calculation Mode''': PeakGradient (Default) or UseConstantBAT
** '''Constant BAT''': Constant Bolus Arrival Time Index (frame number)
** '''Output R-squared goodness of fit image''': each pixel will be initialized to a value between 0 and 1 characterizing the goodness of fit. Larger values correspond to a better fit (see [http://en.wikipedia.org/wiki/Coefficient_of_determination R^2 measure description])
** '''Output Bolus Arrival Time Image''': the bolus arrival time calculated at each pixel
|}

The following acquisition parameters should be available in the NRRD header of the input data (if you are analyzing a DICOM time series, they will typically be extracted from the DICOM data):
* TR Value: Repetition time (milliseconds)
* TE Value: Echo time (milliseconds)
* FA Value: Flip angle (degrees)
* Timestamps for the dynamic series (in milliseconds)

Here is an example how this information is represented in the NRRD header:
<pre>
MultiVolume.DICOM.EchoTime:=2.93
MultiVolume.DICOM.FlipAngle:=10
MultiVolume.DICOM.RepetitionTime:=6.13
MultiVolume.FrameIdentifyingDICOMTagName:=AcquisitionTime
MultiVolume.FrameIdentifyingDICOMTagUnits:=ms
</pre>


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


{{documentation/{{documentation/version}}/module-section|References}}
* [1] Knopp MV, Giesel FL, Marcos H et al: Dynamic contrast-enhanced magnetic resonance imaging in oncology. Top Magn Reson Imaging, 2001; 12:301-308.
* [2] 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.
* [3] de Bazelaire, C.M., et al., MR imaging relaxation times of abdominal and pelvic tissues measured in vivo at 3.0 T: preliminary results. Radiology, 2004. 230(3): p. 652-9.
* [4] Pintaske J, Martirosian P, Graf H, Erb G, Lodemann K-P, Claussen CD, Schick F. Relaxivity of Gadopentetate Dimeglumine (Magnevist), Gadobutrol (Gadovist), and Gadobenate Dimeglumine (MultiHance) in human blood plasma at 0.2, 1.5, and 3 Tesla. Investigative radiology. 2006 March;41(3):213–21.
* [5] Parker GJ, Roberts C, Macdonald A, Buonaccorsi GA, Cheung S, Buckley DL, Jackson A, Watson Y, Davies K, Jayson GC. Experimentally-derived functional form for a population-averaged high-temporal-resolution arterial input function for dynamic contrast-enhanced MRI. Magnetic Resonance in Medicine, 2006 Nov; 56(5):993-1000.
* [6] Huang, W., Li, X., Chen, Y., Li, X., Chang, M.-C., Oborski, M. J., … Kalpathy-Cramer, J. (2014). Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge. Translational Oncology, 7(1), 153–66. doi:10.1593/tlo.13838 http://dx.doi.org/10.1593/tlo.13838
* [7] Tofts, P. S., Brix, G., Buckley, D. L., Evelhoch, J. L., Henderson, E., Knopp, M. V, … Weisskoff, R. M. (1999). Estimating kinetic parameters from Contrast-Enhanced T 1 -Weighted MRI of a Diffusable Tracer : Standardized Quantities and Symbols. J Magn Reson Imaging, 10(3), 223–232.

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

Source code: https://github.com/millerjv/PkModeling

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

File:PkModelingUI061912.png

2016-01-04T21:14:18Z

Stevedaxiao: Stevedaxiao uploaded a new version of File:PkModelingUI061912.png

Documentation/4.4/Modules/T1Mapping

2015-09-11T05:32:04Z

Stevedaxiao:

Documentation/Nightly/Modules/T1Mapping

2015-09-11T05:31:44Z

Stevedaxiao:

Documentation/4.4/Extensions/T1Mapping

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Documentation/Nightly/Modules/T1Mapping

2015-09-11T05:19:48Z

Stevedaxiao:

Documentation/Nightly/Modules/T1Mapping

2015-09-11T05:18:21Z

Stevedaxiao:

File:T1 Mapping CPP GUI.png

2015-09-11T05:16:54Z

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Documentation/Nightly/Modules/T1Mapping

2015-09-11T03:52:31Z

Stevedaxiao:

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Documentation/Nightly/Modules/T1Mapping

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File:DSC logo Resized.png

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2015-09-02T22:24:38Z

Stevedaxiao: uploaded a new version of "File:T1 Mapping Logo Resized CPP.png": Reverted to version as of 21:05, 31 August 2015

File:T1 Mapping Logo Resized CPP.png

2015-09-02T22:18:37Z

Stevedaxiao: uploaded a new version of "File:T1 Mapping Logo Resized CPP.png"

Documentation/4.4/Modules/DSC MRI Analysis

2015-09-02T04:28:22Z

Stevedaxiao:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

{|
|
[[Image:DSC logo.png | 100px]]
|
Extension: [[Documentation/{{documentation/version}}/Extensions/DSC_MRI_Analysis|DSC_MRI_Analysis]] 

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, and by National Cancer Institute as part of the Quantitative Imaging Network initiative (U01CA154601) and QIICR (U24CA180918). 

Implementation of the DSC MRI Analysis was contributed by Xiao Da from MGH. 

Author: Xiao Da (MGH), Yangming Ou (MGH), Andriy Fedorov (BWH), Steve Pieper (Isomics), Jayashree Kalpathy-Cramer (MGH) 
Contact: Xiao Da, <email>XDA@mgh.harvard.edu</email> 
|}

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|martinos}}|{{collaborator|longname|martinos}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dynamic Susceptibility Contrast (DSC) MRI imaging is an important functional imaging method that enables quantitative assessment of tissue hemodynamic patterns. Abnormality of blood flow, volume and permeability is frequently observed during tumor growth, and characterization of these perfusion attributes has become clinically important for both diagnosis and therapy planning. In the context of glial neoplasms, perfusion characteristics have been shown to correlate with tumor type and grade and hence influence treatment decisions. 
DSC MRI imaging is based on the principle that flow of a paramagnetic contrast agent through a capillary bed will transiently change the magnetic susceptibility of the given tissue. Decreased signal intensity on spin-echo or gradient-echo images after the first pass of the contrast agent, frequently described as susceptibility-induced T2* shortening, is the result of this temporal change in magnetic susceptibility. This signal time curve is then converted into a concentration time curve, and use of tracer kinetic analysis various hemodynamic variables, such as cerebral blood volume, cerebral blood flow, and mean transit time, as well as metrics that address vessel leakage may be estimated. Combined, these metrics enable microvascular imaging, providing a visual correlate of blood flow, volume, and vessel permeability.




{{documentation/{{documentation/version}}/module-section|Use Cases}}
*Estimation of quantitative parameters(rCBV,rCBF and MTT) from DSC MRI.
*Guide diagnosis, prognosis and therapy planning.
*Brain Tumor, Stroke, Adrenoleukodystrophy and other diseases.
{|
|[[Image:DSC Result.png|thumb|500px|Framework to Estimate DSC Parametric Maps]]
|}


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

{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:DSC GUI V0.png|thumb|400px|DSC MRI Analysis GUI]]
|
* '''PkModeling Parameters''':
** '''CBF/CBV Time Interval Value''': Time interval for CBF/CBV calculation.
** '''Use Population AIF''': A mean AIF is calculated from a functional form instead of from the input using the aifMask or a prescribed AIF.
* '''IO'''
** '''Input 4D image''': 4D DSC MRI Image.
** '''ROI Mask Image''': Mask designating the location for DSC analysis.
** '''AIF Mask Image''': Mask designating the location of the arterial input function (AIF). AIF can either be calculated from the input using the aifMask, prescribed directly in concentration units using the prescribedAIF option, or via a population AIF.
** '''Prescribed AIF''': Prescribed arterial input function (AIF).
** '''Output K2 image''': Leakage map.
** '''Output RCBV image''': Relative Cerebral Blood Volume (rCBV) map.
** '''Output RCBF image''': Relative Cerebral Blood Flow (rCBF) map.
** '''Output MTT image''': Mean Transit Time (MTT) map.
*'''Advanced options'''
** '''BAT Calculation Mode''': PeakGradient(Default) or UseConstantBAT.
** '''Constant BAT''': Constant bolus arrival time value.
** '''Output Bolus Arrival Time Image''': The bolus arrival time calculated at each pixel.
** '''Output Concentration 4D Image''': Delta R2* concentration image.
** '''Output Fitted Data 4D Image''': Fitted Delta R2* concentration image.
|}


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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://www.healthcare.siemens.com/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/groups/public/@global/@imaging/@mri/documents/download/mdaw/mtix/~edisp/brain_perfusion_how_why-00093544.pdf Introduction of DSC MRI from Siemens]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657863/ Equations for conversion of signal to concentration for DSC]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208985/pdf/nihms596683.pdf Other method to investigate DSC MRI]
* [http://www.ncbi.nlm.nih.gov/pubmed/16611779 Leakage correction for DSC MRI]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
* [https://github.com/stevedaxiao/DSC_Analysis.git Source code for analysis of DSC MRI]


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

Documentation/Nightly/Modules/DSC MRI Analysis

2015-09-02T04:27:38Z

Stevedaxiao:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

{|
|
[[Image:DSC logo.png | 100px]]
|
Extension: [[Documentation/{{documentation/version}}/Extensions/DSC_MRI_Analysis|DSC_MRI_Analysis]] 

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, and by National Cancer Institute as part of the Quantitative Imaging Network initiative (U01CA154601) and QIICR (U24CA180918). 

Implementation of the DSC MRI Analysis was contributed by Xiao Da from MGH. 

Author: Xiao Da (MGH), Yangming Ou (MGH), Andriy Fedorov (BWH), Steve Pieper (Isomics), Jayashree Kalpathy-Cramer (MGH) 
Contact: Xiao Da, <email>XDA@mgh.harvard.edu</email> 
|}

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|martinos}}|{{collaborator|longname|martinos}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dynamic Susceptibility Contrast (DSC) MRI imaging is an important functional imaging method that enables quantitative assessment of tissue hemodynamic patterns. Abnormality of blood flow, volume and permeability is frequently observed during tumor growth, and characterization of these perfusion attributes has become clinically important for both diagnosis and therapy planning. In the context of glial neoplasms, perfusion characteristics have been shown to correlate with tumor type and grade and hence influence treatment decisions. 
DSC MRI imaging is based on the principle that flow of a paramagnetic contrast agent through a capillary bed will transiently change the magnetic susceptibility of the given tissue. Decreased signal intensity on spin-echo or gradient-echo images after the first pass of the contrast agent, frequently described as susceptibility-induced T2* shortening, is the result of this temporal change in magnetic susceptibility. This signal time curve is then converted into a concentration time curve, and use of tracer kinetic analysis various hemodynamic variables, such as cerebral blood volume, cerebral blood flow, and mean transit time, as well as metrics that address vessel leakage may be estimated. Combined, these metrics enable microvascular imaging, providing a visual correlate of blood flow, volume, and vessel permeability.




{{documentation/{{documentation/version}}/module-section|Use Cases}}
*Estimation of quantitative parameters(rCBV,rCBF and MTT) from DSC MRI.
*Guide diagnosis, prognosis and therapy planning.
*Brain Tumor, Stroke, Adrenoleukodystrophy and other diseases.
{|
|[[Image:DSC Result.png|thumb|500px|Framework to Estimate DSC Parametric Maps]]
|}


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

{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:DSC GUI V0.png|thumb|400px|DSC MRI Analysis GUI]]
|
* '''PkModeling Parameters''':
** '''CBF/CBV Time Interval Value''': Time interval for CBF/CBV calculation.
** '''Use Population AIF''': A mean AIF is calculated from a functional form instead of from the input using the aifMask or a prescribed AIF.
* '''IO'''
** '''Input 4D image''': 4D DSC MRI Image.
** '''ROI Mask Image''': Mask designating the location for DSC analysis.
** '''AIF Mask Image''': Mask designating the location of the arterial input function (AIF). AIF can either be calculated from the input using the aifMask, prescribed directly in concentration units using the prescribedAIF option, or via a population AIF.
** '''Prescribed AIF''': Prescribed arterial input function (AIF).
** '''Output K2 image''': Leakage map.
** '''Output RCBV image''': Relative Cerebral Blood Volume (rCBV) map.
** '''Output RCBF image''': Relative Cerebral Blood Flow (rCBF) map.
** '''Output MTT image''': Mean Transit Time (MTT) map.
*'''Advanced options'''
** '''BAT Calculation Mode''': PeakGradient(Default) or UseConstantBAT.
** '''Constant BAT''': Constant bolus arrival time value.
** '''Output Bolus Arrival Time Image''': The bolus arrival time calculated at each pixel.
** '''Output Concentration 4D Image''': Delta R2* concentration image.
** '''Output Fitted Data 4D Image''': Fitted Delta R2* concentration image.
|}


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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://www.healthcare.siemens.com/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/groups/public/@global/@imaging/@mri/documents/download/mdaw/mtix/~edisp/brain_perfusion_how_why-00093544.pdf Introduction of DSC MRI from Siemens]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657863/ Equations for conversion of signal to concentration for DSC]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208985/pdf/nihms596683.pdf Other method to investigate DSC MRI]
* [http://www.ncbi.nlm.nih.gov/pubmed/16611779 Leakage correction for DSC MRI]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
* [https://github.com/stevedaxiao/DSC_Analysis.git Source code for analysis of DSC MRI]


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

File:DSC GUI V0.png

2015-09-02T04:25:08Z

Stevedaxiao: uploaded a new version of "File:DSC GUI V0.png"

Documentation/4.4/Modules/T1 Mapping CPP

2015-09-02T04:18:58Z

Stevedaxiao:

File:DSC logo Resized.png

2015-09-01T21:59:38Z

Stevedaxiao:

File:T1 Mapping CPP Logo Resized.png

2015-08-31T21:09:08Z

Stevedaxiao:

File:T1 Mapping Logo Resized CPP.png

2015-08-31T21:05:19Z

Stevedaxiao: uploaded a new version of "File:T1 Mapping Logo Resized CPP.png"

Documentation/Nightly/Modules/T1Mapping

2015-08-31T19:45:11Z

Stevedaxiao:

File:T1 Mapping Logo Resized CPP.png

2015-08-31T19:44:23Z

Stevedaxiao:

Documentation/4.4/Extensions/DSC MRI Analysis

2015-08-20T22:50:48Z

Stevedaxiao: Redirected page to Documentation/Nightly/Modules/DSC MRI Analysis

#REDIRECT [[Documentation/Nightly/Modules/DSC_MRI_Analysis]]

Documentation/Nightly/Extensions/DSC MRI Analysis

2015-08-20T22:48:38Z

Stevedaxiao: Redirected page to Documentation/Nightly/Modules/DSC MRI Analysis

#REDIRECT [[Documentation/Nightly/Modules/DSC_MRI_Analysis]]

Documentation/4.4/Modules/DSC MRI Analysis

2015-08-20T22:42:33Z

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

{|
|
[[Image:DSC logo.png | 100px]]
|
Extension: [[Documentation/{{documentation/version}}/Extensions/DSC_MRI_Analysis|DSC_MRI_Analysis]] 

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, and by National Cancer Institute as part of the Quantitative Imaging Network initiative (U01CA154601) and QIICR (U24CA180918). 

Implementation of the DSC MRI Analysis was contributed by Xiao Da from MGH. 

Author: Xiao Da (MGH), Yangming Ou (MGH), Andriy Fedorov (BWH), Steve Pieper (Isomics), Jayashree Kalpathy-Cramer (MGH) 
Contact: Xiao Da, <email>XDA@mgh.harvard.edu</email> 
|}

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|martinos}}|{{collaborator|longname|martinos}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dynamic Susceptibility Contrast (DSC) MRI imaging is an important functional imaging method that enables quantitative assessment of tissue hemodynamic patterns. Abnormality of blood flow, volume and permeability is frequently observed during tumor growth, and characterization of these perfusion attributes has become clinically important for both diagnosis and therapy planning. In the context of glial neoplasms, perfusion characteristics have been shown to correlate with tumor type and grade and hence influence treatment decisions. 
DSC MRI imaging is based on the principle that flow of a paramagnetic contrast agent through a capillary bed will transiently change the magnetic susceptibility of the given tissue. Decreased signal intensity on spin-echo or gradient-echo images after the first pass of the contrast agent, frequently described as susceptibility-induced T2* shortening, is the result of this temporal change in magnetic susceptibility. This signal time curve is then converted into a concentration time curve, and use of tracer kinetic analysis various hemodynamic variables, such as cerebral blood volume, cerebral blood flow, and mean transit time, as well as metrics that address vessel leakage may be estimated. Combined, these metrics enable microvascular imaging, providing a visual correlate of blood flow, volume, and vessel permeability.




{{documentation/{{documentation/version}}/module-section|Use Cases}}
*Estimation of quantitative parameters(rCBV,rCBF and MTT) from DSC MRI.
*Guide diagnosis, prognosis and therapy planning.
*Brain Tumor, Stroke, Adrenoleukodystrophy and other diseases.
{|
|[[Image:DSC Result.png|thumb|500px|Framework to Estimate DSC Parametric Maps]]
|}


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

{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:DSC GUI V0.png|thumb|400px|DSC MRI Analysis GUI]]
|
* '''PkModeling Parameters''':
** '''CBF/CBV Time Interval Value''': Time interval for CBF/CBV calculation.
** '''Use Population AIF''': A mean AIF is calculated from a functional form instead of from the input using the aifMask or a prescribed AIF.
* '''IO'''
** '''Input 4D image''': 4D DSC MRI Image.
** '''ROI Mask Image''': Mask designating the location for DSC analysis.
** '''AIF Mask Image''': Mask designating the location of the arterial input function (AIF). AIF can either be calculated from the input using the aifMask, prescribed directly in concentration units using the prescribedAIF option, or via a population AIF.
** '''Prescribed AIF''': Prescribed arterial input function (AIF).
** '''Output RCBV image''': Relative Cerebral Blood Volume (rCBV) map.
** '''Output RCBF image''': Relative Cerebral Blood Flow (rCBF) map.
** '''Output MTT image''': Mean Transit Time (MTT) map.
*'''Advanced options'''
** '''BAT Calculation Mode''': PeakGradient(Default) or UseConstantBAT.
** '''Constant BAT''': Constant bolus arrival time value.
** '''Output Bolus Arrival Time Image''': The bolus arrival time calculated at each pixel.
** '''Output Concentration 4D Image''': Delta R2* concentration image.
** '''Output Fitted Data 4D Image''': Fitted Delta R2* concentration image.
|}


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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://www.healthcare.siemens.com/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/groups/public/@global/@imaging/@mri/documents/download/mdaw/mtix/~edisp/brain_perfusion_how_why-00093544.pdf Introduction of DSC MRI from Siemens]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657863/ Equations for conversion of signal to concentration for DSC]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208985/pdf/nihms596683.pdf Other method to investigate DSC MRI]
* [http://www.ncbi.nlm.nih.gov/pubmed/16611779 Leakage correction for DSC MRI]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
* [https://github.com/stevedaxiao/DSC_Analysis.git Source code for analysis of DSC MRI]


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

Documentation/Nightly/Modules/DSC MRI Analysis

2015-08-20T22:34:59Z

Stevedaxiao:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

{|
|
[[Image:DSC logo.png | 100px]]
|
Extension: [[Documentation/{{documentation/version}}/Extensions/DSC_MRI_Analysis|DSC_MRI_Analysis]] 

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, and by National Cancer Institute as part of the Quantitative Imaging Network initiative (U01CA154601) and QIICR (U24CA180918). 

Implementation of the DSC MRI Analysis was contributed by Xiao Da from MGH. 

Author: Xiao Da (MGH), Yangming Ou (MGH), Andriy Fedorov (BWH), Steve Pieper (Isomics), Jayashree Kalpathy-Cramer (MGH) 
Contact: Xiao Da, <email>XDA@mgh.harvard.edu</email> 
|}

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|martinos}}|{{collaborator|longname|martinos}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dynamic Susceptibility Contrast (DSC) MRI imaging is an important functional imaging method that enables quantitative assessment of tissue hemodynamic patterns. Abnormality of blood flow, volume and permeability is frequently observed during tumor growth, and characterization of these perfusion attributes has become clinically important for both diagnosis and therapy planning. In the context of glial neoplasms, perfusion characteristics have been shown to correlate with tumor type and grade and hence influence treatment decisions. 
DSC MRI imaging is based on the principle that flow of a paramagnetic contrast agent through a capillary bed will transiently change the magnetic susceptibility of the given tissue. Decreased signal intensity on spin-echo or gradient-echo images after the first pass of the contrast agent, frequently described as susceptibility-induced T2* shortening, is the result of this temporal change in magnetic susceptibility. This signal time curve is then converted into a concentration time curve, and use of tracer kinetic analysis various hemodynamic variables, such as cerebral blood volume, cerebral blood flow, and mean transit time, as well as metrics that address vessel leakage may be estimated. Combined, these metrics enable microvascular imaging, providing a visual correlate of blood flow, volume, and vessel permeability.




{{documentation/{{documentation/version}}/module-section|Use Cases}}
*Estimation of quantitative parameters(rCBV,rCBF and MTT) from DSC MRI.
*Guide diagnosis, prognosis and therapy planning.
*Brain Tumor, Stroke, Adrenoleukodystrophy and other diseases.
{|
|[[Image:DSC Result.png|thumb|500px|Framework to Estimate DSC Parametric Maps]]
|}


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

{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:DSC GUI V0.png|thumb|400px|DSC MRI Analysis GUI]]
|
* '''PkModeling Parameters''':
** '''CBF/CBV Time Interval Value''': Time interval for CBF/CBV calculation.
** '''Use Population AIF''': A mean AIF is calculated from a functional form instead of from the input using the aifMask or a prescribed AIF.
* '''IO'''
** '''Input 4D image''': 4D DSC MRI Image.
** '''ROI Mask Image''': Mask designating the location for DSC analysis.
** '''AIF Mask Image''': Mask designating the location of the arterial input function (AIF). AIF can either be calculated from the input using the aifMask, prescribed directly in concentration units using the prescribedAIF option, or via a population AIF.
** '''Prescribed AIF''': Prescribed arterial input function (AIF).
** '''Output RCBV image''': Relative Cerebral Blood Volume (rCBV) map.
** '''Output RCBF image''': Relative Cerebral Blood Flow (rCBF) map.
** '''Output MTT image''': Mean Transit Time (MTT) map.
*'''Advanced options'''
** '''BAT Calculation Mode''': PeakGradient(Default) or UseConstantBAT.
** '''Constant BAT''': Constant bolus arrival time value.
** '''Output Bolus Arrival Time Image''': The bolus arrival time calculated at each pixel.
** '''Output Concentration 4D Image''': Delta R2* concentration image.
** '''Output Fitted Data 4D Image''': Fitted Delta R2* concentration image.
|}


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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://www.healthcare.siemens.com/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/groups/public/@global/@imaging/@mri/documents/download/mdaw/mtix/~edisp/brain_perfusion_how_why-00093544.pdf Introduction of DSC MRI from Siemens]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657863/ Equations for conversion of signal to concentration for DSC]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208985/pdf/nihms596683.pdf Other method to investigate DSC MRI]
* [http://www.ncbi.nlm.nih.gov/pubmed/16611779 Leakage correction for DSC MRI]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
* [https://github.com/stevedaxiao/DSC_Analysis.git Source code for analysis of DSC MRI]


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

Documentation/Nightly/Modules/DSC MRI Analysis

2015-08-20T22:29:56Z

Stevedaxiao:

Documentation/Nightly/Modules/DSC MRI Analysis

2015-08-20T21:45:13Z

File:DSC GUI V0.png

2015-08-20T21:38:56Z

Stevedaxiao:

File:DSC Result.png

2015-08-20T21:36:16Z

Stevedaxiao:

File:DSC logo.png

2015-08-20T20:30:52Z

Stevedaxiao:

Documentation/Nightly/Extensions

2015-08-20T20:24:29Z

Stevedaxiao: /* Cat 2 */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
* [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Kevin Wang, Adam Rankin, Greg Sharp, Andras Lasso, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]


** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)
** [[Documentation/{{documentation/version}}/Extensions/PathRecorder|Path Recorder]] (Alireza Mehrtash)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTI-Reg|DTI-Reg]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]] (Francois Budin, Pengdong Xiao, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]] (Andras Lasso, Matt Lougheed)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]] - formerly Multidimensional data (Andras Lasso, Matthew Holden, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Atsushi Yamada, Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)
** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]
** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]
* [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)
* [[Documentation/{{documentation/version}}/Extensions/ResectionPlanner|ResectionVolume]] (Matt Lougheed)
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM]] (Andrey Fedorov, Ethan Ulrich)
* [[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PETTumorSegmentation]] (Christian Bauer)
* [[Documentation/{{documentation/version}}/Extensions/PET-IndiC|PET-IndiC]] (Ethan Ulrich)
* [[Documentation/{{documentation/version}}/Extensions/CornerAnnotation|CornerAnnotation]] (Atsushi Yamada)
* [[Documentation/{{documentation/version}}/Extensions/Wasp|Watershed Annotation and Segmentation Plugin.]] (Thomas Lawson)
* [[Documentation/{{documentation/version}}/Extensions/SlicerPetSpectAnalysis|SlicerPetSpectAnalysis]] (Martín Bertran,Natalia Martínez, Guillermo Carbajal, Álvaro Gómez)
** [[Documentation/{{documentation/version}}/Modules/dPetBrainQuantification|dPetBrainQuantification]]
* [[Documentation/{{documentation/version}}/Extensions/IGTWizard|IGTWizard]] (Junichi Tokuda and Atsushi Yamada)
* [[Documentation/{{documentation/version}}/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Modules/T1_Mapping|T1_Mapping]] (Xiao Da, Artem Mamonov, Jayashree Kalpathy-Cramer and Andriy Fedorov)
* [[Documentation/{{documentation/version}}/Modules/T1_Mapping_CPP|T1_Mapping_CPP]] (Xiao Da, Yangming Ou, Andriy Fedorov and Jayashree Kalpathy-Cramer)
* [[Documentation/{{documentation/version}}/Extensions/PickAndPaint|PickAndPaint]] (Lucie Macron)
* [[Documentation/{{documentation/version}}/Extensions/EasyClip|EasyClip]] (Julia Lopinto)
* [[Documentation/{{documentation/version}}/Extensions/MeshStatistics|MeshStatistics]] (Lucie Macron)
* [[Documentation/{{documentation/version}}/Extensions/AnglePlanes|AnglePlanes]] (Julia Lopinto)
* [[Documentation/{{documentation/version}}/Extensions/Q3DC|Q3DC]] (Lucie Macron)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

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