Slicer Wiki - User contributions [en]

Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions/ExperimentalFolderAccess

2014-01-09T22:47:25Z

Cvachet:

<p>If not already done, send an email on the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel slicer developers list] asking to be granted write permission on the [http://slicer.kitware.com/midas3/folder/253 experimental folder].</p>
<pre>
To: slicer-devel@bwh.harvard.edu
Subject: Extension NAME-OF-YOUR-EXTENSION - Asking permission to write to the Experimental folder
Hi,

This extension will allow to [...]

Could you grant user YourUserName write access to the Experimental folder ?

</pre>

Modules:ARCTIC-Documentation-3.6

2010-08-26T20:06:34Z

Cvachet: /* References */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
[[Image:ARCTIC.png|thumb|280px|ARCTIC User Interface]]
* '''Inputs''': Two modes exist to select input images needed to perform the cortical thickness analysis
** '''Input mode 1 - Raw Images:''' set input images representing the different modalities of the same subject
*** ''T1-weighted image:'' set input T1 image, if available
*** ''T2-weighted image:'' set input T2 image, if available
*** ''PD-weighted image:'' set input PD image, if available
*** ''Tissue segmentation atlas directory:'' set directory containing gray-scale atlas to perform the tissue segmentation
*** ''Segmentation atlas type (T1 or T2, default: T1):'' set segmentation atlas type (should match subject input image)
** '''Input mode 2 - Segmented Images:''' set tissue segmentation label image with its related raw image
*** ''Tissue segmentation image:'' set tissue segmentation label image
*** ''White matter label (default: 1):'' set tissue segmentation white matter label
*** ''Gray matter label (default: 2):'' set tissue segmentation gray matter label
*** ''CSF label (default: 3):'' set tissue segmentation CSF label
*** ''Raw image:'' set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** ''Cortical thickness on white matter boundary:'' set output image which represents cortical thickness measurement on the white matter boundary
** ''Cortical thickness on gray matter boundary:'' set output image which represents cortical thickness measurement on the gray matter boundary
** ''Cortical thickness results directory:'' set output directory to save cortical thickness measurements
** ''ID number:'' set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** ''Case parcellation image:'' set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** ''Atlas parcellation image:'' set the atlas parcellation image
*** ''Atlas image:'' set the grayscale atlas image

[[Image:ARCTIC_AdvancedParams.png|thumb|280px|ARCTIC Advanced Parameters User Interface]]
* '''Advanced tissue segmentation parameters'''
** ''Filter options:'' specifies smoothing parameters prior to the segmentation
** ''Priors:'' set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** ''Maximum bias degree:'' set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** ''Atlas warping parameters:'' enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** ''Mask dilation (default: disabled):'' check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** ''InterpOff (default: disabled):'' check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** ''Threshold (default: 1.8):'' set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** ''Initialization:'' choose between different initialization methods (see registration pipeline discussion)

|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases on MIDAS:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://skylla.ia.unc.edu/CDash/index.php?project=ARCTIC Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===

* H.C. Hazlett, C. Vachet, C. Mathieu, M. Styner, J. Piven, Use of the Slicer3 Toolkit to Produce Regional Cortical Thickness Measurement of Pediatric MRI Data, presented at the 8th Annual International Meeting for Autism Research (IMFAR) Chicago, IL 2009.
* C. Mathieu, C. Vachet, H.C. Hazlett, G. Geric, J. Piven, and M. Styner, ARCTIC – Automatic Regional Cortical ThICkness Tool, UNC Radiology Research Day 2009 abstract

Modules:ARCTIC-Documentation-3.6

2010-04-06T21:48:39Z

Cvachet: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
[[Image:ARCTIC.png|thumb|280px|ARCTIC User Interface]]
* '''Inputs''': Two modes exist to select input images needed to perform the cortical thickness analysis
** '''Input mode 1 - Raw Images:''' set input images representing the different modalities of the same subject
*** ''T1-weighted image:'' set input T1 image, if available
*** ''T2-weighted image:'' set input T2 image, if available
*** ''PD-weighted image:'' set input PD image, if available
*** ''Tissue segmentation atlas directory:'' set directory containing gray-scale atlas to perform the tissue segmentation
*** ''Segmentation atlas type (T1 or T2, default: T1):'' set segmentation atlas type (should match subject input image)
** '''Input mode 2 - Segmented Images:''' set tissue segmentation label image with its related raw image
*** ''Tissue segmentation image:'' set tissue segmentation label image
*** ''White matter label (default: 1):'' set tissue segmentation white matter label
*** ''Gray matter label (default: 2):'' set tissue segmentation gray matter label
*** ''CSF label (default: 3):'' set tissue segmentation CSF label
*** ''Raw image:'' set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** ''Cortical thickness on white matter boundary:'' set output image which represents cortical thickness measurement on the white matter boundary
** ''Cortical thickness on gray matter boundary:'' set output image which represents cortical thickness measurement on the gray matter boundary
** ''Cortical thickness results directory:'' set output directory to save cortical thickness measurements
** ''ID number:'' set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** ''Case parcellation image:'' set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** ''Atlas parcellation image:'' set the atlas parcellation image
*** ''Atlas image:'' set the grayscale atlas image

[[Image:ARCTIC_AdvancedParams.png|thumb|280px|ARCTIC Advanced Parameters User Interface]]
* '''Advanced tissue segmentation parameters'''
** ''Filter options:'' specifies smoothing parameters prior to the segmentation
** ''Priors:'' set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** ''Maximum bias degree:'' set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** ''Atlas warping parameters:'' enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** ''Mask dilation (default: disabled):'' check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** ''InterpOff (default: disabled):'' check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** ''Threshold (default: 1.8):'' set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** ''Initialization:'' choose between different initialization methods (see registration pipeline discussion)

|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases on MIDAS:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://skylla.ia.unc.edu/CDash/index.php?project=ARCTIC Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-06T21:36:16Z

Cvachet: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
[[Image:ARCTIC.png|thumb|280px|ARCTIC User Interface]]
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image

[[Image:ARCTIC_AdvancedParams.png|thumb|280px|ARCTIC Advanced Parameters User Interface]]
* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases on MIDAS:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://skylla.ia.unc.edu/CDash/index.php?project=ARCTIC Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-06T21:31:26Z

Cvachet: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
[[Image:ARCTIC.png|thumb|280px|ARCTIC User Interface]]
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image

[[Image:ARCTIC_AdvancedParams.png|thumb|280px|User Interface]]
* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases on MIDAS:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://skylla.ia.unc.edu/CDash/index.php?project=ARCTIC Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

File:ARCTIC.png

2010-04-06T21:29:39Z

Cvachet: uploaded a new version of "File:ARCTIC.png"

File:ARCTIC AdvancedParams.png

2010-04-06T21:24:37Z

Cvachet:

File:ARCTIC AdvancedTissueSegParam.png

2010-04-06T21:05:30Z

Cvachet:

File:ARCTIC AdvancedSkullStrippingParam.png

2010-04-06T21:05:18Z

Cvachet:

File:ARCTIC AdvancedCortThickParam.png

2010-04-06T21:05:07Z

Cvachet:

File:ARCTIC AdvancedAtlasRegParam.png

2010-04-06T21:04:57Z

Cvachet:

File:ARCTIC.png

2010-04-06T21:04:37Z

Cvachet:

Modules:ARCTIC-Documentation-3.6

2010-04-06T18:22:35Z

Cvachet: /* Tests */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:

* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases on MIDAS:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://skylla.ia.unc.edu/CDash/index.php?project=ARCTIC Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-06T18:20:17Z

Cvachet: /* Source code & documentation */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:

* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases on MIDAS:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-06T18:14:19Z

Cvachet: /* Dependencies */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:

* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases on MIDAS:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-06T18:13:49Z

Cvachet: /* Tutorials */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
* [http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage Wiki page on NITRC]

===Quick Tour of Features and Use===

{|
|
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:

* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-01T16:23:26Z

Cvachet: /* Module Type & Category */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Workflow

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

{|
|
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:

* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-01T16:03:46Z

Cvachet: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

{|
|
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image, if available
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the subject space coordinate
** If a parcellation needs to be defined (i.e atlas registration will be performed):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:

* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''
** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation

* '''Advanced atlas registration parameters:'''
** Choose between different initialization methods : see registration pipeline discussion

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-04-01T14:50:40Z

Cvachet: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

{|
|
* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
** T1-weighted image: set input T1 image
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set atlas type

* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform the lobar analysis, i.e to perform the atlas orientation)

* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of the output images

* '''Parcellation:''' set parameters to perform a lobar analysis
** If a parcellation is already defined for the subject:
*** Case parcellation image: set the parcellation image defined in the case space coordinate
** If a parcellation needs to be defined (i.e atlas registration):
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:

* '''Advanced tissue segmentation parameters'''
** Filter options: specifies smoothing parameters prior to the segmentation
** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).

* '''Advanced skull-stripping parameters'''
** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.

* '''Advanced cortical thickness parameters:'''

* '''Advanced atlas registration parameters:'''

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Documentation/3.6

2010-03-31T22:00:25Z

Cvachet: /* Listing of plug-ins */

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* Atlas Creator (Sylvain Jaume)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Gyri Contour Segmentation]] (Peter Karasev)
* Subvolume extraction with ROI widget (Andriy Fedorov)
* Registration Metrics (HD and DSC) (Haytham Elhawary)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)

=List of pre-existing Modules=
==Core==
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']]
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) transition '''Not yet 3.6'''

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''

===Registration===
*[[Slicer3:Registration|Overview of all Registration Modules ]]
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Register Images Robust Affine]] (Casey Goodlett)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Deformable B-Spline Registration]] (Bill Lorensen) '''in progress'''
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial-Based Registration]] (Casey Goodlett)
**[[Modules:Transforms-Documentation-3.6| Transforms Module for interactive rigid registration]] (Alex Yarmarkovich)
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]] (Nicole Aucoin)
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''

===Segmentation===
*Overview (Kilian)
**[[Modules:EMSegment|EM Segment]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Simple|EM Segment Simple]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''
*Analysis

====Tractography====
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''
*[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
*[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles) '''Not yet 3.6'''

===Time Series===
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the icon to start the extensions wizard
[[image:ExtensionsWizard.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu) '''Not yet 3.6'''

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry '''Not yet 3.6'''

* [[Modules:DiffusionWarp|DiffusionWarp]] '''Not yet 3.6'''

* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''

* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''

* [[Modules:LocalRegionSeg|LocalRegionSeg]] '''Not yet 3.6'''

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''

* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''

* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''

* [[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins, Daniel Haehn (haehn@bwh.harvard.edu)

* [[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models, Daniel Haehn (haehn@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''

* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution, Daniel Haehn (haehn@bwh.harvard.edu)

* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Deprecated Extensions'''

* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:58:54Z

Cvachet:

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===ARCTIC: Automatic Regional Cortical ThICkness===

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input 1: Raw Images'''
** T1-weighted image: set input T1 image
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set atlas type
* '''Input 2: Segmented Images'''
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform the lobar analysis, i.e to perform the atlas orientation)
* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of output images
* '''Parcellation:''': parameters need to be set to perform a lobar analysis
** Parcellation already defined for the subject
*** Case parcellation image: set the parcellation image defined in the case space coordinate
** Parcellation needs to be defined: atlas is registered to the case
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:
* '''Advanced tissue segmentation parameters'''
* '''Advanced skull-stripping parameters'''
* '''Advanced registration parameters:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:57:13Z

Cvachet: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input 1: Raw Images'''
** T1-weighted image: set input T1 image
** T2-weighted image: set input T2 image, if available
** PD-weighted image: set input PD image, if available
** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
** Segmentation atlas type (T1 or T2, default: T1): set atlas type
* '''Input 2: Segmented Images'''
** Tissue segmentation image: set tissue segmentation label image
** White matter label (default: 1): set tissue segmentation white matter label
** Gray matter label (default: 2): set tissue segmentation gray matter label
** CSF label (default: 3): set tissue segmentation CSF label
** Raw image: set its related raw image (needed to perform the lobar analysis, i.e to perform the atlas orientation)
* '''Output:'''
** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
** Cortical thickness results directory: set output directory to save cortical thickness measurements
** ID number: set ID number to set prefix of output images
* '''Parcellation:''': parameters need to be set to perform a lobar analysis
** Parcellation already defined for the subject
*** Case parcellation image: set the parcellation image defined in the case space coordinate
** Parcellation needs to be defined: atlas is registered to the case
*** Atlas parcellation image: set the atlas parcellation image
*** Atlas image: set the grayscale atlas image
** Atlas parcellation orientation:
* '''Advanced tissue segmentation parameters'''
* '''Advanced skull-stripping parameters'''
* '''Advanced registration parameters:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:45:46Z

Cvachet: /* Dependencies */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input 1: Raw Images'''
** T1-weighted image:
** T2-weighted image:
** PD-weighted image:
** Tissue segmentation atlas directory:
** Segmentation atlas type (T1 or T2, default: T1): select at
* '''Input 2: Segmented Images'''
** Tissue segmentation image:
** White matter label (default: 1)
** Gray matter label (default: 2)
** CSF label:
** Raw image:
* '''Output:'''
** Cortical thickness on white matter boundary:
** Cortical thickness on gray matter boundary
** Cortical thickness results directory:
** ID number:
* '''Parcellation:'''
** Case parcellation image:
** Atlas parcellation image:
** Atlas image:
** Atlas parcellation orientation:
* '''Advanced tissue segmentation parameters'''
* '''Advanced skull-stripping parameters'''
* '''Advanced registration parameters:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
* Publicly available atlases:
** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]
** [http://www.insight-journal.org/midas/item/view/2330 Elderly atlas]
** [http://www.insight-journal.org/midas/item/view/2283 Primate atlas]

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:40:12Z

Cvachet: /* Dependencies */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input 1: Raw Images'''
** T1-weighted image:
** T2-weighted image:
** PD-weighted image:
** Tissue segmentation atlas directory:
** Segmentation atlas type (T1 or T2, default: T1): select at
* '''Input 2: Segmented Images'''
** Tissue segmentation image:
** White matter label (default: 1)
** Gray matter label (default: 2)
** CSF label:
** Raw image:
* '''Output:'''
** Cortical thickness on white matter boundary:
** Cortical thickness on gray matter boundary
** Cortical thickness results directory:
** ID number:
* '''Parcellation:'''
** Case parcellation image:
** Atlas parcellation image:
** Atlas image:
** Atlas parcellation orientation:
* '''Advanced tissue segmentation parameters'''
* '''Advanced skull-stripping parameters'''
* '''Advanced registration parameters:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
** RegisterImages
** ResampleScalarVectorDWIVolume
* Atlas:
**
* Libraries:

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:31:36Z

Cvachet: /* Dependencies */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input 1: Raw Images'''
** T1-weighted image:
** T2-weighted image:
** PD-weighted image:
** Tissue segmentation atlas directory:
** Segmentation atlas type (T1 or T2, default: T1): select at
* '''Input 2: Segmented Images'''
** Tissue segmentation image:
** White matter label (default: 1)
** Gray matter label (default: 2)
** CSF label:
** Raw image:
* '''Output:'''
** Cortical thickness on white matter boundary:
** Cortical thickness on gray matter boundary
** Cortical thickness results directory:
** ID number:
* '''Parcellation:'''
** Case parcellation image:
** Atlas parcellation image:
** Atlas image:
** Atlas parcellation orientation:
* '''Advanced tissue segmentation parameters'''
* '''Advanced skull-stripping parameters'''
* '''Advanced registration parameters:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Slicer3 modules: RegisterImages and ResampleScalarVectorDWIVolume

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:30:43Z

Cvachet: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ArcticLogo.png|thumb|180px|ARCTIC logo]]
|[[Image:T1Image.png|thumb|200px|T1 skull-stripped image]]
|[[Image:Parcellation.png|thumb|200px|Parcellation image]]
|[[Image:Corticalthickness.png|thumb|200px|Cortical thickness on WM surface]]
|[[Image:ThicknessInformation.png|thumb|200px|Cortical thickness information]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Pipeline

===Authors, Collaborators & Contact===
* Author1: Cedric Mathieu, UNC-Chapel Hill
* Contributor1: Clement Vachet, UNC-Chapel Hill
* Contributor2: Martin Styner, UNC-Chapel Hill
* Contributor3: Heather Cody Hazlett, UNC-Chapel Hill
* Contact: Clement Vachet, cvachet[at]email[dot]unc[dot]edu

===Module Description===
ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate when one wants to perform individual regional cortical thickness analysis. ARCTIC allows efficient QC via precomputed 3D-Slicer scenes.

===Tutorials===

* Tutorials:
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.ppt|‏ ARCTIC-v1.2 ppt]]
** [[Media:ARCTIC-v1.2-Slicer3-Tutorial.pdf‏| ARCTIC-v1.2 PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input 1: Raw Images'''
** T1-weighted image:
** T2-weighted image:
** PD-weighted image:
** Tissue segmentation atlas directory:
** Segmentation atlas type (T1 or T2, default: T1): select at
* '''Input 2: Segmented Images'''
** Tissue segmentation image:
** White matter label (default: 1)
** Gray matter label (default: 2)
** CSF label:
** Raw image:
* '''Output:'''
** Cortical thickness on white matter boundary:
** Cortical thickness on gray matter boundary
** Cortical thickness results directory:
** ID number:
* '''Parcellation:'''
** Case parcellation image:
** Atlas parcellation image:
** Atlas image:
** Atlas parcellation orientation:
* '''Advanced tissue segmentation parameters'''
* '''Advanced skull-stripping parameters'''
* '''Advanced registration parameters:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

None

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Download release source code via svn:
* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:14:03Z

Cvachet: /* Source code & documentation */

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:11:29Z

Cvachet: /* Known bugs */

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:08:24Z

Cvachet: /* Tutorials */

Modules:ARCTIC-Documentation-3.6

2010-03-31T21:06:35Z

Cvachet: /* Tutorials */

File:ARCTIC-v1.2-Slicer3-Tutorial.pdf

2010-03-31T21:05:47Z

Cvachet:

File:ARCTIC-v1.2-Slicer3-Tutorial.ppt

2010-03-31T21:05:34Z

Cvachet:

Modules:ARCTIC-Documentation-3.6

2010-03-31T20:50:19Z

Cvachet: /* Use Cases, Examples */

Modules:ARCTIC-Documentation-3.6

2010-03-31T20:37:54Z

Cvachet: /* Authors, Collaborators & Contact */

Modules:ARCTIC-Documentation-3.6

2010-03-31T20:30:59Z

Cvachet: /* Acknowledgment */

Modules:ARCTIC-Documentation-3.6

2010-03-31T20:28:19Z

Cvachet: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== MyModule {| |[[Image:Arctic…'

File:ThicknessInformation.png

2010-03-31T20:23:17Z

Cvachet:

File:T1Image.png

2010-03-31T20:22:47Z

Cvachet:

File:Parcellation.png

2010-03-31T20:22:35Z

Cvachet:

Documentation/3.6

2010-03-31T19:34:29Z

Cvachet: /* Listing of plug-ins */

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* Atlas Creator (Sylvain Jaume)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Gyri Contour Segmentation]] (Peter Karasev)
* Subvolume extraction with ROI widget (Andriy Fedorov)
* Registration Metrics (HD and DSC) (Haytham Elhawary)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)

=List of pre-existing Modules=
==Core==
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']]
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) transition '''Not yet 3.6'''

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''

===Registration===
*[[Slicer3:Registration|Overview of all Registration Modules ]]
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Register Images Robust Affine]] (Casey Goodlett)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Deformable B-Spline Registration]] (Bill Lorensen) '''in progress'''
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial-Based Registration]] (Casey Goodlett)
**[[Modules:Transforms-Documentation-3.6| Transforms Module for interactive rigid registration]] (Alex Yarmarkovich)
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]] (Nicole Aucoin)
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''

===Segmentation===
*Overview (Kilian)
**[[Modules:EMSegment|EM Segment]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Simple|EM Segment Simple]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''
*Analysis

====Tractography====
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''
*[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
*[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles) '''Not yet 3.6'''

===Time Series===
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the icon to start the extensions wizard
[[image:ExtensionsWizard.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) '''Not yet 3.6'''

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu) '''Not yet 3.6'''

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry '''Not yet 3.6'''

* [[Modules:DiffusionWarp|DiffusionWarp]] '''Not yet 3.6'''

* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''

* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''

* [[Modules:LocalRegionSeg|LocalRegionSeg]] '''Not yet 3.6'''

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''

* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''

* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''

* [[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins, Daniel Haehn (haehn@bwh.harvard.edu)

* [[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models, Daniel Haehn (haehn@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''

* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution, Daniel Haehn (haehn@bwh.harvard.edu)

* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Deprecated Extensions'''

* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''