Slicer Wiki - User contributions [en]

Documentation/Nightly/Modules/DeepInfer

2017-08-12T00:36:16Z

Mehrtash:

<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/DeepInfer|DeepInfer]] 
Acknowledgments:
This work is funded by NIH Grant No.P41EB015898, Natural Sciences andEngineering Research Council (NSERC) of Canada and the Canadian Institutes of Health Research (CIHR). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Mehran Pesteie ({{collaborator|name|ubc}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 
webite: [http://www.deepinfer.org/ DeepInfer Website] 
License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
[[File:Deepinfer-256.png|128px|]]
 
DeepInfer is an open-source deep learning deployment toolkit for medical imaging and image-guided therapy. With DeepInfer 3D Slicer users can deploy trained
deep learning and machine learning models in their workflow. Also, DeepInfer allows machine learning experts to package,
ship, and deploy their models, thereby additionally allowing clinical researchers and biomedical engineers to use
task-specific deep models, without the need for further software development and configuration.

{{documentation/{{documentation/version}}/module-section|Setup Guide}}
In order to use DeepInfer, [https://www.docker.com/ Docker] is required to be installed and configured properly.
==== Windows ====
Docker for Windows requires Windows 10 Pro (64bit) and Microsoft Hyper-V. You also need to enable virtualization in BIOS settings.
* [https://docs.docker.com/docker-for-windows/install/ Docker installation guide for Windows]
* VERY IMPORTANT: Share drive C with docker containers from settings.
[[File:DockerWindows.PNG|600px|]] 

==== Mac OS X ====
* [https://docs.docker.com/docker-for-mac/install/#install-and-run-docker-for-mac Docker installation guide for MAC]

==== Ubuntu ====
* [https://docs.docker.com/engine/installation/linux/ubuntu/ Docker installation guide for Ubuntu]
* Give non-root access to docker using this [http://askubuntu.com/a/477554 guide].

{{documentation/{{documentation/version}}/module-section|Demo}}
* [https://www.youtube.com/watch?v=7k_SLtmM2Kw Demo Video]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
[[File:Deepinfer-panels.png|600px|]]

{{documentation/{{documentation/version}}/module-section|Deployed Models}}
==== Prostate Segmentation in Targeted MRI-Guided Biopsy ====
This model is trained for the task of rough delineation of the prostate gland that is a necessary step in MRI-guided targeted biopsy. The deployed model is trained on transaxial T2-weighted MRIs of the prostate (without endorectal coil on a 3T MRI machine) collected during MR-guided prostate biopsy procedures. The network based on a customized variant of the U-Net architecture. The network is trained on N = 224 patients on a total number of 26250 2D slices of prostate images and achieved 76.25% accuracy on N = 57 validation patients (2184 2D slices). 

[[File:Prostate-deepinfer.png|800px|]] 


{{documentation/{{documentation/version}}/module-section|Citing DeepInfer}}
To acknowledge DeepInfer and 3D Slicer, please cite the please cite the [http://www.deepinfer.org DeepInfer web site] and following publications when publishing work that uses or incorporates DeepInfer and 3D Slicer:

* Mehrtash, A., Pesteie, M., Hetherington, J., Behringer, P.A., Kapur, T., Wells, W.M., Rohling, R., Fedorov, A. and Abolmaesumi, P., 2017, March. [http://www.spl.harvard.edu/publications/item/view/3076 DeepInfer: open-source deep learning deployment toolkit for image-guided therapy.] In SPIE Medical Imaging (pp. 101351K-101351K). International Society for Optics and Photonics.

* Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network.] Magn Reson Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
==== Architecture ====
The figure below shows the architecture of the DeepInfer toolkit, which has three components: the Docker engine,
the DeepInfer 3D Slicer extension [1], and the cloud model registry [2].
The Docker engine consists of local Docker containers that include the deployed models, as well as all of the required deep learning frameworks, which
process incoming data and produce respective results.
Data streaming between the Docker engine and the GUI is achieved by sharing a local folder with the specific Docker image. 
[[File:Deepifner-arch.png|800px|]] 

# [https://github.com/deepinfer/Slicer-DeepInfer Slicer-DeepInfer Module Source Code]
# [https://github.com/DeepInfer/Model-Registry Model Registry]

==== Packaging and Deployment Example ====
[https://github.com/mehrtash/Prostate-Segmenter Prostate Segmenter Repository] is an example of the code that can be used as a reference to package and deploy a model in DeepInfer.
It shows how you can build a docker and package trained weights inside.

* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/docker/Dockerfile.cpu Example of a CPU DockerFile]
* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/fit.py Example of a python file that is called by running Docker]


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

File:DockerWindows.PNG

2017-08-12T00:33:02Z

Mehrtash:

Documentation/Nightly/Modules/DeepInfer

2017-06-05T16:42:57Z

Mehrtash:

<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/DeepInfer|DeepInfer]] 
Acknowledgments:
This work is funded by NIH Grant No.P41EB015898, Natural Sciences andEngineering Research Council (NSERC) of Canada and the Canadian Institutes of Health Research (CIHR). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Mehran Pesteie ({{collaborator|name|ubc}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 
webite: [http://www.deepinfer.org/ DeepInfer Website] 
License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
[[File:Deepinfer-256.png|128px|]]
 
DeepInfer is an open-source deep learning deployment toolkit for medical imaging and image-guided therapy. With DeepInfer 3D Slicer users can deploy trained
deep learning and machine learning models in their workflow. Also, DeepInfer allows machine learning experts to package,
ship, and deploy their models, thereby additionally allowing clinical researchers and biomedical engineers to use
task-specific deep models, without the need for further software development and configuration.

{{documentation/{{documentation/version}}/module-section|Setup Guide}}
In order to use DeepInfer, [https://www.docker.com/ Docker] is required to be installed and configured properly.
==== Windows ====
Docker for Windows requires Windows 10 Pro (64bit) and Microsoft Hyper-V. You also need to enable virtualization in BIOS settings.
* [https://docs.docker.com/docker-for-windows/install/ Docker installation guide for Windows]
* Share drive C with docker containers from settings.

==== Mac OS X ====
* [https://docs.docker.com/docker-for-mac/install/#install-and-run-docker-for-mac Docker installation guide for MAC]

==== Ubuntu ====
* [https://docs.docker.com/engine/installation/linux/ubuntu/ Docker installation guide for Ubuntu]
* Give non-root access to docker using this [http://askubuntu.com/a/477554 guide].

{{documentation/{{documentation/version}}/module-section|Demo}}
* [https://www.youtube.com/watch?v=7k_SLtmM2Kw Demo Video]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
[[File:Deepinfer-panels.png|600px|]]

{{documentation/{{documentation/version}}/module-section|Deployed Models}}
==== Prostate Segmentation in Targeted MRI-Guided Biopsy ====
This model is trained for the task of rough delineation of the prostate gland that is a necessary step in MRI-guided targeted biopsy. The deployed model is trained on transaxial T2-weighted MRIs of the prostate (without endorectal coil on a 3T MRI machine) collected during MR-guided prostate biopsy procedures. The network based on a customized variant of the U-Net architecture. The network is trained on N = 224 patients on a total number of 26250 2D slices of prostate images and achieved 76.25% accuracy on N = 57 validation patients (2184 2D slices). 

[[File:Prostate-deepinfer.png|800px|]] 


{{documentation/{{documentation/version}}/module-section|Citing DeepInfer}}
To acknowledge DeepInfer and 3D Slicer, please cite the please cite the [http://www.deepinfer.org DeepInfer web site] and following publications when publishing work that uses or incorporates DeepInfer and 3D Slicer:

* Mehrtash, A., Pesteie, M., Hetherington, J., Behringer, P.A., Kapur, T., Wells, W.M., Rohling, R., Fedorov, A. and Abolmaesumi, P., 2017, March. [http://www.spl.harvard.edu/publications/item/view/3076 DeepInfer: open-source deep learning deployment toolkit for image-guided therapy.] In SPIE Medical Imaging (pp. 101351K-101351K). International Society for Optics and Photonics.

* Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network.] Magn Reson Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
==== Architecture ====
The figure below shows the architecture of the DeepInfer toolkit, which has three components: the Docker engine,
the DeepInfer 3D Slicer extension [1], and the cloud model registry [2].
The Docker engine consists of local Docker containers that include the deployed models, as well as all of the required deep learning frameworks, which
process incoming data and produce respective results.
Data streaming between the Docker engine and the GUI is achieved by sharing a local folder with the specific Docker image. 
[[File:Deepifner-arch.png|800px|]] 

# [https://github.com/deepinfer/Slicer-DeepInfer Slicer-DeepInfer Module Source Code]
# [https://github.com/DeepInfer/Model-Registry Model Registry]

==== Packaging and Deployment Example ====
[https://github.com/mehrtash/Prostate-Segmenter Prostate Segmenter Repository] is an example of the code that can be used as a reference to package and deploy a model in DeepInfer.
It shows how you can build a docker and package trained weights inside.

* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/docker/Dockerfile.cpu Example of a CPU DockerFile]
* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/fit.py Example of a python file that is called by running Docker]


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

Documentation/Nightly/Modules/DeepInfer

2017-06-05T16:42:16Z

Mehrtash:

<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/DeepInfer|DeepInfer]] 
Acknowledgments:
This work is funded by NIH Grant No.P41EB015898, Natural Sciences andEngineering Research Council (NSERC) of Canada and the Canadian Institutes of Health Research (CIHR). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Mehran Pesteie ({{collaborator|name|ubc}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 
webite: [http://www.deepinfer.org/ DeepInfer Website] 
License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
[[File:Deepinfer-256.png|128px|]]
 
DeepInfer is an open-source deep learning deployment toolkit for medical imaging and Image-Guided Therapy. With DeepInfer 3D Slicer users can deploy trained
deep learning and machine learning models in their workflow. Also, DeepInfer allows machine learning experts to package,
ship, and deploy their models, thereby additionally allowing clinical researchers and biomedical engineers to use
task-specific deep models, without the need for further software development and configuration.

{{documentation/{{documentation/version}}/module-section|Setup Guide}}
In order to use DeepInfer, [https://www.docker.com/ Docker] is required to be installed and configured properly.
==== Windows ====
Docker for Windows requires Windows 10 Pro (64bit) and Microsoft Hyper-V. You also need to enable virtualization in BIOS settings.
* [https://docs.docker.com/docker-for-windows/install/ Docker installation guide for Windows]
* Share drive C with docker containers from settings.

==== Mac OS X ====
* [https://docs.docker.com/docker-for-mac/install/#install-and-run-docker-for-mac Docker installation guide for MAC]

==== Ubuntu ====
* [https://docs.docker.com/engine/installation/linux/ubuntu/ Docker installation guide for Ubuntu]
* Give non-root access to docker using this [http://askubuntu.com/a/477554 guide].

{{documentation/{{documentation/version}}/module-section|Demo}}
* [https://www.youtube.com/watch?v=7k_SLtmM2Kw Demo Video]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
[[File:Deepinfer-panels.png|600px|]]

{{documentation/{{documentation/version}}/module-section|Deployed Models}}
==== Prostate Segmentation in Targeted MRI-Guided Biopsy ====
This model is trained for the task of rough delineation of the prostate gland that is a necessary step in MRI-guided targeted biopsy. The deployed model is trained on transaxial T2-weighted MRIs of the prostate (without endorectal coil on a 3T MRI machine) collected during MR-guided prostate biopsy procedures. The network based on a customized variant of the U-Net architecture. The network is trained on N = 224 patients on a total number of 26250 2D slices of prostate images and achieved 76.25% accuracy on N = 57 validation patients (2184 2D slices). 

[[File:Prostate-deepinfer.png|800px|]] 


{{documentation/{{documentation/version}}/module-section|Citing DeepInfer}}
To acknowledge DeepInfer and 3D Slicer, please cite the please cite the [http://www.deepinfer.org DeepInfer web site] and following publications when publishing work that uses or incorporates DeepInfer and 3D Slicer:

* Mehrtash, A., Pesteie, M., Hetherington, J., Behringer, P.A., Kapur, T., Wells, W.M., Rohling, R., Fedorov, A. and Abolmaesumi, P., 2017, March. [http://www.spl.harvard.edu/publications/item/view/3076 DeepInfer: open-source deep learning deployment toolkit for image-guided therapy.] In SPIE Medical Imaging (pp. 101351K-101351K). International Society for Optics and Photonics.

* Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network.] Magn Reson Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
==== Architecture ====
The figure below shows the architecture of the DeepInfer toolkit, which has three components: the Docker engine,
the DeepInfer 3D Slicer extension [1], and the cloud model registry [2].
The Docker engine consists of local Docker containers that include the deployed models, as well as all of the required deep learning frameworks, which
process incoming data and produce respective results.
Data streaming between the Docker engine and the GUI is achieved by sharing a local folder with the specific Docker image. 
[[File:Deepifner-arch.png|800px|]] 

# [https://github.com/deepinfer/Slicer-DeepInfer Slicer-DeepInfer Module Source Code]
# [https://github.com/DeepInfer/Model-Registry Model Registry]

==== Packaging and Deployment Example ====
[https://github.com/mehrtash/Prostate-Segmenter Prostate Segmenter Repository] is an example of the code that can be used as a reference to package and deploy a model in DeepInfer.
It shows how you can build a docker and package trained weights inside.

* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/docker/Dockerfile.cpu Example of a CPU DockerFile]
* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/fit.py Example of a python file that is called by running Docker]


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

Documentation/Nightly/Modules/DeepInfer

2017-04-11T22:57:17Z

Mehrtash:

<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/DeepInfer|DeepInfer]] 
Acknowledgments:
This work is funded by NIH Grant No.P41EB015898, Natural Sciences andEngineering Research Council (NSERC) of Canada and the Canadian Institutes of Health Research (CIHR). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Mehran Pesteie ({{collaborator|name|ubc}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 
webite: [http://www.deepinfer.org/ DeepInfer Website] 
License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
[[File:Deepinfer-256.png|128px|]]
 
DeepInfer is an Open-Source Deep Learning Deployment Toolkit for medical imaging and Image-Guided Therapy. With DeepInfer 3D Slicer users can deploy trained
deep learning and machine learning models in their workflow. Also, DeepInfer allows machine learning experts to package,
ship, and deploy their models, thereby additionally allowing clinical researchers and biomedical engineers to use
task-specific deep models, without the need for further software development and configuration.

{{documentation/{{documentation/version}}/module-section|Setup Guide}}
In order to use DeepInfer, [https://www.docker.com/ Docker] is required to be installed and configured properly.
==== Windows ====
Docker for Windows requires Windows 10 Pro (64bit) and Microsoft Hyper-V. You also need to enable virtualization in BIOS settings.
* [https://docs.docker.com/docker-for-windows/install/ Docker installation guide for Windows]
* Share drive C with docker containers from settings.

==== Mac OS X ====
* [https://docs.docker.com/docker-for-mac/install/#install-and-run-docker-for-mac Docker installation guide for MAC]

==== Ubuntu ====
* [https://docs.docker.com/engine/installation/linux/ubuntu/ Docker installation guide for Ubuntu]
* Give non-root access to docker using this [http://askubuntu.com/a/477554 guide].

{{documentation/{{documentation/version}}/module-section|Demo}}
* [https://www.youtube.com/watch?v=7k_SLtmM2Kw Demo Video]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
[[File:Deepinfer-panels.png|600px|]]

{{documentation/{{documentation/version}}/module-section|Deployed Models}}
==== Prostate Segmentation in Targeted MRI-Guided Biopsy ====
This model is trained for the task of rough delineation of the prostate gland that is a necessary step in MRI-guided targeted biopsy. The deployed model is trained on transaxial T2-weighted MRIs of the prostate (without endorectal coil on a 3T MRI machine) collected during MR-guided prostate biopsy procedures. The network based on a customized variant of the U-Net architecture. The network is trained on N = 224 patients on a total number of 26250 2D slices of prostate images and achieved 76.25% accuracy on N = 57 validation patients (2184 2D slices). 

[[File:Prostate-deepinfer.png|800px|]] 


{{documentation/{{documentation/version}}/module-section|Citing DeepInfer}}
To acknowledge DeepInfer and 3D Slicer, please cite the please cite the [http://www.deepinfer.org DeepInfer web site] and following publications when publishing work that uses or incorporates DeepInfer and 3D Slicer:

* Mehrtash, A., Pesteie, M., Hetherington, J., Behringer, P.A., Kapur, T., Wells, W.M., Rohling, R., Fedorov, A. and Abolmaesumi, P., 2017, March. [http://www.spl.harvard.edu/publications/item/view/3076 DeepInfer: open-source deep learning deployment toolkit for image-guided therapy.] In SPIE Medical Imaging (pp. 101351K-101351K). International Society for Optics and Photonics.

* Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network.] Magn Reson Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
==== Architecture ====
The figure below shows the architecture of the DeepInfer toolkit, which has three components: the Docker engine,
the DeepInfer 3D Slicer extension [1], and the cloud model registry [2].
The Docker engine consists of local Docker containers that include the deployed models, as well as all of the required deep learning frameworks, which
process incoming data and produce respective results.
Data streaming between the Docker engine and the GUI is achieved by sharing a local folder with the specific Docker image. 
[[File:Deepifner-arch.png|800px|]] 

# [https://github.com/deepinfer/Slicer-DeepInfer Slicer-DeepInfer Module Source Code]
# [https://github.com/DeepInfer/Model-Registry Model Registry]

==== Packaging and Deployment Example ====
[https://github.com/mehrtash/Prostate-Segmenter Prostate Segmenter Repository] is an example of the code that can be used as a reference to package and deploy a model in DeepInfer.
It shows how you can build a docker and package trained weights inside.

* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/docker/Dockerfile.cpu Example of a CPU DockerFile]
* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/fit.py Example of a python file that is called by running Docker]


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

File:Deepinfer-panels.png

2017-04-11T22:55:15Z

Mehrtash:

Documentation/Nightly/Modules/DeepInfer

2017-04-11T22:52:31Z

Mehrtash:

<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/DeepInfer|DeepInfer]] 
Acknowledgments:
This work is funded by NIH Grant No.P41EB015898, Natural Sciences andEngineering Research Council (NSERC) of Canada and the Canadian Institutes of Health Research (CIHR). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Mehran Pesteie ({{collaborator|name|ubc}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 
webite: [http://www.deepinfer.org/ DeepInfer Website] 
License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
}}

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
[[File:Deepinfer-256.png|128px|]]
 
DeepInfer is an Open-Source Deep Learning Deployment Toolkit for medical imaging and Image-Guided Therapy. With DeepInfer 3D Slicer users can deploy trained
deep learning and machine learning models in their workflow. Also, DeepInfer allows machine learning experts to package,
ship, and deploy their models, thereby additionally allowing clinical researchers and biomedical engineers to use
task-specific deep models, without the need for further software development and configuration.

{{documentation/{{documentation/version}}/module-section|Setup Guide}}
In order to use DeepInfer, [https://www.docker.com/ Docker] is required to be installed and configured properly.
==== Windows ====
Docker for Windows requires Windows 10 Pro (64bit) and Microsoft Hyper-V. You also need to enable virtualization in BIOS settings.
* [https://docs.docker.com/docker-for-windows/install/ Docker installation guide for Windows]
* Share drive C with docker containers from settings.

==== Mac OS X ====
* [https://docs.docker.com/docker-for-mac/install/#install-and-run-docker-for-mac Docker installation guide for MAC]

==== Ubuntu ====
* [https://docs.docker.com/engine/installation/linux/ubuntu/ Docker installation guide for Ubuntu]
* Give non-root access to docker using this [http://askubuntu.com/a/477554 guide].

{{documentation/{{documentation/version}}/module-section|Demo}}
* [https://www.youtube.com/watch?v=7k_SLtmM2Kw Demo Video]


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

{{documentation/{{documentation/version}}/module-section|Deployed Models}}
==== Prostate Segmentation in Targeted MRI-Guided Biopsy ====
This model is trained for the task of rough delineation of the prostate gland that is a necessary step in MRI-guided targeted biopsy. The deployed model is trained on transaxial T2-weighted MRIs of the prostate (without endorectal coil on a 3T MRI machine) collected during MR-guided prostate biopsy procedures. The network based on a customized variant of the U-Net architecture. The network is trained on N = 224 patients on a total number of 26250 2D slices of prostate images and achieved 76.25% accuracy on N = 57 validation patients (2184 2D slices). 

[[File:Prostate-deepinfer.png|800px|]] 


{{documentation/{{documentation/version}}/module-section|Citing DeepInfer}}
To acknowledge DeepInfer and 3D Slicer, please cite the please cite the [http://www.deepinfer.org DeepInfer web site] and following publications when publishing work that uses or incorporates DeepInfer and 3D Slicer:

* Mehrtash, A., Pesteie, M., Hetherington, J., Behringer, P.A., Kapur, T., Wells, W.M., Rohling, R., Fedorov, A. and Abolmaesumi, P., 2017, March. [http://www.spl.harvard.edu/publications/item/view/3076 DeepInfer: open-source deep learning deployment toolkit for image-guided therapy.] In SPIE Medical Imaging (pp. 101351K-101351K). International Society for Optics and Photonics.

* Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network.] Magn Reson Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
==== Architecture ====
The figure below shows the architecture of the DeepInfer toolkit, which has three components: the Docker engine,
the DeepInfer 3D Slicer extension [1], and the cloud model registry [2].
The Docker engine consists of local Docker containers that include the deployed models, as well as all of the required deep learning frameworks, which
process incoming data and produce respective results.
Data streaming between the Docker engine and the GUI is achieved by sharing a local folder with the specific Docker image. 
[[File:Deepifner-arch.png|800px|]] 

# [https://github.com/deepinfer/Slicer-DeepInfer Slicer-DeepInfer Module Source Code]
# [https://github.com/DeepInfer/Model-Registry Model Registry]

==== Packaging and Deployment Example ====
[https://github.com/mehrtash/Prostate-Segmenter Prostate Segmenter Repository] is an example of the code that can be used as a reference to package and deploy a model in DeepInfer.
It shows how you can build a docker and package trained weights inside.

* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/docker/Dockerfile.cpu Example of a CPU DockerFile]
* [https://github.com/mehrtash/Prostate-Segmenter/blob/master/fit.py Example of a python file that is called by running Docker]


{{documentation/{{documentation/version}}/module-footer}}
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Mehrtash: /* Modules by category */

__NOTOC__
<noinclude>{{:Documentation/Nightly/ModuleExtensionListing/TOC}}</noinclude>
= Modules by category =
36 categories:
* [[#Modules_by_category_Cardiac|Cardiac]]
* [[#Modules_by_category_Cardiac_MRI_Toolkit|Cardiac MRI Toolkit]]
* [[#Modules_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Modules_by_category_ML|Machine Learning]]
** [[#Modules_by_category_Chest_Imaging_Platform_Modules|Modules]]
** [[#Modules_by_category_Chest_Imaging_Platform_Toolkit|Toolkit]]
*** [[#Modules_by_category_Toolkit_Particles|Particles]]
*** [[#Modules_by_category_Toolkit_Processing|Processing]]
*** [[#Modules_by_category_Toolkit_Quantification|Quantification]]
*** [[#Modules_by_category_Toolkit_Registration|Registration]]
*** [[#Modules_by_category_Toolkit_Segmentation|Segmentation]]
*** [[#Modules_by_category_Toolkit_Utils|Utils]]
* [[#Modules_by_category_CIP|CIP]]
* [[#Modules_by_category_Converters|Converters]]
* [[#Modules_by_category_Developer_Tools|Developer Tools]]
** [[#Modules_by_category_Developer_Tools_DICOM_Plugins|DICOM Plugins]]
** [[#Modules_by_category_Developer_Tools_Editor_Extensions|Editor Extensions]]
** [[#Modules_by_category_Developer_Tools_Matlab|Matlab]]
* [[#Modules_by_category_Diffusion|Diffusion]]
** [[#Modules_by_category_Diffusion_Diffusion_Data_Conversion|Diffusion Data Conversion]]
** [[#Modules_by_category_Diffusion_Diffusion_Tensor_Images|Diffusion Tensor Images]]
** [[#Modules_by_category_Diffusion_Diffusion_Weighted_Images|Diffusion Weighted Images]]
** [[#Modules_by_category_Diffusion_Process|Process]]
** [[#Modules_by_category_Diffusion_Quantify|Quantify]]
** [[#Modules_by_category_Diffusion_Tractography|Tractography]]
*** [[#Modules_by_category_Diffusion_Tractography_Region_based|Region-based]]
** [[#Modules_by_category_Diffusion_Utilities|Utilities]]
* [[#Modules_by_category_Editor_Effects|Editor Effects]]
* [[#Modules_by_category_EditorEffect|Editor Effect]]
* [[#Modules_by_category_Endoscopy|Endoscopy]]
* [[#Modules_by_category_Examples|Examples]]
* [[#Modules_by_category_Exporter|Exporter]]
* [[#Modules_by_category_Filter|Filter]]
* [[#Modules_by_category_Filtering|Filtering]]
** [[#Modules_by_category_Filtering_Arithmetic|Arithmetic]]
** [[#Modules_by_category_Filtering_Denoising|Denoising]]
** [[#Modules_by_category_Filtering_Morphology|Morphology]]
* [[#Modules_by_category_IGT|IGT]]
* [[#Modules_by_category_Informatics|Informatics]]
** [[#Modules_by_category_Informatics_Converters|Converters]]
* [[#Modules_by_category_Legacy|Legacy]]
** [[#Modules_by_category_Legacy_Converters|Converters]]
** [[#Modules_by_category_Legacy_Filtering|Filtering]]
** [[#Modules_by_category_Legacy_Registration|Registration]]
** [[#Modules_by_category_Legacy_Work_in_Progress|Work in Progress]]
*** [[#Modules_by_category_Work_in_Progress_Diffusion_Tensor|Diffusion Tensor]]
**** [[#Modules_by_category_Diffusion_Tensor_Test|Test]]
* [[#Modules_by_category_Margin_Calculator|Margin Calculator]]
* [[#Modules_by_category_Mesh_Generation|Mesh Generation]]
* [[#Modules_by_category_MeshGeneration|Mesh Generation]]
* [[#Modules_by_category_Microscopy|Microscopy]]
* [[#Modules_by_category_MultiVolume_Support|Multi Volume Support]]
* [[#Modules_by_category_Plastimatch|Plastimatch]]
** [[#Modules_by_category_Plastimatch_Registration|Registration]]
** [[#Modules_by_category_Plastimatch_Utilities|Utilities]]
* [[#Modules_by_category_Quantification|Quantification]]
** [[#Modules_by_category_Quantification_ChangeQuantification|Change Quantification]]
* [[#Modules_by_category_Radiotherapy|Radiotherapy]]
* [[#Modules_by_category_Registration|Registration]]
** [[#Modules_by_category_Registration_CMF_Registration|CMF Registration]]
*** [[#Modules_by_category_CMF_Registration_Voxelbase_Registration|Voxelbase Registration]]
** [[#Modules_by_category_Registration_Label_Registration|Label Registration]]
** [[#Modules_by_category_Registration_Specialized|Specialized]]
* [[#Modules_by_category_Segmentation|Segmentation]]
** [[#Modules_by_category_Segmentation_Specialized|Specialized]]
* [[#Modules_by_category_Sequences|Sequences]]
* [[#Modules_by_category_Shape_Analysis|Shape Analysis]]
* [[#Modules_by_category_Slicelets|Slicelets]]
* [[#Modules_by_category_Surface_Models|Surface Models]]
* [[#Modules_by_category_TestCases|Test Cases]]
* [[#Modules_by_category_Testing|Testing]]
** [[#Modules_by_category_Testing_IGT_Tests|IGT Tests]]
** [[#Modules_by_category_Testing_SlicerRT_Tests|Slicer RT Tests]]
** [[#Modules_by_category_Testing_TestCases|Test Cases]]
* [[#Modules_by_category_Utilities|Utilities]]
** [[#Modules_by_category_Utilities_BRAINS|BRAINS]]
* [[#Modules_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Modules_by_category_Wizards|Wizards]]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Philips4d Us Dicom Patcher]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]] extension)
* [[Documentation/Nightly/Extensions/SlicerHeart|Valve View]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]] extension)

== Cardiac MRI Toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit PVAntrum Cut] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Boolean REMOVEFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentation Workflow]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration BRAINSFit] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Automatic Left Atrial Scar] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Connected Threshold Filter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Wizard] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Isolated Connected Filter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Inhomogeneity Correction] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Axial Dilate] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [[Documentation/Nightly/Modules/ScarVisualization|Scar Visualization]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit LASegmentation Graph Cuts] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)

== Machine Learning ==
* [[Documentation/Nightly/Modules/DeepInfer|DeepInfer]]


== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Interactive Lobe Segmentation] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Airway Inspector] (loadable, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

=== Modules ===
* [http://www.chestimagingplatform.org CIP MIPViewer] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Body Composition] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Trachea Stent Planning] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Lesion Model] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP PAARatio] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Parenchyma Subtype Training] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

=== Toolkit ===

==== Particles ====
* [http://www.chestimagingplatform.org Extract Particles From Chest Region Chest Type] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Filter Vessel Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Remove Particles From Particles Data Set] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Merge Particle Data Sets] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Perturb Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Filter Airway Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Fit Lobe Surface Models To Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Classify Fissure Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Stenciled Label Map From Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Filter Fissure Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

==== Processing ====
* [http://www.chestimagingplatform.org Resample Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Rescale Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Median Filtered Image] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Label Map From Region And Type Points] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Crop Lung] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate NLMFiltered Image] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Remove Chest Type From Label Map Using Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Atlas Convex Hull] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Fissure Feature Vectors] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Lobe Surface Models] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Filter Connected Components] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Extract Chest Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Perform Morphological] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Extract Fissure Boundary From Lobe Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Enhance Fissures In Image] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Remap Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Distance Map From Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Resample CT] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Feature Strength] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Distance Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Quality Control] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Image Sub Volumes] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

==== Quantification ====
* [http://www.chestimagingplatform.org Evaluate Lung Lobe Segmentation Results] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Transformation Kappa] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read Write Image Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Intensity Statistics] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Cross Sectional Area] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Label Particles By Chest Region Chest Type] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Transformation Similarity Metric] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Region Histograms And Parenchyma Phenotypes] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Transformation Kappa2D] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

==== Registration ====
* [http://www.chestimagingplatform.org Register Lung Atlas] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Register Label Maps] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Register CT] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

==== Segmentation ====
* [http://www.chestimagingplatform.org Generate Otsu Lung Cast] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Segment Lung Lobes] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Partial Lung Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Split Left Lung Right Lung] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Binary Thinning3D] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Lesion Segmentation] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

==== Utils ====
* [http://www.chestimagingplatform.org Convert Dicom] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Region Type Locations To ROIVolume] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read VTKWrite NRRDs] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Overlay Images] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Execute System Command] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Structures In Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Find Patch Match] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Convert Chest Region Chest Type To Label Map Value] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Mask Out Label Map Structures] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read NRRDs Write VTK] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Convert Label Map Value To Chest Region Chest Type] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read Write Region And Type Points] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Merge Chest Label Maps] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read Vida Write CIP] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read Dicom Write Tags] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Transfer Region And Type Indices To From Points] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

== CIP ==
* [http://www.chestimagingplatform.org CIP Common] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

== Converters ==
* [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|Quad Edge Surface Mesher]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)
* [[Documentation/Nightly/Modules/CropVolume|Crop Volume]] (loadable, built-in)
* [[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/UKFTractography|Convert VTK]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Modules/VectorToScalarVolume|Vector To Scalar Volume]] (scripted, built-in)
* [[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOMSeries]] (cli, built-in)
* [http://www.chestimagingplatform.org Particles Display] (loadable, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Region Type] (loadable, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)

== Developer Tools ==
* [[Documentation/Nightly/Modules/Cameras|Cameras]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ExecutionModelTour|Execution Model Tour]] (cli, built-in)
* [[Documentation/Nightly/Extensions/DebuggingTools|Node Modified Statistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]] extension)
* [[Documentation/Nightly/Extensions/DebuggingTools|Py Dev Remote Debug]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]] extension)
* [[Documentation/Nightly/Modules/ExtensionWizard|Extension Wizard]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ImageMaker|Image Maker]] (cli, bundled in [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]] extension)
* [[Documentation/Nightly/Modules/ExtensionStats|Extension Stats]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]] extension)
* [[Documentation/Nightly/Modules/DeveloperToolsForExtensions|Developer Tools For Extensions]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]] extension)
* [[Documentation/Nightly/Modules/EventBroker|Event Broker]]
* Double Arrays (loadable, built-in)

=== DICOM Plugins ===
* Dicom Ultrasound Plugin
* DICOMSegmentation Plugin
* DICOMSlicer Data Bundle Plugin
* [[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]
* DICOMDiffusion Volume Plugin
* DICOMLongitudinal PETCTPlugin
* Dicom Sro Import Plugin
* DICOMScalar Volume Plugin
* [[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]
* Dicom Rt Import Export Plugin
* Multi Volume Importer Plugin

=== Editor Extensions ===
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect] (scripted, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice Effect] (scripted, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)
* [[Documentation/Nightly/Modules/PETTumorSegmentationEffect|PETTumor Segmentation Effect]] (scripted, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]] extension)
* [[Documentation/Nightly/Extensions/IASEM|Binary Watershed Effect]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|Double Threshold Effect]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)

=== Matlab ===
* [[Documentation/Nightly/Modules/MatlabModuleGenerator|Matlab Module Generator]] (loadable, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]] extension)
* [[Documentation/Nightly/Modules/MatlabCommander|Matlab Commander]] (cli, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]] extension)

== Diffusion ==


=== Diffusion Data Conversion ===
* [[Documentation/Nightly/Modules/DWIConverter|DWIConverter]] (cli, built-in)


=== Diffusion Tensor Images ===
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]] (cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]] extension)


=== Diffusion Weighted Images ===
* BRAINSDWICleanup (cli, built-in)
* [[Documentation/Nightly/Modules/FinslerBacktracing|Finsler Backtracing]] (cli, bundled in [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]] extension)
* [[Documentation/Nightly/Modules/FinslerTractography|Finsler Tractography]] (cli, bundled in [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]] extension)


=== Process ===
* [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|Diffusion Brain Masking]] (cli, built-in)
* [[Documentation/Nightly/Modules/DWIToDTIEstimation|Diffusion Tensor Estimation]] (cli, built-in)


=== Quantify ===
* [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Maps]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiberTractMeasurements|Tractography Measurements]] (cli, built-in)


=== Tractography ===
* [[Documentation/Nightly/Modules/TractographyDisplay|Tractography Display]] (loadable, built-in)
* [[Documentation/Nightly/Modules/TractographyInteractiveSeeding|Tractography Seeding]] (loadable, built-in)
* [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)

==== Region-based ====
* [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|Tractography ROI Seeding]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiberBundleLabelSelect|Tractography ROI Selection]] (cli, built-in)


=== Utilities ===
* [[Documentation/Nightly/Modules/TractographyDICOMLoad|Tractography DICOM Load]] (cli, built-in)
* [[Documentation/Nightly/Modules/TractographyDICOMSave|Tractography DICOM Save]] (cli, built-in)
* DWI to Full Brain Tractography (cli, built-in)
* [[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTIVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiberBundleToLabelMap|Tractography to Mask Image]] (scripted, built-in)



== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]] (scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]] extension)

== EditorEffect ==
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]] extension)

== Endoscopy ==
* [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted, built-in)

== Examples ==
* [[Documentation/Nightly/Modules/FastGrowCut|Fast Grow Cut]] (loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Fast Grow Cut Segmenter] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Interactive Segmenter] (loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment] extension)

== Exporter ==
* [[Documentation/Nightly/Modules/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] extension)

== Filter ==
* Island Removal (cli, built-in)

== Filtering ==
* [[Documentation/Nightly/Modules/SegmentationSmoothing|Segmentation Smoothing]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)
* [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBias Field Correction]] (cli, built-in)
* [[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] (cli, built-in)
* [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (cli, built-in)
* [[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] (cli, built-in)
* [[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] (cli, built-in)
* [[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (cli, built-in)
* [[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] (cli, built-in)

=== Arithmetic ===
* [[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] (cli, built-in)
* [[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] (cli, built-in)

=== Denoising ===
* [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (cli, built-in)
* [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] (cli, built-in)
* [[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (cli, built-in)

=== Morphology ===
* [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (cli, built-in)

== IGT ==
* [https://github.com/SlicerIGT/LumpNav Viewpoint] (scripted, bundled in [https://github.com/SlicerIGT/LumpNav Lump Nav] extension)
* [[Documentation/Nightly/Modules/CollectFiducials|Collect Fiducials]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [https://github.com/SlicerIGT/LumpNav Lump Nav] (scripted, bundled in [https://github.com/SlicerIGT/LumpNav Lump Nav] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Transform Fusion]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/GyroGuide|Gyro Guide]] (scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Create Models]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]] (scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]] extension)
* [[Documentation/Nightly/Modules/TrackerStabilizer|Tracker Stabilizer]] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer] extension)
* [[Documentation/Nightly/Modules/PathExplorer|Path Explorer]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Ultrasound Snapshots]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [https://github.com/SlicerIGT/LumpNav Breach Warning Light] (scripted, bundled in [https://github.com/SlicerIGT/LumpNav Lump Nav] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Breach Warning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Model Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Pivot Calibration]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/VolumeResliceDriver|Volume Reslice Driver]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Fiducial Registration Wizard]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkRemote|Open IGTLink Remote]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/Watchdog|Watchdog]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/CornerAnnotation|Corner Annotation]] (scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkIF|Open IGTLink IF]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]] (scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|i Gyne]] extension)
* [[Documentation/Nightly/Modules/PlusRemote|Plus Remote]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Fiducials To Model Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Markups To Model]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)

== Informatics ==
* [[Documentation/Nightly/Extensions/mpReview|mp Review Preprocessor]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mp Review]] extension)
* [[Documentation/Nightly/Modules/Tables|Tables]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mp Review]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mp Review]] extension)
* [[Documentation/Nightly/Modules/Data|Data]] (loadable, built-in)
* [[Documentation/Nightly/Modules/Units|Units]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DICOM|DICOM]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SampleData|Sample Data]] (scripted, built-in)
* [[Documentation/Nightly/Modules/Colors|Colors]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]] (scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]] extension)
* [[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable, built-in)
* [[Documentation/Nightly/Modules/Markups|Markups]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SubjectHierarchy|Subject Hierarchy]] (loadable, built-in)

=== Converters ===


== Legacy ==

=== Converters ===
* [[Documentation/Nightly/Modules/BSplineToDeformationField|BSpline To Deformation Field]] (cli, built-in)

=== Filtering ===
* [[Documentation/Nightly/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (cli, built-in)
* [[Documentation/Nightly/Modules/ResampleScalarVolume|Resample Scalar Volume]] (cli, built-in)

=== Registration ===
* Test Grid Transform Registration (cli, built-in)
* [[Documentation/Nightly/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] (cli, built-in)

=== Work in Progress ===

==== Diffusion Tensor ====

===== Test =====
* Diffusion Tensor Test (cli, built-in)

== Margin Calculator ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Dose Morphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Dose Population Histogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Motion Simulator]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Synthetic RTDose]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Motion Simulator Double Array]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver CLI]] (cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]] extension)

== MeshGeneration ==
* [[Documentation/Nightly/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)
* [[Documentation/Nightly/Modules/MeshCompression|Mesh Compression]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport Series]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|Bin Shrink]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|Label Object Statistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|Spacing Aware Curvature Diffusion]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)

== MultiVolume Support ==
* [[Documentation/Nightly/Modules/MultiVolumeImporter|Multi Volume Importer]] (scripted, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeExplorer|Multi Volume Explorer]] (loadable, built-in)

== Plastimatch ==
* [[Documentation/Nightly/Modules/DicomSroExport|Dicom Sro Export]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Plm Register]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)

=== Registration ===
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch slicer bspline]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch slicer landwarp]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)

=== Utilities ===
* [[Documentation/Nightly/Extensions/SlicerRT|Plastimatch Py]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] (cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)
* [[Documentation/Nightly/Extensions/PET-IndiC|PETIndi C]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]] extension)
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] (scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)
* [[Documentation/Nightly/Modules/HeterogeneityCAD|Heterogeneity CAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]] (cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]] extension)
* [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandard Uptake Value Computation]] (cli, built-in)
* [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactor Calculator]] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)
* [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]] extension)
* [[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DWModeling|DWModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)
* BRAINSLabel Stats (cli, built-in)
* [[Documentation/Nightly/Modules/PkModeling|Pk Modeling]] (cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]] extension)
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImage Maker]] (cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]] extension)
* [[Documentation/Nightly/Modules/DataProbe|Data Probe]] (scripted, built-in)
* [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] (cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension] extension)
* [[Documentation/Nightly/Modules/dPetBrainQuantification|d Pet Brain Quantification]] (scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension] extension)
* [[Documentation/Nightly/Modules/DiceComputation|Dice Computation]] (loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]] extension)

=== ChangeQuantification ===
* [[Documentation/Nightly/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]] extension)

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/SlicerRT|Beams]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Dvh Comparison]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/Isodose|Isodose]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DoseVolumeHistogram|Dose Volume Histogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Dicom Rt Import Export]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DoseAccumulation|Dose Accumulation]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/SegmentComparison|Segment Comparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Planar Image]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/SegmentMorphology|Segment Morphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DoseComparison|Dose Comparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DicomSroImport|Dicom Sro Import]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)

== Registration ==
* [[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable, built-in)
* BRAINSResize (cli, built-in)
* Perform Metric Test (cli, built-in)
* [[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] (cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)
* [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] (cli, built-in)

=== CMF Registration ===
* [[Documentation/Nightly/Extensions/CMFreg|Apply Matrix]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelAddition|Label Addition]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/Downsize|Downsize]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/SurfaceRegistration|Surface Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelExtraction|Label Extraction]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)

==== Voxelbase Registration ====
* [[Documentation/Nightly/Modules/NonGrowing|Non Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/Growing|Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/MaskCreation|Mask Creation]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)

=== Label Registration ===
* [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|Distance Map Based Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)

=== Specialized ===
* [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemon Warp]] (cli, built-in)
* [[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable, built-in)
* VBRAINSDemon Warp (cli, built-in)

== Segmentation ==
* EMSegment Quick (loadable, built-in)
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip With Model]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]] extension)
* [http://www.nitrc.org/projects/abc ABC] (cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation CLI] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation] extension)
* [[Documentation/Nightly/Modules/LAScarSegmenter|LAScar Segmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]] extension)
* [[Documentation/Nightly/Modules/SegmentEditor|Segment Editor]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/AirwaySegmentation|Airway Segmentation]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation] extension)
* [[Documentation/Nightly/Modules/SkullStripper|Skull Stripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip With Roi]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]] extension)
* [[Documentation/Nightly/Modules/SegmentCAD|Segment CAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]] extension)
* [[Documentation/Nightly/Modules/SwissSkullStripper|Swiss Skull Stripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]] extension)
* [https://github.com/Tomnl/Slicer-Wasp Wasp] (scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)
* [[Documentation/Nightly/Modules/Editor|Editor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (cli, built-in)
* [[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]] extension)

=== Specialized ===
* BRAINSROIAuto (cli, built-in)
* [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (cli, built-in)
* EMSegment Command Line (cli, built-in)


== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|Sequence Browser]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|Metafile Importer]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]] (cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]] extension)

== Slicelets ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis Algo] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)

== Surface Models ==
* [[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] (scripted, built-in)
* [[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] (cli, built-in)
* [[Documentation/Nightly/Modules/ModelMaker|Model Maker]] (cli, built-in)
* [[Documentation/Nightly/Modules/ModelToLabelMap|Model To Label Map]] (cli, built-in)
* [[Documentation/Nightly/Modules/MergeModels|Merge Models]] (cli, built-in)
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]] (scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]] extension)
* [[Documentation/Nightly/Modules/LabelMapSmoothing|Label Map Smoothing]] (cli, built-in)
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]] (cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]] extension)
* [[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] (cli, built-in)

== TestCases ==
* SEGExporter Self Test

== Testing ==
* CLI4Test
* Threshold Threading Test
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis Monitoring]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* Slicer MRBSave Restore Check Paths Test
* CLIROITest (cli, built-in)
* Performance Tests
* Slicer MRBMultiple Save Restore Test
* Slicer MRBTest
* SEGExporter Self Test
* Self Tests
* Slicer MRBMultiple Save Restore Loop Test

=== IGT Tests ===
* Breach Warning Self Test
* Watchdog Self Test

=== SlicerRT Tests ===
* IGRTWorkflow Self Test
* Dicom Rt Import Self Test
* [[Documentation/Nightly/Extensions/SlicerRT|Batch Structure Set Conversion]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)

=== TestCases ===
* Atlas Tests
* Add Storable Data After Scene View Test
* test tractography display
* RSNAQuant Tutorial
* Neurosurgical Planning Tutorial Markups Self Test
* Change Tracker Self Test
* Fiducial Layout Switch Bug1914
* Graph Cut Segment Self Test
* Charting (scripted, built-in)
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures] (scripted, bundled in [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures] extension)
* fiber visibility crash2438
* RSNAVis Tutorial
* JRC2013Vis
* Add Many Markups Fiducial Test
* Slicer4Minute (scripted, built-in)
* Crop Volume Self Test
* Slice Link Logic (scripted, built-in)
* Volume Rendering Scene Close (scripted, built-in)
* slicer Close Crash Bug2590
* CLIEvent Test
* Markups Widgets Self Test
* Tables Self Test
* Markups In Views Self Test
* Two CLIs In Parallel Test
* Subject Hierarchy Core Plugins Self Test
* Subject Hierarchy Generic Self Test
* Scene Performance (scripted, built-in)
* Markups In Compare Viewers Self Test
* scene Import2428
* RSNA2012Prostate Demo
* DTINot Reproducible Issue3977
* Two CLIs In ARow Test
* Colors Scalar Bar Self Test
* BRAINSFit Rigid Registration Crash Issue4139
* View Controllers Slice Interpolation Bug1926

== Utilities ==
* [[Documentation/Nightly/Modules/DataStore|Data Store]] (loadable, built-in)
* BRAINSStrip Rotation (cli, built-in)
* EMSegment Transform To New Format (cli, built-in)

=== BRAINS ===
* BRAINSTransform Convert (cli, built-in)

== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ Centerline Computation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [http://slicer.vmtk.org/ Vesselness Filtering] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [http://slicer.vmtk.org/ Level Set Segmentation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)

== Wizards ==
* [[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ChangeTracker|Change Tracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]] extension)

= Modules by name =
311 modules:
* [http://www.nitrc.org/projects/abc ABC] (cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)
* [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] (cli, built-in)
* [[Documentation/Nightly/Modules/AddScalarVolumes|Add Scalar Volumes]] (cli, built-in)
* [http://www.chestimagingplatform.org Airway Inspector] (loadable, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/AirwaySegmentation|Airway Segmentation]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation CLI] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension] extension)
* [[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/CMFreg|Apply Matrix]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Beams]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/IASEM|Bin Shrink]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)
* [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemon Warp]] (cli, built-in)
* BRAINSDWICleanup (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] (cli, built-in)
* BRAINSLabel Stats (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] (cli, built-in)
* BRAINSResize (cli, built-in)
* BRAINSROIAuto (cli, built-in)
* BRAINSStrip Rotation (cli, built-in)
* BRAINSTransform Convert (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|Breach Warning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [https://github.com/SlicerIGT/LumpNav Breach Warning Light] (scripted, bundled in [https://github.com/SlicerIGT/LumpNav Lump Nav] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)
* [[Documentation/Nightly/Modules/CastScalarVolume|Cast Scalar Volume]] (cli, built-in)
* [http://slicer.vmtk.org/ Centerline Computation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Modules/ChangeTracker|Change Tracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]] extension)
* [[Documentation/Nightly/Modules/CheckerBoardFilter|Checker Board Filter]] (cli, built-in)
* [http://www.chestimagingplatform.org CIP Body Composition] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Common] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Lesion Model] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP MIPViewer] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP PAARatio] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Parenchyma Subtype Training] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org CIP Trachea Stent Planning] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Classify Fissure Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver CLI]] (cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Automatic Left Atrial Scar] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Axial Dilate] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Boolean REMOVEFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Connected Threshold Filter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Inhomogeneity Correction] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Isolated Connected Filter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit LASegmentation Graph Cuts] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit PVAntrum Cut] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration BRAINSFit] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Wizard] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [[Documentation/Nightly/Modules/CollectFiducials|Collect Fiducials]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/Colors|Colors]] (loadable, built-in)
* [[Documentation/Nightly/Modules/CompareVolumes|Compare Volumes]] (scripted, built-in)
* [http://www.chestimagingplatform.org Compute Cross Sectional Area] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Distance Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Feature Strength] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Fissure Feature Vectors] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Compute Intensity Statistics] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Convert Chest Region Chest Type To Label Map Value] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Convert Dicom] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Convert Label Map Value To Chest Region Chest Type] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Extensions/UKFTractography|Convert VTK]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Modules/CornerAnnotation|Corner Annotation]] (scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]] extension)
* [[Documentation/Nightly/Modules/CreateDICOMSeries|Create DICOMSeries]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|Create Models]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [http://www.chestimagingplatform.org Crop Lung] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/CropVolume|Crop Volume]] (loadable, built-in)
* [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (cli, built-in)
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]] (scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]] extension)
* [[Documentation/Nightly/Modules/Data|Data]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DataProbe|Data Probe]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DataStore|Data Store]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DiceComputation|Dice Computation]] (loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]] extension)
* [[Documentation/Nightly/Modules/DICOM|DICOM]] (scripted, built-in)
* DICOM2Full Brain Tractography (scripted, built-in)
* [[Documentation/Nightly/Extensions/SlicerRT|Dicom Rt Import Export]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DicomSroExport|Dicom Sro Export]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DicomSroImport|Dicom Sro Import]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (cli, built-in)
* [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (cli, built-in)
* [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|Distance Map Based Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)
* [[Documentation/Nightly/Modules/DoseAccumulation|Dose Accumulation]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/DoseComparison|Dose Comparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Dose Morphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Dose Population Histogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Modules/DoseVolumeHistogram|Dose Volume Histogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/Downsize|Downsize]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/dPetBrainQuantification|d Pet Brain Quantification]] (scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis] extension)
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] (cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Dvh Comparison]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* DWIConvert (cli, built-in)
* [[Documentation/Nightly/Modules/DWIToDTIEstimation|DWITo DTIEstimation]] (cli, built-in)
* [[Documentation/Nightly/Modules/DWModeling|DWModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]] (scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]] extension)
* [[Documentation/Nightly/Modules/Editor|Editor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable, built-in)
* EMSegment Command Line (cli, built-in)
* EMSegment Quick (loadable, built-in)
* EMSegment Transform To New Format (cli, built-in)
* [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted, built-in)
* [http://www.chestimagingplatform.org Enhance Fissures In Image] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Evaluate Lung Lobe Segmentation Results] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Execute System Command] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Extract Chest Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Extract Fissure Boundary From Lobe Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Extract Particles From Chest Region Chest Type] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/ExtractSkeleton|Extract Skeleton]] (cli, built-in)
* [[Documentation/Nightly/Modules/FastGrowCut|Fast Grow Cut]] (loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Fast Grow Cut Segmenter] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)
* Fiber Bundle Label Select (cli, built-in)
* [[Documentation/Nightly/Modules/FiberBundleToLabelMap|Fiber Bundle To Label Map]] (scripted, built-in)
* [[Documentation/Nightly/Modules/FiberTractMeasurements|Fiber Tract Measurements]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiducialRegistration|Fiducial Registration]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|Fiducial Registration Wizard]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Fiducials To Model Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [http://www.chestimagingplatform.org Filter Airway Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Filter Connected Components] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Filter Fissure Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Filter Vessel Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Find Patch Match] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/FinslerBacktracing|Finsler Backtracing]] (cli, bundled in [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]] extension)
* [[Documentation/Nightly/Modules/FinslerTractography|Finsler Tractography]] (cli, bundled in [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]] extension)
* [http://www.chestimagingplatform.org Fit Lobe Surface Models To Particle Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (cli, built-in)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis Algo] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)
* [http://www.chestimagingplatform.org Generate Atlas Convex Hull] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Binary Thinning3D] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Distance Map From Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Image Sub Volumes] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Lesion Segmentation] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Lobe Surface Models] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Median Filtered Image] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate NLMFiltered Image] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Otsu Lung Cast] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Overlay Images] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Partial Lung Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Region Histograms And Parenchyma Phenotypes] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Generate Stenciled Label Map From Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Structures In Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Transformation Kappa] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Transformation Kappa2D] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Get Transformation Similarity Metric] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] (cli, built-in)
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Interactive Segmenter] (loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment] extension)
* [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleModelMaker|Grayscale Model Maker]] (cli, built-in)
* [[Documentation/Nightly/Modules/Growing|Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/GyroGuide|Gyro Guide]] (scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]] extension)
* [[Documentation/Nightly/Modules/HeterogeneityCAD|Heterogeneity CAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]] extension)
* [[Documentation/Nightly/Modules/HistogramMatching|Histogram Matching]] (cli, built-in)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport Series]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]] (scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|i Gyne]] extension)
* [[Documentation/Nightly/Modules/ImageLabelCombine|Image Label Combine]] (cli, built-in)
* [[Documentation/Nightly/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]] extension)
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]] extension)
* [http://www.chestimagingplatform.org Interactive Lobe Segmentation] (scripted, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* Island Removal (cli, built-in)
* [[Documentation/Nightly/Modules/Isodose|Isodose]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter KUtil] (scripted, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)
* [[Documentation/Nightly/Modules/LabelAddition|Label Addition]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelExtraction|Label Extraction]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [http://www.chestimagingplatform.org Label Map From Region And Type Points] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/LabelMapSmoothing|Label Map Smoothing]] (cli, built-in)
* [[Documentation/Nightly/Extensions/IASEM|Label Object Statistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [http://www.chestimagingplatform.org Label Particles By Chest Region Chest Type] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/LabelStatistics|Label Statistics]] (scripted, built-in)
* [[Documentation/Nightly/Modules/LandmarkRegistration|Landmark Registration]] (scripted, built-in)
* [[Documentation/Nightly/Modules/LAScarSegmenter|LAScar Segmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]] extension)
* [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentation Workflow]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [http://slicer.vmtk.org/ Level Set Segmentation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [https://github.com/SlicerIGT/LumpNav Lump Nav] (scripted, bundled in [https://github.com/SlicerIGT/LumpNav Lump Nav] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Modules/Markups|Markups]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|Markups To Model]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/MaskCreation|Mask Creation]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [http://www.chestimagingplatform.org Mask Out Label Map Structures] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/MaskScalarVolume|Mask Scalar Volume]] (cli, built-in)
* [[Documentation/Nightly/Modules/MedianImageFilter|Median Image Filter]] (cli, built-in)
* [http://www.chestimagingplatform.org Merge Chest Label Maps] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/MergeModels|Merge Models]] (cli, built-in)
* [http://www.chestimagingplatform.org Merge Particle Data Sets] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/MeshCompression|Mesh Compression]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]] (cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]] extension)
* [[Documentation/Nightly/Extensions/Sequences|Metafile Importer]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Modules/ModelMaker|Model Maker]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|Model Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/Models|Models]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ModelToLabelMap|Model To Label Map]] (cli, built-in)
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]] (cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Motion Simulator]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Motion Simulator Double Array]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mp Review]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mp Review]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mp Review Preprocessor]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mp Review]] extension)
* [[Documentation/Nightly/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeExplorer|Multi Volume Explorer]] (loadable, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeImporter|Multi Volume Importer]] (scripted, built-in)
* [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBias Field Correction]] (cli, built-in)
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]] (scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]] extension)
* [[Documentation/Nightly/Modules/NonGrowing|Non Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkIF|Open IGTLink IF]] (loadable, built-in)
* [[Documentation/Nightly/Modules/OpenIGTLinkRemote|Open IGTLink Remote]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/OrientScalarVolume|Orient Scalar Volume]] (cli, built-in)
* [http://www.chestimagingplatform.org Particles Display] (loadable, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/PathExplorer|Path Explorer]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] (cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)
* Perform Metric Test (cli, built-in)
* [http://www.chestimagingplatform.org Perform Morphological] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Perturb Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Extensions/PET-IndiC|PETIndi C]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]] extension)
* [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandard Uptake Value Computation]] (cli, built-in)
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImage Maker]] (cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]] extension)
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]] extension)
* [[Documentation/Nightly/Extensions/SlicerHeart|Philips4d Us Dicom Patcher]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Pivot Calibration]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/PkModeling|Pk Modeling]] (cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Planar Image]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch slicer bspline]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch slicer landwarp]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Plastimatch Py]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Plm Register]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/PlusRemote|Plus Remote]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/ProbeVolumeWithModel|Probe Volume With Model]] (cli, built-in)
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] (scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)
* [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|Quad Edge Surface Mesher]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)
* [http://www.chestimagingplatform.org Quality Control] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]] (cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]] extension)
* [http://www.chestimagingplatform.org Read Dicom Write Tags] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read NRRDs Write VTK] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read Vida Write CIP] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read VTKWrite NRRDs] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read Write Image Data] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Read Write Region And Type Points] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable, built-in)
* [http://www.chestimagingplatform.org Region Type] (loadable, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Region Type Locations To ROIVolume] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Register CT] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Register Label Maps] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Register Lung Atlas] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Remap Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Remove Chest Type From Label Map Using Particles] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Remove Particles From Particles Data Set] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [http://www.chestimagingplatform.org Resample CT] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]] (cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]] extension)
* [[Documentation/Nightly/Modules/ResampleDTIVolume|Resample DTIVolume]] (cli, built-in)
* [http://www.chestimagingplatform.org Resample Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWIVolume]] (cli, built-in)
* [http://www.chestimagingplatform.org Rescale Label Map] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (cli, built-in)
* [[Documentation/Nightly/Modules/SampleData|Sample Data]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ScarVisualization|Scar Visualization]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)
* [[Documentation/Nightly/Modules/SceneViews|Scene Views]] (loadable, built-in)
* [[Documentation/Nightly/Modules/Segmentations|Segmentations]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/SegmentationSmoothing|Segmentation Smoothing]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]] extension)
* [[Documentation/Nightly/Modules/SegmentCAD|Segment CAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]] extension)
* [[Documentation/Nightly/Modules/SegmentComparison|Segment Comparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Segment Editor]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [http://www.chestimagingplatform.org Segment Lung Lobes] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/SegmentMorphology|Segment Morphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Extensions/Sequences|Sequence Browser]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|Sequences]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Modules/SimpleFilters|Simple Filters]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (cli, built-in)
* [[Documentation/Nightly/Modules/SkullStripper|Skull Stripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]] extension)
* [[Documentation/Nightly/Modules/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] extension)
* [[Documentation/Nightly/Extensions/IASEM|Spacing Aware Curvature Diffusion]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* [http://www.chestimagingplatform.org Split Left Lung Right Lung] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Modules/SubjectHierarchy|Subject Hierarchy]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/SurfaceRegistration|Surface Registration]] (scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/SurfaceToolbox|Surface Toolbox]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactor Calculator]] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)
* [[Documentation/Nightly/Modules/SwissSkullStripper|Swiss Skull Stripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|Synthetic RTDose]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]] extension)
* [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] (cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)
* [[Documentation/Nightly/Modules/Tables|Tables]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)
* [[Documentation/Nightly/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (cli, built-in)
* [[Documentation/Nightly/Modules/TrackerStabilizer|Tracker Stabilizer]] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer] extension)
* [[Documentation/Nightly/Modules/TractographyDisplay|Tractography Display]] (loadable, built-in)
* Tractography Interactive Seeding (loadable, built-in)
* [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (cli, built-in)
* [http://www.chestimagingplatform.org Transfer Region And Type Indices To From Points] (cli, bundled in [http://www.chestimagingplatform.org Chest Imaging Platform] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Transform Fusion]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable, built-in)
* [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|Ultrasound Snapshots]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/Units|Units]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerHeart|Valve View]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]] extension)
* VBRAINSDemon Warp (cli, built-in)
* [[Documentation/Nightly/Modules/VectorToScalarVolume|Vector To Scalar Volume]] (scripted, built-in)
* [http://slicer.vmtk.org/ Vesselness Filtering] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Vff File Reader]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]] extension)
* [[Documentation/Nightly/Modules/ViewControllers|View Controllers]] (loadable, built-in)
* [https://github.com/SlicerIGT/LumpNav Viewpoint] (scripted, bundled in [https://github.com/SlicerIGT/LumpNav Lump Nav] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip With Model]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip With Roi]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]] extension)
* [[Documentation/Nightly/Modules/VolumeRendering|Volume Rendering]] (loadable, built-in)
* [[Documentation/Nightly/Modules/VolumeResliceDriver|Volume Reslice Driver]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/Volumes|Volumes]] (loadable, built-in)
* [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (cli, built-in)
* [https://github.com/Tomnl/Slicer-Wasp Wasp] (scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)
* [[Documentation/Nightly/Modules/Watchdog|Watchdog]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]] extension)
* [[Documentation/Nightly/Modules/Welcome|Welcome]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]] (scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]] extension)

Documentation/Nightly/Extensions/DeepInfer

2017-04-09T23:34:44Z

Mehrtash: Mehrtash moved page Documentation/Nightly/Extensions/DeepInfer to Documentation/Nightly/Modules/DeepInfer

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

Documentation/Nightly/Modules/DeepInfer

2017-04-09T23:34:43Z

Mehrtash: Mehrtash moved page Documentation/Nightly/Extensions/DeepInfer to Documentation/Nightly/Modules/DeepInfer

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2017-04-09T23:34:19Z

Mehrtash: /* Extensions by category */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]
* [[Documentation/Nightly/Extensions/DatabaseInteractor|Database Interactor]]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

File:Deepinfer-256.png

2017-02-04T14:00:50Z

Mehrtash:

Documentation/4.6/ModuleExtensionListing/Extensions by category

2017-02-04T13:39:23Z

Mehrtash:

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]


== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://github.com/KitwareMedical/SlicerITKUltrasound SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2017-02-04T13:37:14Z

Mehrtash: /* Extensions by category */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]


== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]
== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]
* [[Documentation/Nightly/Extensions/DatabaseInteractor|Database Interactor]]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2017-02-04T13:36:23Z

Mehrtash: /* Extensions by category */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]
* [[Documentation/Nightly/Extensions/DatabaseInteractor|Database Interactor]]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2017-02-04T13:34:47Z

Mehrtash: /* Extensions by category */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer]]
== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]


== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]
* [[Documentation/Nightly/Extensions/DatabaseInteractor|Database Interactor]]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Documentation/Nightly/Modules/DeepInfer

2017-02-04T13:32:48Z

Mehrtash: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."

Documentation/4.6/ModuleExtensionListing/Extensions by category

2017-02-04T13:23:49Z

Mehrtash: /* Extensions by category */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]
== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]


== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://github.com/KitwareMedical/SlicerITKUltrasound SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Documentation/4.6/ModuleExtensionListing/Extensions by category

2017-02-04T13:21:56Z

Mehrtash: Added machine learning category.

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]


== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://github.com/KitwareMedical/SlicerITKUltrasound SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Documentation/Nightly/Extensions/TCIABrowser

2016-07-31T20:43:04Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

[https://cancerimagingarchive.net/dashboard2/ TCIA metrics dashboard] provides extensive details on the types of imaging data by anatomy and other characteristics that are available within TCIA.





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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|'''Browsing Collections, patients and studies.''' (A) Collection selector combobox (B) Cache server response to the local storage (C) Icon for Clinical Information from TCGA (D) Tables are expandable (E) Status of the series (Available on local database / Available on TCIA server) (F) Download and Index to the Slicer DICOM database (local storage) (G) Download and load into the Slicer scene.
|File:TCIA-Browser-2.png|alt2= Downloading Series|'''Downloading Series.''' Multiple series from multiple patients and studies can be downloaded at the same time. (A) Progress bars showing download status of the selected series (B) Status bar showing the current process and the status of server responses (C) Cancel downloads button.
|File:TCIA-Browser-3.png|alt3= Extra clinical information from TCGA|'''Extra clinical information from TCGA.'''
|File:TCIA-Browser-4.png|alt4= Settings|'''Settings.''' (A) Show Browser button to pop up browser. (B) Selecting folder on the local file system for storing DICOM images and json responses. (C) Adding custom API keys for accessing non-public data.
}}

|}

{|

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]
Checking the API from the python console:
<pre>
import TCIABrowserLib as tblib
client = tblib.TCIAClient()
client.get_collection_values()
response = client.get_collection_values()
response_string = response.read()[:]
print(response_string)
</pre>


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

Documentation/4.4/Extensions/TCIABrowser

2015-05-18T14:29:42Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections (Updated February 2014)
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}





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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|'''Browsing Collections, patients and studies.''' (A) Collection selector combobox (B) Cache server response to the local storage (C) Icon for Clinical Information from TCGA (D) Tables are expandable (E) Status of the series (Available on local database / Available on TCIA server) (F) Download and Index to the Slicer DICOM database (local storage) (G) Download and load into the Slicer scene.
|File:TCIA-Browser-2.png|alt2= Downloading Series|'''Downloading Series.''' Multiple series from multiple patients and studies can be downloaded at the same time. (A) Progress bars showing download status of the selected series (B) Status bar showing the current process and the status of server responses (C) Cancel downloads button.
|File:TCIA-Browser-3.png|alt3= Extra clinical information from TCGA|'''Extra clinical information from TCGA.'''
|File:TCIA-Browser-4.png|alt4= Settings|'''Settings.''' (A) Show Browser button to pop up browser. (B) Selecting folder on the local file system for storing DICOM images and json responses. (C) Adding custom API keys for accessing non-public data.
}}

|}

{|

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T14:28:40Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections (Updated February 2014)
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}





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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|'''Browsing Collections, patients and studies.''' (A) Collection selector combobox (B) Cache server response to the local storage (C) Icon for Clinical Information from TCGA (D) Tables are expandable (E) Status of the series (Available on local database / Available on TCIA server) (F) Download and Index to the Slicer DICOM database (local storage) (G) Download and load into the Slicer scene.
|File:TCIA-Browser-2.png|alt2= Downloading Series|'''Downloading Series.''' Multiple series from multiple patients and studies can be downloaded at the same time. (A) Progress bars showing download status of the selected series (B) Status bar showing the current process and the status of server responses (C) Cancel downloads button.
|File:TCIA-Browser-3.png|alt3= Extra clinical information from TCGA|'''Extra clinical information from TCGA.'''
|File:TCIA-Browser-4.png|alt4= Settings|'''Settings.''' (A) Show Browser button to pop up browser. (B) Selecting folder on the local file system for storing DICOM images and json responses. (C) Adding custom API keys for accessing non-public data.
}}

|}

{|

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T14:20:13Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections (Updated February 2014)
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}





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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|Browsing Collections, patients and studies. (A) Collection selector combobox (B) Cache server response to the local storage (C) Icon for Clinical Information from TCGA (D) Tables are expandable (E) Status of the series (Available on local database / Available on TCIA server) (F) Download and Index to the Slicer DICOM database (local storage) (G) Download and load into the Slicer scene.
|File:TCIA-Browser-2.png|alt2= Downloading Series|Downloading Series.
|File:TCIA-Browser-3.png|alt3= Extra clinical information from TCGA|Extra clinical information from TCGA.
|File:TCIA-Browser-4.png|alt4= Settings|Settings.
}}

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".

|}

{|
* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T14:14:30Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections (Updated February 2014)
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}





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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|Browsing Collections, patients and studies.
|File:TCIA-Browser-2.png|alt2= Downloading Series|Downloading Series.
|File:TCIA-Browser-3.png|alt3= Extra clinical information from TCGA|Extra clinical information from TCGA.
|File:TCIA-Browser-4.png|alt4= Settings|Settings.
}}

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".

|}

{|
* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

File:TCIA-Browser-4.png

2015-05-18T14:11:56Z

Mehrtash:

File:TCIA-Browser-3.png

2015-05-18T14:11:40Z

Mehrtash:

File:TCIA-Browser-2.png

2015-05-18T14:11:18Z

Mehrtash:

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T14:01:59Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections (Updated February 2014)
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}





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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New03.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New04.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
}}

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".

|}

{|
* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T14:01:03Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}





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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New03.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New04.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
}}

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".

|}

{|
* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T14:00:11Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}




{{documentation/{{documentation/version}}/module-section|Tutorials}}
Not available at this time.

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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New03.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New04.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
}}

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".

|}

{|
* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T13:59:10Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections
|width=360
|height=360
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}




{{documentation/{{documentation/version}}/module-section|Tutorials}}
Not available at this time.

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

{{Gallery
|title=TCIA Browser Screesnshots
|width=480
|height=360
|lines=4
|align=center
|File:TCIA-Browser-1.png|alt1= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New03.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
|Image:TCIA-New04.png|alt2= Browsing Collections|Browsing Collections, patients and studies.
}}

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".

|}

{|
* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T13:52:34Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections
|width=480
|height=480
|lines=4
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections|Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities|Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts|Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers|Manufacuterers.
}}




{{documentation/{{documentation/version}}/module-section|Tutorials}}
Not available at this time.

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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

|[[File:TCIA-Browser-1.png|thumb|6000px|Module GUI]]

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
|[[Image:TCIA-New03.png|thumb|600px|Module GUI]]
|[[Image:TCIA-New04.png|thumb|600px|Module GUI]]
|}

{|

* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T13:47:10Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

{{Gallery
|title=Summary Statistics of Data Available from TCIA Public Collections
|width=480
|height=480
|lines=2
|align=center
|Image:TCIA_public_collections-collections.png|alt1= Collections.
|Image:TCIA_public_collections-modalities.png|alt2= Modalities.
|Image:TCIA_public_collections-body_parts.png|alt3= Body Parts.
|Image:TCIA_public_collections-manufacturers.png|alt4= Manufacuterers.
}}




{{documentation/{{documentation/version}}/module-section|Tutorials}}
Not available at this time.

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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

|[[File:TCIA-Browser-1.png|thumb|6000px|Module GUI]]

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
|[[Image:TCIA-New03.png|thumb|600px|Module GUI]]
|[[Image:TCIA-New04.png|thumb|600px|Module GUI]]
|}

{|

* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/Nightly/Extensions/TCIABrowser

2015-05-18T13:41:33Z

Mehrtash:

<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/TCIABrowser|TCIABrowser]] 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov). 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}}) 
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

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

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


{{documentation/{{documentation/version}}/module-section|Module Description}}

[[Image:TCIABrowser_logo.png]]

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):

* QIBA CT-1C
* TCGA-GBM *
* RIDER PHANTOM PET-CT
* RIDER PHANTOM MRI
* Phantom FDA
* TCGA-LGG *
* TCGA-KIRC *
* TCGA-BRCA *
* BREAST-DIAGNOSIS
* PROSTATE-DIAGNOSIS
* LIDC-IDRI
* TCGA-LUAD *
* RIDER Lung CT
* RIDER NEURO MRI
* RIDER Lung PET-CT
* CT COLONOGRAPHY
* REMBRANDT
* RIDER Breast MRI

For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

<gallery widths="480px" heights="480px" perrow="2">
Image:TCIA_public_collections-collections.png
Image:TCIA_public_collections-modalities.png
Image:TCIA_public_collections-body_parts.png
Image:TCIA_public_collections-manufacturers.png
</gallery>



{{documentation/{{documentation/version}}/module-section|Tutorials}}
Not available at this time.

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

{|
* '''Browsing Collections, patients and studies'''
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox (A) select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon [[Image:Report-icon-tcia.png|thumb|25px|TCGA Data Available]] besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
The use Cache checkbox (B) will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

|[[File:TCIA-Browser-1.png|thumb|6000px|Module GUI]]

* '''Downloading Series'''
After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

|}

{|
* '''Access Clinical Data from TCGA'''
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
|[[Image:TCIA-New03.png|thumb|600px|Module GUI]]
|[[Image:TCIA-New04.png|thumb|600px|Module GUI]]
|}

{|

* '''Settings '''
If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
|}


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

* [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
* [http://cancerimagingarchive.net/ TCIA Home Page]
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* [https://github.com/QIICR/TCIABrowser Source Code]

Tip: The REST API can be checked by [https://chrome.google.com/webstore/detail/rest-console/cokgbflfommojglbmbpenpphppikmonn?utm_source=plus REST Console] Google Chrome extension.
{{documentation/{{documentation/version}}/module-developerinfo}}


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