Slicer Wiki - User contributions [en]

File:CMFregData.zip

2013-11-18T22:12:19Z

Vboen: uploaded a new version of "File:CMFregData.zip"

Documentation/Nightly/Modules/Downsize

2013-11-11T16:17:57Z

Vboen:

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

===Downsize===
Downsize

{|
|[[Image:DownsizeInterface.png|thumb|280px|User Interface]]
|[[Image:InputVolumeBadResolutionCMFreg.png|thumb|280px|Input Scan Bad Voxel Based Resolution]]
|[[Image:OutputScanDownsizedCMFreg.png|thumb|280px|Output Scan Downsized]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration pre steps (voxel resolution)

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Parameters''''':
** '''Size''' [-s --spacing] : The value of each voxel resolution for 3 dimensions
** '''Input Volume''' [index: 0] : Input volume to be resampled.
* '''''Output''''':
** '''Output Volume''' [index: 1] : Resampled Output Volume

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

Documentation/Nightly/Modules/NonGrowing

2013-10-31T15:31:19Z

Vboen:

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

===NonGrowing===
NonGrowing

{|
|[[Image:NonGrowingInterface.png|thumb|280px|User Interface]]
|[[Image:BaselineCBCTCMFreg.png|thumb|280px|Baseline CBCT Scan - Input Scan]]
|[[Image:FollowupCBCTCMFreg.png|thumb|280px|Follow up CBCT Scan - Input Scan]]
|[[Image:BaselineSegmentationMaskCMFreg.png|thumb|280px|Baseline Segmentation Mask - Input Seg]]
|[[Image:FollowupSegmentationMaskCMFreg.png|thumb|280px|Followup Segmentation Mask - Input Seg]]
|[[Image:BaselineFollowupSCANCMFreg2.png|thumb|280px|Baseline and Followup CBCT Scans - Baseline Input Scan + Followup Input Scan]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg2.png|thumb|280px|Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan]]
|}

== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Parameters''''':
** '''Baseline Scan (fixed)''' [-f --fixedVolume] : The fixed scan image for registration.
** '''Follow up Scan (moving)''' [-m --movingVolume] : The moving scan image for registration.
** '''Baseline Segmentation (fixed)''' [--fixedBinaryVolume] : The fixed one label segmentation image for registration used to specify the region of interest.
** '''Follow up Segmentation (moving)''' [--movingBinaryVolume] : The moving one label segmentation image for registration used to specify the region of interest.

* '''''Output Registration Matrix''''':
** '''Registration Matrix''' [-t --transformPath] : File name for the rigid component of the estimated registration matrix. Can be used to rigidly register the moving image to the fixed image.

* '''''Apply Registration Matrix''''':
** '''Input Segmentatiton to be Registered''' [--segmentation] : Input segmentation image to be modified with the registration matrix.
** '''Output Registered Scan''' [--segmentationOut] : Output segmentation image. This segmentaiton image is the 'Input Segmentation to be Registered' with the registration matrix already applied.
** '''Output Registered Scan''' [--outputVolume] : Output image for registration. This image is the Follow up Scan with the registration matrix already applied.

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

Documentation/4.3/Modules/ApplyRegistrationMatrix

2013-10-31T15:18:36Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===Apply Matrix=== Apply Matrix {| |User Interface |} == Gener…'

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

===Apply Matrix===
Apply Matrix

{|
|[[Image:ApplyMatrixInterfaceNew.png|thumb|280px|User Interface]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: Volume Applying Registration matrix

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Volumes and Matrix''''':
** '''Input Volume''' [index 0] : Volume (scan or seg) which the registration matrix will be applied to.
** '''Check it if the input Volume is a segmentation''' [--isSeg] : Check box which must be selected if the input Volume is a segmentation.
** '''Registration Matrix''' [-f --transformationFile] : DOF file with the coordinate matrix which will be applied to the Input Volume.
** '''Reference Volume (To set Output Parameters)''' [-R --Reference] : Resampled Output Volume

* '''''Output Volume''''':
** '''Output Volume''' [index: 1] : Resampled Output Volume modified by the registration matrix

Documentation/4.3/Extensions/CMFreg

2013-10-31T15:16:31Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]


{{documentation/{{documentation/version}}/extension-section|Tutorials}}
The Dental and Craniofacial Bionetwork for Image Analysis's websit has a [https://sites.google.com/a/umich.edu/dentistry-image-computing/Clinical-Applications/3d-registration---longitudinal-and-across-subjects CMFreg Tutorial]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-10-31T15:15:08Z

Vboen:

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-10-31T15:10:13Z

Vboen:

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

===Apply Matrix===
Apply Matrix

{|
|[[Image:ApplyMatrixInterfaceNew.png|thumb|280px|User Interface]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: Volume Applying Registration matrix

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Volumes and Matrix''''':
** '''Input Volume''' [index 0] : Volume (scan or seg) which the registration matrix will be applied to.
** '''Registration Matrix''' [-f --transformationFile] : DOF file with the coordinate matrix which will be applied to the Input Volume.
** '''Reference Volume (To set Output Parameters)''' [-R --Reference] : Resampled Output Volume

* '''''Output Volume''''':
** '''Output Volume''' [index: 1] : Resampled Output Volume modified by the registration matrix

File:ApplyMatrixInterfaceNew.png

2013-10-31T15:09:31Z

Vboen:

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-10-04T14:08:49Z

Vboen:

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

===Apply Matrix===
Apply Matrix

{|
|[[Image:ApplyMatrixInterface.png|thumb|280px|User Interface]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: Volume Applying Registration matrix

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Volumes and Matrix''''':
** '''Input Volume''' [index 0] : Volume (scan or seg) which the registration matrix will be applied to.
** '''Registration Matrix''' [-f --transformationFile] : DOF file with the coordinate matrix which will be applied to the Input Volume.
** '''Reference Volume (To set Output Parameters)''' [-R --Reference] : Resampled Output Volume

* '''''Output Volume''''':
** '''Output Volume''' [index: 1] : Resampled Output Volume modified by the registration matrix

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-10-04T14:08:28Z

Vboen:

File:ApplyMatrixInterface.png

2013-10-04T14:08:03Z

Vboen:

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-10-04T14:01:46Z

Vboen:

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

===Apply Matrix===
Apply Matrix

{|
|[[Image:DownsizeInterface.png|thumb|280px|User Interface]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: Volume Applying Registration matrix

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Volumes and Matrix''''':
** '''Input Volume''' [index 0] : Volume (scan or seg) which the registration matrix will be applied to.
** '''Registration Matrix''' [-f --transformationFile] : DOF file with the coordinate matrix which will be applied to the Input Volume.
** '''Reference Volume (To set Output Parameters)''' [-R --Reference] : Resampled Output Volume

* '''''Output Volume''''':
** '''Output Volume''' [index: 1] : Resampled Output Volume modified by the registration matrix

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

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-10-04T14:00:43Z

Vboen:

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

===Apply Matrix===
Apply Matrix

{|
|[[Image:DownsizeInterface.png|thumb|280px|User Interface]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Applying Scan Registration matrix

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Volumes and Matrix''''':
** '''Input Volume''' [index 0] : Volume (scan or seg) which the registration matrix will be applied to.
** '''Registration Matrix''' [-f --transformationFile] : DOF file with the coordinate matrix which will be applied to the Input Volume.
** '''Reference Volume (To set Output Parameters)''' [-R --Reference] : Resampled Output Volume

* '''''Output Volume''''':
** '''Output Volume''' [index: 1] : Resampled Output Volume modified by the registration matrix

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

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-10-04T13:56:51Z

Vboen:

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

===Apply Matrix===
Apply Matrix

{|
|[[Image:DownsizeInterface.png|thumb|280px|User Interface]]
|[[Image:InputVolumeBadResolutionCMFreg.png|thumb|280px|Input Scan Bad Voxel Based Resolution]]
|[[Image:OutputScanDownsizedCMFreg.png|thumb|280px|Output Scan Downsized]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Applying Scan Registration matrix

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Volumes and Matrix''''':
** '''Input Volume''' [index 0] : Scan which the registration matrix will be applied to.
** '''Registration Matrix''' [-f --transformationFile] : DOF file with the coordinate matrix which will be applied to the Input Volume.
** '''Reference Volume (To set Output Parameters)''' [-R --Reference] : Resampled Output Volume

* '''''Output Volume''''':
** '''Output Volume''' [index: 1] : Resampled Output Volume modified by the registration matrix

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

Documentation/Nightly/Extensions/CMFreg

2013-10-03T14:22:37Z

Vboen:

Documentation/Nightly/Extensions/CMFreg

2013-10-03T14:13:21Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]


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


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T19:55:10Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T19:30:28Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]


{{documentation/{{documentation/version}}/extension-section|Data}}
*[[media:CMFregData.zip|Dataset]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T19:29:35Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]


*[[media:CMFregData.zip|Dataset]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T19:14:48Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]
*[[media:CMFregData.zip|Dataset]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T19:02:47Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]
http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T18:58:24Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]

*[[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip]]

*[[Images/{{Images/version}}/c/c1/CMFregData.zip|Data]]

http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T18:56:18Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]
*[[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/CMFreg

2013-10-02T18:49:18Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]
*[[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip|CMFregData]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/ApplyRegistrationMatrix

2013-09-27T15:01:41Z

Vboen: Created page with '...'

...

Documentation/Nightly/Extensions/CMFreg

2013-09-27T14:55:56Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/ApplyRegistrationMatrix|ApplyRegistrationMatrix]]
*[[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/NonGrowing

2013-09-23T21:30:08Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===NonGrowing=== NonGrowing {| |User Interface |[[Image:BaselineCB…'

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

===NonGrowing===
NonGrowing

{|
|[[Image:NonGrowingInterface.png|thumb|280px|User Interface]]
|[[Image:BaselineCBCTCMFreg.png|thumb|280px|Baseline CBCT Scan - Input Scan]]
|[[Image:FollowupCBCTCMFreg.png|thumb|280px|Follow up CBCT Scan - Input Scan]]
|[[Image:BaselineSegmentationMaskCMFreg.png|thumb|280px|Baseline Segmentation Mask - Input Seg]]
|[[Image:FollowupSegmentationMaskCMFreg.png|thumb|280px|Followup Segmentation Mask - Input Seg]]
|[[Image:BaselineFollowupSCANCMFreg2.png|thumb|280px|Baseline and Followup CBCT Scans - Baseline Input Scan + Followup Input Scan]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg.png|thumb|280px|Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan]]
|}

== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Parameters''''':
** '''Baseline Scan (fixed)''' [-f --fixedVolume] : The fixed scan image for registration.
** '''Follow up Scan (moving)''' [-m --movingVolume] : The moving scan image for registration.
** '''Baseline Segmentation (fixed)''' [--fixedBinaryVolume] : The fixed one label segmentation image for registration used to specify the region of interest.
** '''Follow up Segmentation (moving)''' [--movingBinaryVolume] : The moving one label segmentation image for registration used to specify the region of interest.

* '''''Output Registration Matrix''''':
** '''Registration Matrix''' [-t --transformPath] : File name for the rigid component of the estimated registration matrix. Can be used to rigidly register the moving image to the fixed image.

* '''''Apply Registration Matrix''''':
** '''Input Segmentatiton to be Registered''' [--segmentation] : Input segmentation image to be modified with the registration matrix.
** '''Output Registered Scan''' [--segmentationOut] : Output segmentation image. This segmentaiton image is the 'Input Segmentation to be Registered' with the registration matrix already applied.
** '''Output Registered Scan''' [--outputVolume] : Output image for registration. This image is the Follow up Scan with the registration matrix already applied.

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

Documentation/Nightly/Modules/Growing

2013-09-23T21:29:43Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===Growing=== Growing {| |User Interface |[[Image:BaselineCBCTCMFreg.…'

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

===Growing===
Growing

{|
|[[Image:GrowingInterface.png|thumb|280px|User Interface]]
|[[Image:BaselineCBCTCMFreg.png|thumb|280px|Baseline CBCT Scan - Input Scan]]
|[[Image:FollowupCBCTCMFreg.png|thumb|280px|Follow up CBCT Scan - Input Scan]]
|[[Image:BaselineSegmentationMaskCMFreg.png|thumb|280px|Baseline Segmentation Mask - Input Seg]]
|[[Image:FollowupSegmentationMaskCMFreg.png|thumb|280px|Followup Segmentation Mask - Input Seg]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg.png|thumb|280px|Baseline Input Scan + Followup Input Scan]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg2.png|thumb|280px|Baseline and Followup CBCT Scans - Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan]]
|}

== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Parameters''''':
** '''Baseline Scan (fixed)''' [-f --fixedVolume] : The fixed scan image for registration.
** '''Follow up Scan (moving)''' [-m --movingVolume] : The moving scan image for registration.
** '''Baseline Segmentation (fixed)''' [--fixedBinaryVolume] : The fixed one label segmentation image for registration used to specify the region of interest.
** '''Follow up Segmentation (moving)''' [--movingBinaryVolume] : The moving one label segmentation image for registration used to specify the region of interest.

* '''''Voxel Based Registration Options''''':
** '''Rigid + Scale (7DOF)''' [--useScaleVersor3D] : Perform a ScaleVersor3D registration as part of the sequential registration steps.
** '''Rigid + Skew + Scale (10DOF)''' [--useScaleSkewVersor3D] : Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.
** '''Affine (12DOF)''' [--useAffine] : Perform an Affine registration as part of the sequential registration steps.

* '''''Output Registration Matrix''''':
** '''Registration Matrix''' [-t --transformPath] : File name for the rigid component of the estimated registration matrix. Can be used to rigidly register the moving image to the fixed image.

* '''''Apply Registration Matrix''''':
** '''Input Segmentatiton to be Registered''' [--segmentation] : Input segmentation image to be modified with the registration matrix.
** '''Output Registered Scan''' [--segmentationOut] : Output segmentation image. This segmentaiton image is the 'Input Segmentation to be Registered' with the registration matrix already applied.
** '''Output Registered Scan''' [--outputVolume] : Output image for registration. This image is the Follow up Scan with the registration matrix already applied.

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

Documentation/Nightly/Modules/MaskCreation

2013-09-23T21:28:24Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===Mask Creation=== Mask Creation {| |User Interface |[[Image:Fo…'

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

===Mask Creation===
Mask Creation

{|
|[[Image:MaskCreationInterface.png|thumb|280px|User Interface]]
|[[Image:FollowupMaskCMFreg.png|thumb|280px|Input Scan to be masked]]
|[[Image:OutputLabelMap1plus2CMFreg.png|thumb|280px|Input mask single label segmentation]]
|[[Image:OutputMaskedScanCMFreg.png|thumb|280px|Output Scan masked]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration pre steps (mask processing)

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Interface Description''''':
** '''InputVolume''' [index 0] : Input Scan to be masked.
** '''Mask Volume''' [index 1] : Single label segmentation to be used as mask.
** '''Masked Volume''' [index 2] : Output Scan mask.
** '''Label Value''' [-l --label] : Label number.

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

Documentation/Nightly/Modules/LabelExtraction

2013-09-23T21:28:01Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===Label Extraction=== Label Extraction {| |User Interface |[…'

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

===Label Extraction===
Label Extraction

{|
|[[Image:LabelExtractionInterface.png|thumb|280px|User Interface]]
|[[Image:InputSegToExtractionCMFreg.png|thumb|280px|Input Segmentation to be computed]]
|[[Image:InputLabelMap1CMFreg.png|thumb|280px|Output segmentaiton with the single label extracted]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration pre steps (label maps processing)

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Interface Description''''':
** '''Input Volume''' [--inputVolume] : Input Segmentation to be computed.
** '''label''' [--labelNumber] : Single label to be extracted from segmentation input.
** '''outputVolume''' [--outputVolume] : Output segmentaiton with single label extracted.

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

Documentation/Nightly/Modules/LabelAddition

2013-09-23T21:27:27Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===Label Addition=== Label Addition {| |User Interface |[[Image…'

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

===Label Addition===
Label Addition

{|
|[[Image:LabelAdditionInterface.png|thumb|280px|User Interface]]
|[[Image:InputLabelMap1CMFreg.png|thumb|280px|Input Scan Bad Voxel Based Resolution]]
|[[Image:InputLabelMap2CMFreg.png|thumb|280px|Input Scan Bad Voxel Based Resolution]]
|[[Image:OutputLabelMap1plus2CMFreg.png|thumb|280px|Output Scan Downsized]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration pre steps (label maps processing)

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Interface Description''''':
** '''Input Label Map A''' [index 0] : First segmentaiton file to be addicted.
** '''Input Label Map B''' [index 1] : Second segmentaiton file to be addicted.
** '''Output Label Map''' [index 2] : Output segmentaiton file with label A plus B.

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

Documentation/Nightly/Modules/Downsize

2013-09-23T21:26:47Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===Downsize=== Downsize {| |User Interface |[[Image:InputVolumeBadRe…'

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

===Downsize===
Downsize

{|
|[[Image:DownsizeInterface.png|thumb|280px|User Interface]]
|[[Image:InputVolumeBadResolutionCMFreg.png|thumb|280px|Input Scan Bad Voxel Based Resolution]]
|[[Image:OutputScanDownsizedCMFreg.png|thumb|280px|Output Scan Downsized]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration pre steps (voxel resolution)

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Parameters''''':
** '''Size''' [-s --spacing] : The value of each voxel resolution for 3 dimensions
** '''Input Volume''' [index: 0] : Input volume to be resampled.
** '''Output Volume''' [index: 1] : Resampled Output Volume

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

Documentation/Nightly/Extensions/CMFreg

2013-09-23T21:26:05Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- ----------------------…'

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip|CMFreg Data]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.3/Extensions/CMFreg

2013-09-23T20:04:02Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip|CMFreg Data]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.3/Extensions/CMFreg

2013-09-23T20:03:32Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.3/Extensions/CMFreg

2013-09-23T20:01:01Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[File:CMFregData.zip|CMFreg Data]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.3/Extensions/CMFreg

2013-09-23T19:38:56Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[File:CMFregData.zip]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

File:CMFregData.zip

2013-09-23T19:37:41Z

Vboen:

Documentation/4.3/Modules/CMFregData

2013-09-23T19:31:43Z

Vboen: Created page with 'Media:CMFregData.zip'

[[Media:CMFregData.zip]]

Documentation/4.3/Extensions/CMFreg

2013-09-23T18:56:47Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/CMFregData|Data]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.3/Extensions/CMFreg

2013-09-23T18:56:03Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]
*[[Documentation/{{documentation/version}}/Modules/Data|Data]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.3/Modules/Growing

2013-09-20T19:01:29Z

Vboen:

Documentation/4.3/Modules/Growing

2013-09-20T19:00:56Z

Vboen:

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

===Growing===
Growing

{|
|[[Image:GrowingInterface.png|thumb|280px|User Interface]]
|[[Image:BaselineCBCTCMFreg.png|thumb|280px|Baseline CBCT Scan - Input Scan]]
|[[Image:FollowupCBCTCMFreg.png|thumb|280px|Follow up CBCT Scan - Input Scan]]
|[[Image:BaselineSegmentationMaskCMFreg.png|thumb|280px|Baseline Segmentation Mask - Input Seg]]
|[[Image:FollowupSegmentationMaskCMFreg.png|thumb|280px|Followup Segmentation Mask - Input Seg]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg2.png|thumb|280px|Baseline and Followup CBCT Scans - Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg.png|thumb|280px|Baseline Input Scan + Followup Input Scan]]
|}

== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Parameters''''':
** '''Baseline Scan (fixed)''' [-f --fixedVolume] : The fixed scan image for registration.
** '''Follow up Scan (moving)''' [-m --movingVolume] : The moving scan image for registration.
** '''Baseline Segmentation (fixed)''' [--fixedBinaryVolume] : The fixed one label segmentation image for registration used to specify the region of interest.
** '''Follow up Segmentation (moving)''' [--movingBinaryVolume] : The moving one label segmentation image for registration used to specify the region of interest.

* '''''Voxel Based Registration Options''''':
** '''Rigid + Scale (7DOF)''' [--useScaleVersor3D] : Perform a ScaleVersor3D registration as part of the sequential registration steps.
** '''Rigid + Skew + Scale (10DOF)''' [--useScaleSkewVersor3D] : Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.
** '''Affine (12DOF)''' [--useAffine] : Perform an Affine registration as part of the sequential registration steps.

* '''''Output Registration Matrix''''':
** '''Registration Matrix''' [-t --transformPath] : File name for the rigid component of the estimated registration matrix. Can be used to rigidly register the moving image to the fixed image.

* '''''Apply Registration Matrix''''':
** '''Input Segmentatiton to be Registered''' [--segmentation] : Input segmentation image to be modified with the registration matrix.
** '''Output Registered Scan''' [--segmentationOut] : Output segmentation image. This segmentaiton image is the 'Input Segmentation to be Registered' with the registration matrix already applied.
** '''Output Registered Scan''' [--outputVolume] : Output image for registration. This image is the Follow up Scan with the registration matrix already applied.

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

Documentation/4.3/Modules/Growing

2013-09-20T19:00:14Z

Vboen:

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

===Growing===
Growing

{|
|[[Image:GrowingInterface.png|thumb|280px|User Interface]]
|[[Image:BaselineCBCTCMFreg.png|thumb|280px|Baseline CBCT Scan - Input Scan]]
|[[Image:FollowupCBCTCMFreg.png|thumb|280px|Follow up CBCT Scan - Input Scan]]
|[[Image:BaselineSegmentationMaskCMFreg.png|thumb|280px|Baseline Segmentation Mask - Input Seg]]
|[[Image:FollowupSegmentationMaskCMFreg.png|thumb|280px|Followup Segmentation Mask - Input Seg]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg2.png|thumb|280px|Baseline and Followup CBCT Scans - Baseline Input Scan + Followup Input Scan]]
|[[Image:BaselineFollowupSCANRegisteredCMFreg.png|thumb|280px|Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan]]
|}

== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Input Parameters''''':
** '''Baseline Scan (fixed)''' [-f --fixedVolume] : The fixed scan image for registration.
** '''Follow up Scan (moving)''' [-m --movingVolume] : The moving scan image for registration.
** '''Baseline Segmentation (fixed)''' [--fixedBinaryVolume] : The fixed one label segmentation image for registration used to specify the region of interest.
** '''Follow up Segmentation (moving)''' [--movingBinaryVolume] : The moving one label segmentation image for registration used to specify the region of interest.

* '''''Voxel Based Registration Options''''':
** '''Rigid + Scale (7DOF)''' [--useScaleVersor3D] : Perform a ScaleVersor3D registration as part of the sequential registration steps.
** '''Rigid + Skew + Scale (10DOF)''' [--useScaleSkewVersor3D] : Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.
** '''Affine (12DOF)''' [--useAffine] : Perform an Affine registration as part of the sequential registration steps.

* '''''Output Registration Matrix''''':
** '''Registration Matrix''' [-t --transformPath] : File name for the rigid component of the estimated registration matrix. Can be used to rigidly register the moving image to the fixed image.

* '''''Apply Registration Matrix''''':
** '''Input Segmentatiton to be Registered''' [--segmentation] : Input segmentation image to be modified with the registration matrix.
** '''Output Registered Scan''' [--segmentationOut] : Output segmentation image. This segmentaiton image is the 'Input Segmentation to be Registered' with the registration matrix already applied.
** '''Output Registered Scan''' [--outputVolume] : Output image for registration. This image is the Follow up Scan with the registration matrix already applied.

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

Documentation/4.3/Extensions/CMFreg

2013-09-18T19:37:13Z

Vboen:

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

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


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Vinicius Boen, University of Michigan 
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry) 
Contact: Vinicius Boen, <email>vboen@umich.edu</email> 
Website: http://www.nitrc.org/projects/cmfreg/ 
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
Image:UofM-logo.png|UofM
</gallery>

{{documentation/{{documentation/version}}/extension-section|Extension Description}}

For assessment of overall facial changes, cranial base segmented models are only used to mask anatomic structures that change with growth and treatment. The registration procedures actually compare voxel by voxel of gray-level CBCT images, containing only the cranial base, to calculate rotation and translation parameters between the 2 images. Cranial base registration yields information of facial displacements relative to the cranial base. For subjects in whom cranial base growth is complete, registration is done using the gray level CBCT datasets of the whole cranial base ( Nongrowing registration module). The larger the number of voxels used for the registration, the more robust the registration is. For this reason, for adult patients the whole cranial base “mask CBCT” is used for registration. For growing patients ( Growing registration module), the registration includes two steps in the same module: in the first, an initial head alignment is done using the whole cranial base, and then a finer registration is performed at the stable structure on the anterior cranial base.
For assessment of localized facial changes, such as mandibular or maxillary growth or bone remodeling of the mandibular condyle or tooth movement, specific anatomic regions can be used to create localized masks and aid regional superimpositions. The challenge in regional superimpositions is to determine which structures offer stable reference for registration.

The CMFregistration modules also include the following functionalities:

* Downsize image: for high resolution image files with large size, downsizing facilitates image analysis, making it more robust and saving computing processing time. In this tool, any voxel size can be entered to resample the volume.

* Label extraction and Label addition: segmentation files can be modified to extract or add a anatomic region of interest into a new file.

* Mask creation: segmentation files are used to : 1: generate CBCT files that can be used to mask anatomic regions that changed with growth and treatment ; or 2: generate a CBCT file that contains only the anatomic region of interest for regional superimpositions.


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/Downsize|Downsize]]
*[[Documentation/{{documentation/version}}/Modules/LabelAddition|LabelAddition]]
*[[Documentation/{{documentation/version}}/Modules/LabelExtraction|LabelExtraction]]
*[[Documentation/{{documentation/version}}/Modules/MaskCreation|MaskCreation]]
*[[Documentation/{{documentation/version}}/Modules/Growing|Growing]]
*[[Documentation/{{documentation/version}}/Modules/NonGrowing|NonGrowing]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:GrowingInterface.png|Growing Registration Interface
Image:BaselineCBCTCMFreg.png|Baseline CBCT Scan
Image:FollowupCBCTCMFreg.png|Follow up CBCT Scan
Image:BaselineFollowupSCANCMFreg.png|Baseline and Followup CBCT Scans
Image:BaselineSegmentationMaskCMFreg.png|Baseline Segmentation Mask
Image:FollowupSegmentationMaskCMFreg.png|Followup Segmentation Mask
Image:BaselineFollowupSCANRegisteredCMFreg2.png|Baseline and Followup CBCT Scans Registered
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

More information as well as the source code can found on the project webpage: https://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage


{{documentation/{{documentation/version}}/extension-footer}}

File:BaselineFollowupSCANRegisteredCMFreg2.png

2013-09-18T19:36:41Z

Vboen:

Documentation/4.3/Modules/MaskCreation

2013-09-18T19:35:23Z

Vboen:

Documentation/4.3/Modules/MaskCreation

2013-09-18T19:32:50Z

Vboen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> __NOTOC__ ===Mask Creation=== Mask Creation {| |User Interface |[[Image:Fo…'

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

===Mask Creation===
Mask Creation

{|
|[[Image:MaskCreationInterface.png|thumb|280px|User Interface]]
|[[Image:FollowupMaskCMFreg.png|thumb|280px|Input Scan to be masked]]
|[[Image:InputLabelMap2CMFreg.png|thumb|280px|Input mask single label segmentation]]
|[[Image:OutputMaskedScanCMFreg.png|thumb|280px|Output Scan masked]]
|}
== General Information ==

===Module Type & Category===

Type: Extension

Category: CBCT Scan Registration pre steps (label maps processing)

===Authors, Collaborators & Contact===

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

===Module Description===
* '''''Interface Description''''':
** '''Input Label Map A''' [index 0] : First segmentaiton file to be addicted.
** '''Input Label Map B''' [index 1] : Second segmentaiton file to be addicted.
** '''Output Label Map''' [index 2] : Output segmentaiton file with label A plus B.

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

File:FollowupMaskCMFreg.png

2013-09-18T19:31:49Z

Vboen:

File:OutputMaskedScanCMFreg.png

2013-09-18T19:30:12Z

Vboen: