Slicer Wiki - User contributions [en]

Documentation/4.1/Modules/TrainModel

2012-06-22T22:23:19Z

Mscully: Expanded use cases.

Documentation/4.1/Modules/TrainModel

2012-06-22T19:55:27Z

Mscully:

Documentation/4.1/Modules/PredictLesions

2012-06-22T19:52:54Z

Mscully: Added panel information and screenshot

File:PredictModelInterface.png

2012-06-22T19:52:08Z

Mscully: The interface for the Slicer4.1 LesionSegmentation->PredictLesions module.

The interface for the Slicer4.1 LesionSegmentation->PredictLesions module.

Documentation/4.1/Modules/TrainModel

2012-06-22T19:45:39Z

Mscully: Added panel info and screenshot

File:TrainModelInterface.png

2012-06-22T19:43:48Z

Mscully: The interface panel for the Slicer4.1 LesionSegmentation TrainModel module.

The interface panel for the Slicer4.1 LesionSegmentation TrainModel module.

Documentation/4.1/Extensions/LesionSegmentation

2012-06-21T20:05:24Z

Mscully: Changed to extensions with multiple modules format

Documentation/4.1/Modules/PredictLesions

2012-06-21T19:53:58Z

Mscully: Initial version

Documentation/4.1/Modules/TrainModel

2012-06-21T19:53:46Z

Mscully: Initial version

Documentation/4.1/HowTo

2012-06-21T19:30:41Z

Mscully: /* Miscellaneous */

{{documentation/{{documentation/version}}/header}}


{{Infobox
|name = 3D Slicer {{documentation/version}}
|above = 3D Slicer
|abovestyle =

|image = [[File:3DSlicer41Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
|imagestyle =
|headerstyle = background:#E7DCC3;
|labelstyle =
|datastyle =

|header1 = Description
|label1 =
|data1 =
|header2 =
|label2 =
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3 =
|data3 = Free and extensible open source package.
|header4 =
|label4 = Multi-platform
|data4 = Linux, MacOSX, Windows
|header5 =
|label5 = Version
|data5 = {{documentation/version}}
|header6 =
|label6 = License
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}

= Overview =

This document aims at describing the principle and guidelines to consider when writing Slicer user documentation.

The documentation framework has been designed keeping in mind the following principles:
* Single location for editing documentation (either the wiki or the source code), no duplicative editing.
* Smart use of mediawiki templates to enforce consistency and reduce maintenance work.

__TOC__

= Naming conventions =
# The application '''Slicer''' should be referenced with an uppercase '''S'''.
# All documentation should be added as subpages under '''Documentation/X.Y/''' where '''X''' and '''Y''' are respectively the '''major''' and '''minor''' Slicer version.
# Version of Slicer should NOT be written in plain text, {{[[Template:Documentation/version|documentation/version]]}} template should be used instead.
# [[Documentation/{{documentation/version}}/SlicerApplication]] should be the root of all subpages specific to Slicer application.
# [[Documentation/{{documentation/version}}/Modules]] should be the root of all subpages specific to Slicer modules.
# Module subpage should be named after the '''module name''' used in the associated source repository. Assuming the module is named '''Foo''', the corresponding subpage is expected to be '''Documentation/{{documentation/version}}/Modules/Foo'''
# Collaborator names, logos or URLs should be referenced using the convenient [[Template:Collaborator|Collaborator]] template.
## For example: <nowiki>''{{collaborator|longname|namic}}''</nowiki> generates ''{{collaborator|longname|namic}}''
# Email addresses must be wrapped with the '''<nowiki><email></email></nowiki>''' tags

= Category =
# All subpages should be categorized. See [https://secure.wikimedia.org/wikipedia/mediawiki/wiki/Help:Categories#Adding_a_page_to_a_category]
# The user documentation pages are grouped in the [[:Category:Documentation/{{documentation/version}}/SlicerApplication|Slicer Application]] and [[:Category:Documentation/{{documentation/version}}/Modules|Modules]] categories.

= SlicerApplication page =
# [[Template:Documentation/{{documentation/version}}/slicerapplication-header|slicerapplication-header]] and [[Template:Documentation/{{documentation/version}}/slicerapplication-footer|slicerapplication-footer]] templates should be respectively used at the top and the bottom of the page.

= Module page =
# [[Template:Documentation/{{documentation/version}}/module-header|module-header]] and [[Template:Documentation/{{documentation/version}}/module-footer|module-footer]] templates should be respectively used at the top and the bottom of the page.
# [[Template:Documentation/modulename|modulename]] should be used instead of writing in plain text the name of the module.
# Base your work on either [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME]] or an [[:Category:Documentation/{{documentation/version}}/Modules|existing module]] documentation.
# For CLI modules, the '''SVNREVISION''' revision number is reported on this [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Applications/CLI page]. The module description and the information for developers would be automatically extracted from the corresponding XML description.
# See [[Documentation/{{documentation/version}}/ModulesMetadata|this page]] to define the revision number. The revision number associated to a module is used to extract module information from the source code directly.

== Documentation for a CLI module ==
The main idea is to re-use the documentation of the CLI parameters in the wiki. When a CLI is added into Slicer, please execute the following steps to create the module online documentation.
# Create a CLI in Slicer4/Modules/CLI
# Add your module in [[Documentation/{{documentation/version}}/ModulesMetadata]]. Adding a module consists of adding a module name+revision pair alphabetically in the list. The revision number must correspond to the most up to date revision number of your module.
# Copy the content of the [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|template]] module and paste it in a page you created with the name of your module: [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME]].
# Edit the wiki code to replace the generic information with the module specific information. You can upload screenshots and tutorials.

== Documentation for a loadable module ==
Creating online documentation for loadable modules is similar to CLI modules. The difference is that loadable modules don't have parameter descriptions, it must be added separately.
# In Slicer4, if it doesn't exist yet
## create a ''Documentation'' subdirectory in your module directory (e.g. ''Slicer4/Modules/Loadable/Transforms/Documentation'').
## Copy and rename the ''YourModuleName.{xml,dox}'' files from an existing module documentation.
# Add description for each [[Documentation/{{documentation/version}}/Developers/Style_Guide/UI#Section|section]] of your module (''YourModuleName.xml'') applying the following pattern:
<pre>
<parameters>
<label>Section1 header</label>
<parameter>
<label>Parameter1 name</label>
<description><![CDATA[Parameter1 description]]></description>
</parameter>
</parameters>
<parameters>
<label>Section2 header</label>
<parameter>
<label>Parameter2 name</label>
<description><![CDATA[Parameter2 description]]></description>
</parameter>
<parameter>
<label>Parameter3 name</label>
<description><![CDATA[Parameter3 description]]></description>
</parameter>
...
</pre>

== Documentation for a scripted module ==
The trick used in loadable module documentation is not supported yet for scripted modules. Documentation must be written directly in the created module wiki page.

= Extension page =
# Create a [[#Module_page|regular wiki page]] for each module of the extension using the [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|template]] page. The URLs of the extension modules are the same than the built-in modules.
# Create an extension page
## [[Template:Documentation/{{documentation/version}}/extension-footer|extension-footer]] template should be at the bottom of the page.
## If the extension bundles exactly [[Documentation/{{documentation/version}}/Developers/Tutorials/BundleModulesIntoExtension#Extension_bundles_1_module|one]] module, use [{{fullurl:Documentation/{{documentation/version}}/Extensions/SkullStripper|redirect=no}} this template]
## If the extension bundles [[Documentation/{{documentation/version}}/Developers/Tutorials/BundleModulesIntoExtension#Extension_bundles_N_modules|more]] than one module, use [[Documentation/{{documentation/version}}/Extensions/Plastimatch|this template]].
# Add an extension entry in [[Documentation/{{documentation/version}}/Extensions#Extension_Categories]]
# The extension should now be listed on [[Documentation/{{documentation/version}}]].

= Miscellaneous =
* High resolution logos are in the [[Logo_Gallery|Logo Gallery]]
* There is a python helper script for SEM compliant tools that can save a significant amount of transcription time: Slicer/Utilities/Scripts/SEMToMediaWiki.py
**To use it run "python Slicer/Utilities/Scripts/SEMToMediaWiki.py -x XMLFILE.xml -o OUTPUT.txt" and the mediawiki content will be in OUTPUT.txt

Documentation/4.1/HowTo

2012-06-21T19:19:21Z

Mscully: /* Miscellaneous */

Documentation/4.1/Extensions/LesionSegmentation

2012-06-21T18:28:47Z

Mscully: Initial version

Documentation/4.0/Modules/BRAINSFit

2011-11-22T21:11:53Z

Mscully:

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Hans Johnson, UIOWA 
Contributor1: Kent Williams, UIOWA 
Contributor2: Vincent Magnotta, UIOWA 
Contributor3: Andriy Fedorov, BWH 
Contact: Hans Johnson, <email>(hans-johnson@uiowa.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:UIOWA-logo.png|University of Iowa
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


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

{{documentation/{{documentation/version}}/module-description|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* '''''Use Case 1: Same Subject: Longitudinal'''''

For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT1Longitudinal.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
</pre>
Since these are the same subject and very little has likely changed in the last year we'll use a Rigid registration. If the registration is poor or there are reasons to expect anatomical changes then additional transforms may be needed, in which case they can be added in a comma separated list, such as "Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline".
<pre>
--transformType Rigid \
</pre>
The scans are the same modality so we'll use --histogramMatch to match the intensity profiles as this tends to help registration. If there are lesions or tumors that vary between images this may not be a good idea, as it will make it harder to detect differences between the images.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
--transformType Rigid \
--histogramMatch \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:LongitudinalCheckerboardPreReg.png|thumb|180px|Longitudinal Checkerboard Before registration]]
| [[Image:LogitudinalCheckerboardPostReg.png|thumb|180px|Longitudinal Checkerboard After registration]]
|}

* '''''Use Case 2: Same Subject: MultiModal'''''

For this use case we're registering a T1 scan with a T2 scan collected in the same session. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT2.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
</pre>
Since these are the same subject, same session we'll use a Rigid registration.
<pre>
--transformType Rigid \
</pre>
The scans are different modalities so we absolutely DO NOT want to use --histogramMatch to match the intensity profiles as this would try to map the T2 intensities into T1 intensities, resulting in an image that was neither, and hence useless.

To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
--transformType Rigid \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:T1T2PreRegCheckerboard.png|thumb|180px|Multimodal Checkerboard Before registration]]
| [[Image:T1T2RegCheckerboard.png|thumb|180px|Multimodal Checkerboard After registration]]
|}

* '''''Use Case 3: Mouse Registration'''''

Here we'll register brains from two different mice together. The fixed and moving mouse brains used in this example are available on [http://midas.kitware.com/item/view/483 Midas].

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
</pre>
Since the subjects are different we are going to use transforms all the way through BSpline. Again, building up transforms one type at a time can't hurt and might help, so we're including all transforms from Rigid through BSpline in the transformType parameter.
<pre>
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
</pre>
The scans are the same modality so we'll use --histogramMatch.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHeadAlign. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
<pre>
--initializeTransformMode useMomentsAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
Since the mouse brains are much smaller than human brains there are a few advanced parameters we'll need to tweak, ROIAutoClosingSize and ROIAutoDilateSize (both under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value for mice is 0.9.
<pre>
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
--histogramMatch \
--initializeTransformMode useMomentsAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
--interpolationMode Linear
</pre>

{|
| [[Image:MouseCheckerboardPreRegistration.png|thumb|180px|Mouse Checkerboard Before registration]]
| [[Image:MouseCheckerboardPostRegistration.png|thumb|180px|Mouse Checkerboard After registration]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
* [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.
* Source repository on [https://github.com/BRAINSia/BRAINSStandAlone/tree/master/BRAINSFit github]
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}

Documentation/4.0/Modules/ForegroundMasking

2011-11-22T21:11:06Z

Mscully:

Documentation/4.0/Modules/BRAINSResample

2011-11-21T21:57:53Z

Mscully: Added use case types.

Documentation/4.0/Modules/BRAINSDemonWarp

2011-11-21T21:32:36Z

Mscully: Added use cases from 3.6 documentation.

Documentation/4.0/Modules/ForegroundMasking

2011-11-21T21:25:36Z

Mscully: Removed example panels.

Documentation/4.0/Modules/BRAINSDemonWarp

2011-11-21T21:24:51Z

Mscully: Removed example panels.

Documentation/4.0/Modules/BRAINSResample

2011-11-21T21:24:15Z

Mscully: Removed example panels.

Documentation/4.0/Modules/BRAINSFit

2011-11-21T21:23:49Z

Mscully: Removed example panels.

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Hans Johnson, UIOWA 
Contributor1: Kent Williams, UIOWA 
Contributor2: Vincent Magnotta, UIOWA 
Contributor3: Andriy Fedorov, BWH 
Contact: Hans Johnson, <email>(hans-johnson@uiowa.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:UIOWA-logo.png|University of Iowa
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


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

{{documentation/{{documentation/version}}/module-description|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* '''''Use Case 1: Same Subject: Longitudinal'''''

For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT1Longitudinal.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
</pre>
Since these are the same subject and very little has likely changed in the last year we'll use a Rigid registration. If the registration is poor or there are reasons to expect anatomical changes then additional transforms may be needed, in which case they can be added in a comma separated list, such as "Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline".
<pre>
--transformType Rigid \
</pre>
The scans are the same modality so we'll use --histogramMatch to match the intensity profiles as this tends to help registration. If there are lesions or tumors that vary between images this may not be a good idea, as it will make it harder to detect differences between the images.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
--transformType Rigid \
--histogramMatch \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:LongitudinalCheckerboardPreReg.png|thumb|180px|Longitudinal Checkerboard Before registration]]
| [[Image:LogitudinalCheckerboardPostReg.png|thumb|180px|Longitudinal Checkerboard After registration]]
|}

* '''''Use Case 2: Same Subject: MultiModal'''''

For this use case we're registering a T1 scan with a T2 scan collected in the same session. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT2.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
</pre>
Since these are the same subject, same session we'll use a Rigid registration.
<pre>
--transformType Rigid \
</pre>
The scans are different modalities so we absolutely DO NOT want to use --histogramMatch to match the intensity profiles as this would try to map the T2 intensities into T1 intensities, resulting in an image that was neither, and hence useless.

To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
--transformType Rigid \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:T1T2PreRegCheckerboard.png|thumb|180px|Multimodal Checkerboard Before registration]]
| [[Image:T1T2RegCheckerboard.png|thumb|180px|Multimodal Checkerboard After registration]]
|}

* '''''Use Case 3: Mouse Registration'''''

Here we'll register brains from two different mice together. The fixed and moving mouse brains used in this example are available on [http://midas.kitware.com/item/view/483 Midas].

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
</pre>
Since the subjects are different we are going to use transforms all the way through BSpline. Again, building up transforms one type at a time can't hurt and might help, so we're including all transforms from Rigid through BSpline in the transformType parameter.
<pre>
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
</pre>
The scans are the same modality so we'll use --histogramMatch.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHeadAlign. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
<pre>
--initializeTransformMode useMomentsAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
Since the mouse brains are much smaller than human brains there are a few advanced parameters we'll need to tweak, ROIAutoClosingSize and ROIAutoDilateSize (both under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value for mice is 0.9.
<pre>
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
--histogramMatch \
--initializeTransformMode useMomentsAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
--interpolationMode Linear
</pre>

{|
| [[Image:MouseCheckerboardPreRegistration.png|thumb|180px|Mouse Checkerboard Before registration]]
| [[Image:MouseCheckerboardPostRegistration.png|thumb|180px|Mouse Checkerboard After registration]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
* [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.
* Source repository on [https://github.com/BRAINSia/BRAINSStandAlone/tree/master/BRAINSFit github]
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}

Documentation/4.0/Modules/BRAINSDemonWarp

2011-11-21T21:20:22Z

Mscully: Removed blank contributors.

Documentation/4.0/Modules/ForegroundMasking

2011-11-21T21:19:57Z

Mscully: Removed blank contributors.

Documentation/4.0/Modules/BRAINSResample

2011-11-21T21:17:46Z

Mscully: Added contributors

Documentation/4.0/Modules/BRAINSFit

2011-11-21T21:16:29Z

Mscully: Added contributors

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Hans Johnson, UIOWA 
Contributor1: Kent Williams, UIOWA 
Contributor2: Vincent Magnotta, UIOWA 
Contributor3: Andriy Fedorov, BWH 
Contact: Hans Johnson, <email>(hans-johnson@uiowa.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:UIOWA-logo.png|University of Iowa
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


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

{{documentation/{{documentation/version}}/module-description|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* '''''Use Case 1: Same Subject: Longitudinal'''''

For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT1Longitudinal.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
</pre>
Since these are the same subject and very little has likely changed in the last year we'll use a Rigid registration. If the registration is poor or there are reasons to expect anatomical changes then additional transforms may be needed, in which case they can be added in a comma separated list, such as "Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline".
<pre>
--transformType Rigid \
</pre>
The scans are the same modality so we'll use --histogramMatch to match the intensity profiles as this tends to help registration. If there are lesions or tumors that vary between images this may not be a good idea, as it will make it harder to detect differences between the images.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
--transformType Rigid \
--histogramMatch \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:LongitudinalCheckerboardPreReg.png|thumb|180px|Longitudinal Checkerboard Before registration]]
| [[Image:LogitudinalCheckerboardPostReg.png|thumb|180px|Longitudinal Checkerboard After registration]]
|}

* '''''Use Case 2: Same Subject: MultiModal'''''

For this use case we're registering a T1 scan with a T2 scan collected in the same session. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT2.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
</pre>
Since these are the same subject, same session we'll use a Rigid registration.
<pre>
--transformType Rigid \
</pre>
The scans are different modalities so we absolutely DO NOT want to use --histogramMatch to match the intensity profiles as this would try to map the T2 intensities into T1 intensities, resulting in an image that was neither, and hence useless.

To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
--transformType Rigid \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:T1T2PreRegCheckerboard.png|thumb|180px|Multimodal Checkerboard Before registration]]
| [[Image:T1T2RegCheckerboard.png|thumb|180px|Multimodal Checkerboard After registration]]
|}

* '''''Use Case 3: Mouse Registration'''''

Here we'll register brains from two different mice together. The fixed and moving mouse brains used in this example are available on [http://midas.kitware.com/item/view/483 Midas].

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
</pre>
Since the subjects are different we are going to use transforms all the way through BSpline. Again, building up transforms one type at a time can't hurt and might help, so we're including all transforms from Rigid through BSpline in the transformType parameter.
<pre>
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
</pre>
The scans are the same modality so we'll use --histogramMatch.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHeadAlign. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
<pre>
--initializeTransformMode useMomentsAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
Since the mouse brains are much smaller than human brains there are a few advanced parameters we'll need to tweak, ROIAutoClosingSize and ROIAutoDilateSize (both under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value for mice is 0.9.
<pre>
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
--histogramMatch \
--initializeTransformMode useMomentsAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
--interpolationMode Linear
</pre>

{|
| [[Image:MouseCheckerboardPreRegistration.png|thumb|180px|Mouse Checkerboard Before registration]]
| [[Image:MouseCheckerboardPostRegistration.png|thumb|180px|Mouse Checkerboard After registration]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}

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

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
* [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.
* Source repository on [https://github.com/BRAINSia/BRAINSStandAlone/tree/master/BRAINSFit github]
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}

Documentation/4.0/Modules/BRAINSFit

2011-11-21T21:09:21Z

Mscully: /* Use Cases, Examples */ Changed data source to Midas

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Hans Johnson, UIOWA 
Contributor1: FIRSTNAME LASTNAME, AFFILIATION 
Contributor2: FIRSTNAME LASTNAME, AFFILIATION 
Contact: Hans Johnson, <email>(hans-johnson@uiowa.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:UIOWA-logo.png|University of Iowa
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


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

{{documentation/{{documentation/version}}/module-description|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* '''''Use Case 1: Same Subject: Longitudinal'''''

For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT1Longitudinal.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
</pre>
Since these are the same subject and very little has likely changed in the last year we'll use a Rigid registration. If the registration is poor or there are reasons to expect anatomical changes then additional transforms may be needed, in which case they can be added in a comma separated list, such as "Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline".
<pre>
--transformType Rigid \
</pre>
The scans are the same modality so we'll use --histogramMatch to match the intensity profiles as this tends to help registration. If there are lesions or tumors that vary between images this may not be a good idea, as it will make it harder to detect differences between the images.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
--transformType Rigid \
--histogramMatch \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:LongitudinalCheckerboardPreReg.png|thumb|180px|Longitudinal Checkerboard Before registration]]
| [[Image:LogitudinalCheckerboardPostReg.png|thumb|180px|Longitudinal Checkerboard After registration]]
|}

* '''''Use Case 2: Same Subject: MultiModal'''''

For this use case we're registering a T1 scan with a T2 scan collected in the same session. The two images are again available on [http://midas.kitware.com/item/view/483 Midas] as testT1.nii.gz and testT2.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
</pre>
Since these are the same subject, same session we'll use a Rigid registration.
<pre>
--transformType Rigid \
</pre>
The scans are different modalities so we absolutely DO NOT want to use --histogramMatch to match the intensity profiles as this would try to map the T2 intensities into T1 intensities, resulting in an image that was neither, and hence useless.

To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
--transformType Rigid \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:T1T2PreRegCheckerboard.png|thumb|180px|Multimodal Checkerboard Before registration]]
| [[Image:T1T2RegCheckerboard.png|thumb|180px|Multimodal Checkerboard After registration]]
|}

* '''''Use Case 3: Mouse Registration'''''

Here we'll register brains from two different mice together. The fixed and moving mouse brains used in this example are available on [http://midas.kitware.com/item/view/483 Midas].

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
</pre>
Since the subjects are different we are going to use transforms all the way through BSpline. Again, building up transforms one type at a time can't hurt and might help, so we're including all transforms from Rigid through BSpline in the transformType parameter.
<pre>
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
</pre>
The scans are the same modality so we'll use --histogramMatch.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHeadAlign. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
<pre>
--initializeTransformMode useMomentsAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
Since the mouse brains are much smaller than human brains there are a few advanced parameters we'll need to tweak, ROIAutoClosingSize and ROIAutoDilateSize (both under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value for mice is 0.9.
<pre>
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
--histogramMatch \
--initializeTransformMode useMomentsAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
--interpolationMode Linear
</pre>

{|
| [[Image:MouseCheckerboardPreRegistration.png|thumb|180px|Mouse Checkerboard Before registration]]
| [[Image:MouseCheckerboardPostRegistration.png|thumb|180px|Mouse Checkerboard After registration]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}

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

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
* [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.
* Source repository on [https://github.com/BRAINSia/BRAINSStandAlone/tree/master/BRAINSFit github]
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}

Documentation/4.0/Modules/BRAINSFit

2011-11-21T20:45:57Z

Mscully: Added use cases from 3.6 documentation.

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Hans Johnson, UIOWA 
Contributor1: FIRSTNAME LASTNAME, AFFILIATION 
Contributor2: FIRSTNAME LASTNAME, AFFILIATION 
Contact: Hans Johnson, <email>(hans-johnson@uiowa.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:UIOWA-logo.png|University of Iowa
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


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

{{documentation/{{documentation/version}}/module-description|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* '''''Use Case 1: Same Subject: Longitudinal'''''

For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later. The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT1Longitudinal.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
</pre>
Since these are the same subject and very little has likely changed in the last year we'll use a Rigid registration. If the registration is poor or there are reasons to expect anatomical changes then additional transforms may be needed, in which case they can be added in a comma separated list, such as "Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline".
<pre>
--transformType Rigid \
</pre>
The scans are the same modality so we'll use --histogramMatch to match the intensity profiles as this tends to help registration. If there are lesions or tumors that vary between images this may not be a good idea, as it will make it harder to detect differences between the images.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
--transformType Rigid \
--histogramMatch \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:LongitudinalCheckerboardPreReg.png|thumb|180px|Longitudinal Checkerboard Before registration]]
| [[Image:LogitudinalCheckerboardPostReg.png|thumb|180px|Longitudinal Checkerboard After registration]]
|}

* '''''Use Case 2: Same Subject: MultiModal'''''

For this use case we're registering a T1 scan with a T2 scan collected in the same sesson. The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT2.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
</pre>
Since these are the same subject, same session we'll use a Rigid registration.
<pre>
--transformType Rigid \
</pre>
The scans are different modalities so we absolutely DO NOT want to use --histogramMatch to match the intensity profiles as this would try to map the T2 intensities into T1 intensities, resulting in an image that was neither, and hence useless.

To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHeadAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
--transformType Rigid \
--initializeTransformMode useCenterOfHeadAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:T1T2PreRegCheckerboard.png|thumb|180px|Multimodal Checkerboard Before registration]]
| [[Image:T1T2RegCheckerboard.png|thumb|180px|Multimodal Checkerboard After registration]]
|}

* '''''Use Case 3: Mouse Registration'''''

Here we'll register brains from two different mice together. The fixed and moving mouse brains used in this example are available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory.

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
</pre>
Since the subjects are different we are going to use transforms all the way through BSpline. Again, building up transforms one type at a time can't hurt and might help, so we're including all transforms from Rigid through BSpline in the transformType parameter.
<pre>
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
</pre>
The scans are the same modality so we'll use --histogramMatch.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHeadAlign. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
<pre>
--initializeTransformMode useMomentsAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
Since the mouse brains are much smaller than human brains there are a few advanced parameters we'll need to tweak, ROIAutoClosingSize and ROIAutoDilateSize (both under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value for mice is 0.9.
<pre>
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
--histogramMatch \
--initializeTransformMode useMomentsAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
--interpolationMode Linear
</pre>

{|
| [[Image:MouseCheckerboardPreRegistration.png|thumb|180px|Mouse Checkerboard Before registration]]
| [[Image:MouseCheckerboardPostRegistration.png|thumb|180px|Mouse Checkerboard After registration]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}

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

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
* [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.
* Source repository on [https://github.com/BRAINSia/BRAINSStandAlone/tree/master/BRAINSFit github]
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=https://raw.github.com/BRAINSia/BRAINSStandAlone/master/BRAINSFit/BRAINSFit.xml }}
}}

Documentation/4.0/Modules/ForegroundMasking

2011-11-21T18:13:59Z

Mscully: Added parameters description xml line.

Documentation/4.0/Modules/BRAINSDemonWarp

2011-11-21T18:12:40Z

Mscully: Added parameters description xml line.

Documentation/4.0/Modules/BRAINSResample

2011-11-21T18:11:24Z

Mscully:

Documentation/4.0/Modules/BRAINSFit

2011-11-21T18:10:20Z

Mscully: Added parameters description xml line.

Documentation/4.0/Modules/ForegroundMasking

2011-11-21T17:34:16Z

Mscully: xml urls now point to github

Documentation/4.0/Modules/BRAINSDemonWarp

2011-11-21T17:25:28Z

Mscully: xml urls point to github

Documentation/4.0/Modules/BRAINSResample

2011-11-21T17:22:10Z

Mscully: Changed github urls to point to master.

Documentation/4.0/Modules/BRAINSFit

2011-11-21T17:19:03Z

Mscully: Updated other urls to BRAINSFit.xml so they point to github.

Documentation/4.0/Modules/BRAINSResample

2011-11-21T17:14:01Z

Mscully: Templates now point to BRAINSResample.xml in github.

Documentation/4.0/Modules/BRAINSDemonWarp

2011-11-21T16:55:33Z

Mscully: Updated module description url to point to BRAINSDemonWarp.xml in github.

Documentation/4.0/Modules/BRAINSResample

2011-11-21T16:53:25Z

Mscully: Updated module description url to point to BRANSResample.xml in github.

Documentation/4.0/Modules/BRAINSFit

2011-11-21T16:51:51Z

Mscully: Updated module description url to point to BRANSFit.xml in github.

Template:Documentation/4.0/module-developerinfo

2011-11-21T16:12:11Z

Mscully: Undo revision 23034 by Mscully (Talk)

<includeonly>Type: {{{type}}}

Category: {{{category}}}

==Notes from the Developer(s)==

Developer notes for {{{1}}} will be automatically listed.

== Dependencies ==

Dependencies of {{{1}}} will be automatically listed.

== Bugs ==

Known bugs of {{{1}}} will be automatically listed.

==Tests==

On the [http://cdash.org/slicer4 Slicer4 Dashboard], these tests verify that the module is working on various platforms:

* [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Applications/CLI/{{{1}}}/Testing/ Test source code directory for {{{1}}}]

==Source code & documentation==

Doxygen documentation and source files of {{{1}}} will be automatically listed.</includeonly><noinclude>

__NOTOC__

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-developerinfo|GradientAnisotropicDiffusion|type=CLI|category=Filtering}}</pre>

{{documentation/{{documentation/version}}/module-developerinfo|GradientAnisotropicDiffusion|type=CLI|category=Filtering}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.0/module-developerinfo

2011-11-21T16:03:20Z

Mscully: /* Tests */ Test source points to TestSuite in github

<includeonly>Type: {{{type}}}

Category: {{{category}}}

==Notes from the Developer(s)==

Developer notes for {{{1}}} will be automatically listed.

== Dependencies ==

Dependencies of {{{1}}} will be automatically listed.

== Bugs ==

Known bugs of {{{1}}} will be automatically listed.

==Tests==

On the [http://cdash.org/slicer4 Slicer4 Dashboard], these tests verify that the module is working on various platforms:

* [https://github.com/BRAINSia/BRAINSStandAlone/tree/master/BRAINSFit/TestSuite Test source code directory for BRAINSFit]

==Source code & documentation==

Doxygen documentation and source files of {{{1}}} will be automatically listed.</includeonly><noinclude>

__NOTOC__

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-developerinfo|GradientAnisotropicDiffusion|type=CLI|category=Filtering}}</pre>

{{documentation/{{documentation/version}}/module-developerinfo|GradientAnisotropicDiffusion|type=CLI|category=Filtering}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Documentation/4.0/Modules/BRAINSFit

2011-11-21T15:57:58Z

Mscully:

Documentation/4.0/Modules/BRAINSFit

2011-11-21T15:33:52Z

Mscully: Added reference to paper.

Documentation/4.0

2011-11-21T15:18:58Z

Mscully: /* Segmentation */ Added link for Foreground Masking.

__NOTOC__


[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]

=Table of Content=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|

===Slicer Application===
----
<big>'''
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)

*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)


*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)'''
</big>

===Mailing Lists===
----
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]



|bgcolor="#CCCCCC"|
|valign="top"|

===Module Categories ===
----
<big>'''
* [[#Core Modules|Core Modules]]
* [[#Wizards|Wizards]]
* [[#Informatics|Informatics]]
* [[#Registration|Registration]]
* [[#Segmentation|Segmentation]]
* [[#Quantification|Quantification]]
* [[#Diffusion|Diffusion]]
* [[#IGT|IGT]]
* [[#Filtering|Filtering]]
* [[#Surface Models|Surface Models]]
* [[#Converters|Converters]]
* [[#Endoscopy|Endoscopy]]
* [[#DeveloperTools|Developer Tools]]
* [[#Legacy|Legacy]]
* [[#Utilities|Utility]]
</big>
|bgcolor="#CCCCCC"|
|valign="top"|

===Miscellaneous===
----


* [[Slicer4:VisualBlog|Visual blog]]
: Set of screenshots showing Slicer in action.


* [[Documentation/4.0/Training|Training pages]]
: Information on how to use Slicer {{documentation/version}}

* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
: Set of common questions/answers

===Developers Corner===
----
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]
: Handy Developer Info
|}

=General Information=
{|width="100%"
|rowspan="3"|
{{Infobox
|name = 3D Slicer {{documentation/version}}
|above = 3D Slicer
|abovestyle =

|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
|imagestyle =
|headerstyle = background:#E7DCC3;
|labelstyle =
|datastyle =

|header1 = Description
|label1 =
|data1 =
|header2 =
|label2 =
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3 =
|data3 = Free and extensible open source package.
|header4 =
|label4 = Multi-platform
|data4 = Linux, MacOSX, Windows
|header5 =
|label5 = Version
|data5 = {{documentation/version}}
|header6 =
|label6 = License
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}

|align="center"|
<gallery widths=150px heights=150px perrow="3" frameless="yes">
Image:2011-11-12-CroppingWholeBrainTractography-detail.png
Image:Selection 142.png
Image:prostate_multiparametric_visualization_Slicer4.png
</gallery>
|-
|
{{ombox
|type=content
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].
}}
|-
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{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}
|}

=Requirements for Modules=
* The module is '''feature complete''', i.e. it does everything that it advertises
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].
*Use the logos in the [[Logo_Gallery|Logo Gallery]]

=Modules by Category=
==Core Modules==
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov) [[image:UnderConstruction.png|tumb|10px]]

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)

==Segmentation==
*EMSegment Easy (no atlas) (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**EMSegment Command-line (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Utilities
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]

==IGT==

==Filtering==
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Resample Tools
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Label Map Smoothing
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*Probe Volume with Model (Paint)

==Converters==
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Endoscopy==
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robert) [[image:UnderConstruction.png|tumb|10px]]
*Module Template
*Multiple Models Example
*Performance Tests
*Tractography

==Legacy==
*Converters
**BSpline to Deformation Field
*Diffusion
**Denoising
***Unbiased Non Local Means Filter for DWI
*Filtering
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**Resample Scalar Volume
*Registration
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Nonrigid BSpline Registration
**Expert Automated Registration
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Robust Multiresolution Affine Registration
*Segmentation
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

==Utilities==
*Transform MRML Files to NewSegmenter Standard

=Extensions=

'''Introduction'''

* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
* In case of problems with extensions, please talk directly to the developers of the extensions.
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.

==Collections==
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.

{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyCollection
| This is a collection of extensions that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

==Table Of Extensions==
{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something wonderful with your data
| [[File:ExperimentalExtensionIcon.png|80px]]
| [[File:NoSlicerLicenseIcon.png|80px]]
| filter, anisotropic
| my-email at gmail.com
|-
| 2
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

'''Caption for the table of extensions'''
<gallery heights="50px" perrow="4">
Image:SlicerLicenseIcon.png‎| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess) Use with care Might not work all the time Might not be available for all platforms
Image:StableExtensionIcon.png|Stable Full documentation Works as advertised Compiles on all supported platforms Email support works
</gallery>

Documentation/4.0/Modules/ForegroundMasking

2011-11-21T15:18:32Z

Mscully: Initial template

Modules:LesionSegmentationApplications-Documentation-3.6

2011-11-10T19:24:39Z

Mscully: /* Authors, Collaborators & Contact */ Updated email addr.

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

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

__NOTOC__
===Lupus Lesion Segmentation Applications===

{|
|[[File:LesionFlowChart.jpg|thumb|200px|Lesion Segmentation Method Overview]]
|[[File:LesionsWithVentricles.png|thumb|200px|Segmented Lesion Volume in Brain]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author1: Mark Scully, The University of Iowa
* Author2: H. J. Bockholt, The Mind Research Network
* Contributor1:
* Contact: Mark Scully, mark-scully[at]uiowa[dot]edu

===Module Description===
The lupus lesion segmentation applications are a group of tools for segmenting lesions in lupus patients using the T1-weighted, T2-weighted, and FLAIR images. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

Please see the [http://wiki.na-mic.org/Wiki/index.php/DBP2:MIND:Roadmap DBP description] for more information.

== Usage ==

===Use Cases, Examples===

This module is specifically for segmenting lesions in lupus patients.
===Tutorials===

* Tutorials:
** [[Media:Slicer3Training_WhiteMatterLesions_v2.3.pdf‏| Lesion Segmentation Tutorial PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/860/LesionSegmentationTutorialData.tgz Download Example dataset]

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

{|
|
* '''Input:''' set input images representing the different modalities of the same subject
** Input T1 Volume: set input T1-weighted image, if available
** Input T2 Volume: set input T2-weighted image, if available
** Input FLAIR Volume: set input FLAIR image, if available
** Input Brain Mask Volume: set input Brain Mask image, if available
** Lesion segmentation Model File: set to the model file available with the tutorial

* '''Output:''' set output image
** Output Lesion Mask Volume: The volume that is the result of the segmentation process

|[[File:Predict_lesion_view.jpg|thumb|280px|User Interface]]
|}

== Development ==

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

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

===Dependencies===

* Slicer3 modules:
**

===Tests===

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

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

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

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

===Source code & documentation===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** cvs -d :pserver:anonymous@www.nitrc.org:/cvsroot/lupuslesion login
** cvs -d :pserver:anonymous@www.nitrc.org:/cvsroot/lupuslesion checkout lupuslesion

== More Information ==

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

===References===
Scully M, Anderson B, Lane T, Gasparovic C, Magnotta V, Sibbitt W, Roldan C, Kikinis R and Bockholt HJ (2010) An automated method for segmenting white matter lesions through multi-level morphometric feature classification with application to lupus. Front. Hum. Neurosci. doi:10.3389/fnhum.2010.00027
http://frontiersin.org/neuroscience/humanneuroscience/paper/10.3389/fnhum.2010.00027/

Slicer3:3.6 Final Issues

2011-02-14T21:43:48Z

Mscully: /* TODO: Issues to fix for the 3.6.3 patch release */ Moved BRAINS test fixes to DONE

'''Notes:
* Include the [http://www.na-mic.org/Bug/ mantis] bug number in your svn commit messages
* Test your fixes in the slicer3 trunk - when you are sure they work, (1) move them to the Slicer-3-6 branch (2) move them from the TODO to the DONE category on this page
* The Slicer3 repository is in maintenance mode - please do not add new features. New modules should be added only as [http://www.slicer.org/slicerWiki/index.php/Slicer3:Extensions extensions].
'''

==TODO: Issues to fix for the 3.6.4 patch release==

* Integrate SPECTRE plugin as an extension once MIPAV is open sourced (Nicole)
* Resample widget does not work properly in linked mode. In that situation, the slices should maintain the relative positions as the widget reorients them. (Steve, Jim, Michal)
* Adjust the appearance of slices in 3D view [http://www.na-mic.org/Bug/view.php?id=1061 1061] Steve)
* Interface settings in Application settings are not saved http://na-mic.org/Mantis/view.php?id=1076 (Steve?)
* http://na-mic.org/Mantis/view.php?id=1028 Request to compute checksum or md5sum and save as part of any storable node has registered as a feature request in Mantis. Plan right now is to create a method on MRMLScene->DataIOManager that will check for any data transfer with a status vtkDataTransfer::Failed. This status is set inside Base/Logic/vtkDataIOManagerLogic before data is loaded into slicer. Debugging this now... (Wendy)
* Move vtkEMSegmentLogic::AddDataIOFromScene to base code and replace in Slicer3.cxx corresponding code with function call
** commandlines currently cannot execute links to files with http address (Wendy, Dominique)
* Generate Robust MRI brain registration for EMSegmenter (Kilian, Dominik)

==TODO: Issues to fix for the 3.6.3 patch release==
''Fixes for these issues should be checked in to the Slicer-3-6 release branch by 3pm Eastern time on Monday, Feb 14, 2011''

* BRAINSResample is not available as a shared library (C++ symbol name in .so) [http://www.na-mic.org/Bug/view.php?id=941 941] (Jim)
* CompareView slice spacing issue [http://na-mic.org/Mantis/view.php?id=936 936] (Jim)
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995] (Jim)
* Compareviewer and crosshairs in Navigator mode: 4 compare viewers in wide screen mode (e.g. use [http://www.na-mic.org/Wiki/index.php/File:RSNA2010_fMRICase040Dataset.zip case 40] for data). text is not suppressed, display is slow. (Jim)
* Migrate latest version of GrowCut into release branch (Harini and Jim)

* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.3 (Steve)
* Create distribution binaries and extensions (Steve)

=== DONE: Issues fixed for inclusion in Slicer 3.6.3 ===
* Migrate BRAINS test fixes to the Slicer-3-6 release branch (Hans, Mark)
* File extension saving issues [http://na-mic.org/Mantis/view.php?id=1056 1056] [http://na-mic.org/Mantis/view.php?id=1064 1064] (Alex)
* Warning and block when file type is changed using filename field in the Save dialog [http://www.na-mic.org/Bug/view.php?id=1064 1064] (Alex)
* Display a warning message during installation on Windows if VC redistributable package is not installed (fix committed to the trunk by partyd on October 29, 2010)
* Model Hierarchy issues [http://www.na-mic.org/Bug/view.php?id=961 961] (Alex)
* Warning on unsaved data on scene close and exit (Alex)
* Status of fade slider is not captured by scenesnapshot (Alexy).
* Models Display UI cleanup (Alex)
* models under transforms do not move after save/load scene [http://www.na-mic.org/Bug/view.php?id=1058 1058] (Alex)
* multiple fiber tubes rendering performance (Alex)
* Slicer crash related to fiducials/MRML [http://www.na-mic.org/Bug/view.php?id=1042 1042] (Alex)
* Fixes to Camera/View handling (Alex & Wendy)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [[http://na-mic.org/Mantis/view.php?id=1036 1036], etc. (Alex)
* Modify ProstateNav so that it does not get recompiled all the time. Fixed in rev [http://viewvc.slicer.org/viewcvs.cgi?rev=15446&sortby=rev&sortdir=down&view=rev 15446], now only one file is recompiled. (Andras)
* Fixed BSplineDeformableRegistration (Fast non-rigid registration) CLI module to work correctly with rotated images (with direction cosines different from identity matrix) (Andras)
* Fix for vtkITKBSpline transform save with scene snapshot [http://www.na-mic.org/Bug/view.php?id=1050] (Steve)
* Fix for passing parameters to command line modules from Luca
* Fix to CropVolume module to correctly propagate the name for the output volume (Andrey)
* FastMarching crashes when applied two two different volumes one after another [http://www.na-mic.org/Bug/view.php?id=1057 1057] (Andrey)
* ChangeTracker deformable metric did not work because demons binary was not properly installed (Andrey)
* Setup node selector in LabelStatistics to allow label maps only (Andrey)
* CropVolume would not work anymore after scene is closed (Andrey)
* While in the volume rendering module, the render speed is slow while looking at a composited cross section. [http://www.na-mic.org/Bug/view.php?id=1052 1052]
* http://na-mic.org/Mantis/view.php?id=983 (fixed)
* Migrate DicomToNrrd fixes to the Slicer-3-6 release branch (Xiaodong)
* Migrate MRML Node test fixes to the Slicer-3-6 release branch (Nicole)
* Fix cygwin compile issue http://www.na-mic.org/Bug/view.php?id=1078 (Andras)
* Model Maker naming bug [http://www.na-mic.org/Bug/view.php?id=1043 1043] (Nicole)
* Loading *.mask files via 'Add Data' doesn't work [http://na-mic.org/Mantis/view.php?id=1067 1067] (Vince, Hans, Dominique)
* Expose step size parameter for Endoscopy (Steve)
* Label Grid should be off by default and should not come on automatically (Steve)
* Slice volume selectors are reset after executing CLI http://na-mic.org/Mantis/view.php?id=1077 (Steve)
* 4D Image: origin is not consistent with "Add volume" loaded data [http://www.na-mic.org/Bug/view.php?id=1000 1000] (Steve, Andrey, Junichi, Isaiah)
* Switch to tclkit for running genlib to work around [http://viewvc.slicer.org/viewcvs.cgi?rev=15824&view=rev cygwin tclsh PATH] issue (Steve and Andras)
* fix 3 view layout with endoscopy, external, and volume rendering view in distinct viewers to support Jay's programmaticly defined use-case (Steve) (not all functionality will be exposed in the GUI).
** switching layouts loses observers on scene
** no way to filter display of models or volume rendering in different viewers
* Migrate fixes for oblique volume editing and threshold paint optimization after testing in trunk (Steve, Andrey)
* Integrate Endoscopic layout. (Wendy)
* Move Cache and DataIO manager setup out of Slicer3.cxx and into SlicerApplicationLogic (not MRML). Not done for 3.6.3 but workaround is being used. (Wendy) [http://na-mic.org/Mantis/view.php?id=1033 1033]
* Debug leaks in FetchMI http://na-mic.org/Mantis/view.php?id=1029
* Error messages in FetchMI: http://na-mic.org/Mantis/view.php?id=1027 (related to 1028)
* Model maker pad fix http://na-mic.org/Mantis/view.php?id=813 (Nicole)
* Remove bugs and simplify user interface of Extension manager: (Steve) - committed to trunk for testing
** uninstall does not work
** "Download /install" and "Uninstall" button should be removed and be executed via next button to keep philosophy of workflow wizard
* Fix for level tracing http://na-mic.org/Mantis/view.php?id=1084
* Extensions (Steve / Daniel)
** Download problems http://na-mic.org/Mantis/view.php?id=1080
* Migrate latest version of GrowCut into release branch (Harini)
* Include Atlas Creator (Kilian, Daniel)
* Migrate EMSegment test fixes to the Slicer-3-6 release branch (Dominique, Kilian, Daniel)
* Data loading and FetchMI (Wendy -- fixes have been checked into trunk, and propagated to branch.)
* Slice view toggles [http://www.na-mic.org/Bug/view.php?id=1003 1003] (Nicole)

==TODO: Issues to fix for the 3.6.2 patch release Oct 22/10==

=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===
* Merge "reference" volume attribute feature into CommandLineModule (Andrey)
* 3D Viewer does not update when slice model is visible and dragging the Fg/Bg slider [http://www.na-mic.org/Bug/view.php?id=1019 1019] (Alex)
* N4 module bug in histogram sharpening parameter passing (Andrey)
* Updated versions of BRAINS tools (Hans)
* Detection of some BRAINS modules (e.g. BRAINSResample) (Steve)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [http://na-mic.org/Mantis/view.php?id=1032 1032]
* Import does not correctly update reference [http://www.na-mic.org/Bug/view.php?id=1010 1010] (Alex)
* Changing names of volume nodes is not propagated to GUI [http://www.na-mic.org/Bug/view.php?id=1012 1012] (Steve)
* Editor tweaks:
** add search to the color selector box - color list dynamically filtered when typing in search box
** pick a new default size for the color selector box (or perhaps have it remember the last size/location picked by the user) - color box remembers size selected by user
** give the color box a 'recently used' section - most recently used colors are now added at top of list for easy access
** rename 'check points' to 'undo/redo'
** implement compression (to vtk stencils) for label maps in the undo/redo stack (update: vtk stencils only represent a single value so they won't work for a multi-value labelmap - looking for alternatives). Done: implemented using new vtkImageStash class that uses ZLib to compress scalar image data. Also allows for compression in background thread so it does not get in the way of interactive use.
* Failed memory allocation dialog box (Steve) - in slicer3 trunk
* 3D Viewer disappears [http://www.na-mic.org/Bug/view.php?id=1004 1004] (Alex)
* in the editor module compress saved label maps into stencils (Steve)
* Side-by-side and Widescreen compare view linking problems appear fixed.
* Ron requests default for crosshair to be navigator OFF
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Works for nrrd, not dicom. Release note added.)
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=993 (was listed as 998, but refers to duplicate bug 993] which appears to be fixed now.
* FetchMI problems mentioned here [http://www.na-mic.org/Bug/view.php?id=998 998] and here [http://na-mic.org/Mantis/view.php?id=955 955] are due to (1) no or loss of network connection or (2) a full cache. (Wendy) added tests for network and server availability in fetchmi and for a full cache before attempting to transact with services.
* FetchMI segfaults when uploading mrml file [http://www.na-mic.org/Bug/view.php?id=1011 1011] (Wendy: this problem is due to having no cache space. Clear the cache and make sure your filesystem has enough free space to play with, then the upload works.)
* CompareView issue [http://na-mic.org/Mantis/view.php?id=929 929] (Jim)
* Display tab in the volumes module should be open by default [http://www.na-mic.org/Bug/view.php?id=1001 1001]
* in the editor module replace the words "Check Points" with the word "Undo" (Steve)
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing):
**add thumbnails to show effect of the transfer functions,
**remove unneeded ones, correct a typo.
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions.
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)
* Diffusion Tensor Glyphs not showing (Demian)
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)
* volume rendering: sampling rate and a few other tweaks (Yanling)
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)
* [https://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:GPURayCaster#Open_Issues VTK GPU Ray Cast issues] (Julien)
** Flickering has not been improved since 3.6.1.
** Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.
* Change names of the grow cut gesture volume nodes to be consistent with the naming conventions of label map (Harini)
* Grow Cut: Change the gesture volume node to be displayed on the foreground and the segmented label volume node to be displayed on the label layer of the slice views (Harini)
* Grow Cut: Modify the opacities of the label layer and the foreground layer to overlay the user input gestures, the resulting segmentation on the image background (Harini)
* Grow Cut: Modify user interface for setting inputs to the Grow Cut algorithm (Harini)
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.2 (Steve)
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)
* Resolve EMSegmenter related bug in connection with BRAINSFit [http://na-mic.org/Mantis/view.php?id=1025 1025] (Dominique)
* Resolved GetReferenceSubScene bugs: [http://na-mic.org/Mantis/view.php?id=1023 1023], [http://na-mic.org/Mantis/view.php?id=1031 1031], [http://na-mic.org/Mantis/view.php?id=1031 1034], [http://na-mic.org/Mantis/view.php?id=1035 1035]
* Create extensions for all versions of Slicer for the release (Steve)

==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==

* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex).
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.
* "Change island" effect of Editor is not functioning when the Scope is set to "all"
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]
* EMSegment command line works now with BRAINS (Kilian)
* Removed KWWidgets that do not work under Windows (Kilian)
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)

==3.6 Release issues==
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:

'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]'''

*VTK GPU ray-cast clipping issue
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]
**90% of the flickering when the camera is inside the volume is removed
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

Done:
* Remove unused color and glyph options from fiber bundle display (Alex)
* fiducial behavior
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
** done for 2d, Andras has tested it and says it's fine
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
*getting BRAINS tests to pass (Hans is working on it)
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now!
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
**for Output DTI volume: DTI Volume
**for Output Baseline Volume: Baseline DTI Volume
**for Otsu Threshold Mask: Otsu Threshold Label Volume
*new default color table (Nicole and Mike)
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7
** Steve and Nicole to meet June 9 to integrate default editor color table
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)

Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].

Modules:BRAINSFit

2010-12-29T22:30:27Z

Mscully:

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

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

__NOTOC__
===Module Name===
BRAINSFit

{|
| [[Image:Before.png|thumb|280px|Before registration]]
|-
| [[Image:After.png|thumb|280px|AfterRegistration]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===

Author: Hans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu

Contributors: Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3); Andriy Fedorov(5), fedorov -at- bwh.harvard.edu (Slicer integration); (1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard)

===Module Description===

{| style="color:green" border="1"
|Program title || BRAINSFit
|-
|Program description || Uses the Mattes Mutual Registration algorithm to register a three-dimensional volume to a reference volume. Described in BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007. http://hdl.handle.net/1926/1291
|-
|Program version || 3.0.0
|-
|Program documentation-url || http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit
|-

|}

Insight/Examples/Registration/ImageRegistration8.cxx
This program is the most functional example of multi-modal 3D rigid image registration provided with ITK. ImageRegistration8 is in the Examples directory, and also sec. 8.5.3 in the ITK manual. We have modified and extended this example in several ways:

*defined a new ITK Transform class, based on itkScaleSkewVersor3DTransform which has 3 dimensions of scale but no skew aspect.
*implemented a set of functions to convert between Versor Transforms and the general itk::AffineTransform and deferred converting from specific to more general representations to preserve transform information specificity as long as possible. Our Rigid transform is the narrowest, a Versor rotation plus separate translation.
*Added a template class itkMultiModal3DMutualRegistrationHelper which is templated over the type of ITK transform generated, and the optimizer used.
*Added image masks as an optional input to the Registration algorithm, limiting the volume considered during registration to voxels within the brain.
*Added image mask generation as an optional input to the Registration algorithm when meaningful masks such as for whole brain are not available, allowing the fit to at least be focused on whole head tissue.
*Added the ability to use one transform result, such as the Rigid transform, to initialize a more adaptive transform
*Defined the command line parameters using tools from the Slicer [ 3] program, in order to conform to the Slicer3 Execution model.
Added the ability to write output images in any ITK-supported scalar image format.
*Extensive testing as part of the BRAINS2 application suite, determined reasonable defaults for registration algorithm parameters. http://testing.psychiatry.uiowa.edu/CDash/

== Usage ==
The BRAINSFit distribution contains a directory named TestData, which contains two example images. The first, test.nii.gz is a NIfTI format image volume, which is used the input for the CTest-managed regression test program. The program makexfrmedImage.cxx, included in the BRAINSFit distribution was used to generate test2.nii.gz, by scaling, rotating and translating test.nii.gz. You can see representative Sagittal slices of test.nii.gz (in this case, the fixed image, test2.nii.gz (the moving image), and the two images ’checkerboarded’ together to the right. To register test2.nii.gz to test.nii.gz, you can use the following command:

BRAINSFit --fixedVolume test.nii.gz \
--movingVolume test2.nii.gz \
--outputVolume registered.nii.gz \
--transformType Affine
A representative slice of the registered results image registered.nii.gz is to the right. You can see from the Checkerboard of the Fixed and Registered images that the fit is quite good with Affine transform-based registration. The blurring of the registered images is a consequence of the initial scaling used in generating the moving image from the fixed image, compounded by the interpolation necessitated by the transform operation.

You can see the differences in results if you re-run BRAINSFit using Rigid, ScaleVersor3D, or ScaleSkewVersor3D as the ----transformType parameter. In this case, the authors judged Affine the best method for registering these particular two images; in the BRAINS2 automated processing pipeline, Rigid usually works well for registering research scans.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* '''''Use Case 1: Same Subject: Longitudinal'''''

For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later. The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT1Longitudinal.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
</pre>
Since these are the same subject and very little has likely changed in the last year we'll use a Rigid registration. If the registration is poor or there are reasons to expect anatomical changes then additional transforms may be needed, in which case they can be added in a comma separated list, such as "Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline".
<pre>
--transformType Rigid \
</pre>
The scans are the same modality so we'll use --histogramMatch to match the intensity profiles as this tends to help registration. If there are lesions or tumors that vary between images this may not be a good idea, as it will make it harder to detect differences between the images.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHead, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHead \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
--transformType Rigid \
--histogramMatch \
--initializeTransformMode useCenterOfHead \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:LongitudinalCheckerboardPreReg.png|thumb|180px|Longitudinal Checkerboard Before registration]]
| [[Image:LogitudinalCheckerboardPostReg.png|thumb|180px|Longitudinal Checkerboard After registration]]
|}

* '''''Use Case 2: Same Subject: MultiModal'''''

For this use case we're registering a T1 scan with a T2 scan collected in the same sesson. The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT2.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
</pre>
Since these are the same subject, same session we'll use a Rigid registration.
<pre>
--transformType Rigid \
</pre>
The scans are different modalities so we absolutely DO NOT want to use --histogramMatch to match the intensity profiles as this would try to map the T2 intensities into T1 intensities, resulting in an image that was neither, and hence useless.

To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHead, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHead \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
--transformType Rigid \
--initializeTransformMode useCenterOfHead \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:T1T2PreRegCheckerboard.png|thumb|180px|Multimodal Checkerboard Before registration]]
| [[Image:T1T2RegCheckerboard.png|thumb|180px|Multimodal Checkerboard After registration]]
|}

* '''''Use Case 3: Mouse Registration'''''

Here we'll register brains from two different mice together. The fixed and moving mouse brains used in this example are available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory.

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
</pre>
Since the subjects are different we are going to use transforms all the way through BSpline. Again, building up transforms one type at a time can't hurt and might help, so we're including all transforms from Rigid through BSpline in the transformType parameter.
<pre>
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
</pre>
The scans are the same modality so we'll use --histogramMatch.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHead. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
<pre>
--initializeTransformMode useMomentsAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
Since the mouse brains are much smaller than human brains there are a few advanced parameters we'll need to tweak, ROIAutoClosingSize and ROIAutoDilateSize (both under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value for mice is 0.9.
<pre>
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
--histogramMatch \
--initializeTransformMode useMomentsAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
--interpolationMode Linear
</pre>

{|
| [[Image:MouseCheckerboardPreRegistration.png|thumb|180px|Mouse Checkerboard Before registration]]
| [[Image:MouseCheckerboardPostRegistration.png|thumb|180px|Mouse Checkerboard After registration]]
|}



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

This section was partially generated with a [http://svn.slicer.org/Slicer4/trunk/Scripts/SEMToMediaWiki.py python script to convert Slicer Execution Model xml files into MediaWiki compatible documentation]

{|
|
* '''''Input Parameters''''':
** '''Fixed Image Volume''' [--fixedVolume] : The fixed image for registration by mutual information optimization.
** '''Moving Image Volume''' [--movingVolume] : The moving image for registration by mutual information optimization.

* '''''Registration phases to use''''': Parameters that define which registration steps to use.
** '''Initialize with previously generated transform''' [--initialTransform] : Filename of transform used to initialize the registration. This CAN NOT be used with either CenterOfHeadLAlign, MomentsAlign, GeometryAlign, or initialTransform file.
** '''Intitialze Transform Mode''' [--initializeTransformMode] : Determine how to initialize the transform center. GeometryAlign on assumes that the center of the voxel lattice of the images represent similar structures. MomentsAlign assumes that the center of mass of the images represent similar structures. useCenterOfHeadAlign attempts to use the top of head and shape of neck to drive a center of mass estimate. Off assumes that the physical space of the images are close, and that centering in terms of the image Origins is a good starting point. This flag is mutually exclusive with the initialTransform flag. ''Default value: Off''
** '''Include Rigid registration phase''' [--useRigid] : Perform a rigid registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include ScaleVersor3D registration phase''' [--useScaleVersor3D] : Perform a ScaleVersor3D registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include ScaleSkewVersor3D registration phase''' [--useScaleSkewVersor3D] : Perform a ScaleSkewVersor3D registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include Affine registration phase''' [--useAffine] : Perform an Affine registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include BSpline registration phase''' [--useBSpline] : Perform a BSpline registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
* '''''Output Settings (At least one output must be specified.)''''':
** '''Slicer BSpline Transform''' [--bsplineTransform] : (optional) Filename to which save the estimated transform. NOTE: You must set at least one output object (either a deformed image or a transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS BSpline
** '''Slicer Linear Transform''' [--linearTransform] : (optional) Filename to which save the estimated transform. NOTE: You must set at least one output object (either a deformed image or a transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS ---NOT--- BSpline
** '''Output Transform''' [--outputTransform] : (optional) Filename to which save the (optional) estimated transform. NOTE: You must select either the outputTransform or the outputVolume option.
** '''Output Image Volume''' [--outputVolume] : (optional) Output image for registration. NOTE: You must select either the outputTransform or the outputVolume option.
** '''Output Image Pixel Type''' [--outputVolumePixelType] : The output image Pixel Type is the scalar datatype for representation of the Output Volume. ''Default value: float''
* '''''Registration Parameters''''':
** '''Transform Type''' [--transformType] : Specifies a list of registration types to be used. The valid types are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline. Specifiying more than one in a comma separated list will initialize the next stage with the previous results. If registrationClass flag is used, it overrides this parameter setting.
** '''Number Of Iterations''' [--numberOfIterations] : The maximum number of iterations to try before failing to converge. Use an explicit limit like 500 or 1000 to manage risk of divergence ''Default value: 1500''
** '''Number Of Samples''' [--numberOfSamples] : The number of voxels sampled for mutual information computation. Increase this for a slower, more careful fit. You can also limit the sampling focus with ROI masks and ROIAUTO mask generation. ''Default value: 100000''
** '''Minimum Step Length''' [--minimumStepLength] : Each step in the optimization takes steps at least this big. When none are possible, registration is complete. ''Default value: 0.005''
** '''Transform Scale''' [--translationScale] : How much to scale up changes in position compared to unit rotational changes in radians -- decrease this to put more rotation in the search pattern. ''Default value: 1000.0''
** '''Reproportion Scale''' [--reproportionScale] : ScaleVersor3D 'Scale' compensation factor. Increase this to put more rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern. 1.0 works well with a translationScale of 1000.0 ''Default value: 1.0''
** '''Skew Scale''' [--skewScale] : ScaleSkewVersor3D Skew compensation factor. Increase this to put more skew in a ScaleSkewVersor3D search pattern. 1.0 works well with a translationScale of 1000.0 ''Default value: 1.0''
** '''Number Of Grid Subdivisions''' [--splineGridSize] : The number of subdivisions of the BSpline Grid to be centered on the image space. Each dimension must have at least 3 subdivisions for the BSpline to be correctly computed. ''Default value: 14,10,12''
** '''Maximum B-Spline Displacement''' [--maxBSplineDisplacement] : Sets the maximum allowed displacements in image physical coordinates for BSpline control grid along each axis. A value of 0.0 indicates that the problem should be unbounded. NOTE: This only constrains the BSpline portion, and does not limit the displacement from the associated bulk transform. This can lead to a substantial reduction in computation time in the BSpline optimizer. ''Default value: 0.0''
* '''''Advanced Output Settings''''':
** '''Stripped Output Transform''' [--strippedOutputTransform] : File name for the rigid component of the estimated affine transform. Can be used to rigidly register the moving image to the fixed image. NOTE: This value is overwritten if either bsplineTransform or linearTransform is set.
** '''Background Fill Value''' [--backgroundFillValue] : Background fill value for output image. ''Default value: 0.0''
** '''Inferior Cut Off From Center''' [--maskInferiorCutOffFromCenter] : For use with --useCenterOfHeadAlign (and --maskProcessingMode ROIAUTO): the cut-off below the image centers, in millimeters, ''Default value: 1000.0''
** '''Scale Output Values''' [--scaleOutputValues] : If true, and the voxel values do not fit within the minimum and maximum values of the desired outputVolumePixelType, then linearly scale the min/max output image voxel values to fit within the min/max range of the outputVolumePixelType. ''Default value: false''
** '''Interpolation Mode''' [--interpolationMode] : Type of interpolation to be used when applying transform to moving volume. Options are Linear, NearestNeighbor, BSpline, WindowedSinc, or RigidInPlace. The RigidInPlace option will create an image with the same discrete voxel values and will adjust the origin and direction of the physical space interpretation. ''Default value: Linear''
* '''''Control of Mask Processing''''':
** '''Mask Processing Mode''' [--maskProcessingMode] : What mode to use for using the masks. If ROIAUTO is choosen, then the mask is implicitly defined using a otsu forground and hole filling algorithm. The Region Of Interest mode (choose ROI) uses the masks to define what parts of the image should be used for computing the transform. ''Default value: NOMASK''
** '''Output Fixed Mask (ROIAUTO only)''' [--outputFixedVolumeROI] : The ROI automatically found in fixed image.
** '''Output Moving Mask (ROIAUTO only)''' [--outputMovingVolumeROI] : The ROI automatically found in moving image.
** '''Input Fixed Mask (ROI only)''' [--fixedBinaryVolume] : Fixed Image binary mask volume.
** '''Input Moving Mask (ROI only)''' [--movingBinaryVolume] : Moving Image binary mask volume.

* '''''Special Input Image Parameters''''':
** '''Fixed Image Time Index''' [--fixedVolumeTimeIndex] : The index in the time series for the 3D fixed image to fit, if 4-dimensional. ''Default value: 0''
** '''Moving Image Time Index''' [--movingVolumeTimeIndex] : The index in the time series for the 3D moving image to fit, if 4-dimensional. ''Default value: 0''
** '''Median Filter Size''' [--medianFilterSize] : The radius for the optional MedianImageFilter preprocessing in all 3 directions. ''Default value: 0,0,0''
** '''Histogram Match''' [--histogramMatch] [-e]: Histogram Match the input images. This is suitable for images of the same modality that may have different absolute scales, but the same overall intensity profile. Do NOT use if registering images from different modailties. ''Default value: false''
** '''Number of Histogram Bins''' [--numberOfHistogramBins] : The number of histogram levels ''Default value: 50''
** '''Number of Match Points''' [--numberOfMatchPoints] : the number of match points ''Default value: 10''
* '''''Registration Debugging Parameters''''':
** '''Caching BSpline Weights Mode''' [--useCachingOfBSplineWeightsMode] : This is a 5x speed advantage at the expense of requiring much more memory. Only relevant when transformType is BSpline. ''Default value: ON''
** '''Explicit PDF Derivatives Mode''' [--useExplicitPDFDerivativesMode] : Using mode AUTO means OFF for BSplineDeformableTransforms and ON for the linear transforms. The ON alternative uses more memory to sometimes do a better job. ''Default value: AUTO''
** ''' ROIAuto Dilate Size''' [--ROIAutoDilateSize] : This flag is only relavent when using ROIAUTO mode for initializing masks. It defines the final dilation size to capture a bit of background outside the tissue region. At setting of 10mm has been shown to help regularize a BSpline registration type so that there is some background constraints to match the edges of the head better. ''Default value: 0.0''
** ''' ROIAuto Closing Size''' [--ROIAutoClosingSize] : This flag is only relavent when using ROIAUTO mode for initializing masks. It defines the hole closing size in mm. It is rounded up to the nearest whole pixel size in each direction. The default is to use a closing size of 9mm. For mouse data this value may need to be reset to 0.9 or smaller. ''Default value: 9.0''
** '''Relaxation Factor''' [--relaxationFactor] : Internal debugging parameter, and should probably never be used from the command line. This will be removed in the future. ''Default value: 0.5''
** '''Maximum Step Length''' [--maximumStepLength] : Internal debugging parameter, and should probably never be used from the command line. This will be removed in the future. ''Default value: 0.2''
** '''Failure Exit Code''' [--failureExitCode] : If the fit fails, exit with this status code. (It can be used to force a successfult exit status of (0) if the registration fails due to reaching the maximum number of iterations. ''Default value: -1''
** '''Write Transform On Failure''' [--writeTransformOnFailure] : Flag to save the final transform even if the numberOfIterations are reached without convergence. (Intended for use when --failureExitCode 0 ) ''Default value: 0''
** '''debugNumberOfThreads''' [--debugNumberOfThreads] : Explicitly specify the maximum number of threads to use. ''Default value: -1''
** '''Debug option''' [--debugLevel] : Display debug messages, and produce debug intermediate results. 0=OFF, 1=Minimal, 10=Maximum debugging. ''Default value: 0''
* '''''Risky Expert-only Parameters''''':
** '''DO NOT USE''' [--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00] : DO NOT USE THIS FLAG ''Default value: false''
** '''DO NOT USE''' [--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01] : DO NOT USE THIS FLAG ''Default value: false''
** '''DO NOT USE''' [--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02] : DO NOT USE THIS FLAG ''Default value: false''
** '''Selective Permission for Transform Parameters to Vary''' [--permitParameterVariation] : A bit vector to permit linear transform parameters to vary under optimization. The vector order corresponds with transform parameters, and beyond the end ones fill in as a default. For instance, you can choose to rotate only in x (pitch) with 1,0,0; this is mostly for expert use in turning on and off individual degrees of freedom in rotation, translation or scaling without multiplying the number of transform representations; this trick is probably meaningless when tried with the general affine transform.=
** '''Cost Metric''' [--costMetric] : The cost metric to be used during fitting. Defaults to MMI. Options are MMI (Mattes Mutual Information), MSE (Mean Square Error), NC (Normalized Correlation), MC (Match Cardinality for binary images) ''Default value: MMI''

||[[Image:BRAINSFitUI_part1.png|thumb|280px|User Interface]] [[Image:BRAINSFitUI_part2.png|thumb|280px|User Interface]]
|}

== Development ==

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

This is a thin wrapper program around the BRAINSFitHelper class in BRAINSCommonLib. The BRAINSFitHelper class
is intended to allow all the functionality of BRAINSFit to be easily incorporated into another program by including a single header file, linking against the BRAINSCommonLib library, and adding code similar to the following to your application:
<pre>

typedef itk::BRAINSFitHelper HelperType;
HelperType::Pointer myHelper=HelperType::New();
myHelper->SetTransformType(localTransformType);
myHelper->SetFixedVolume(extractFixedVolume);
myHelper->SetMovingVolume(extractMovingVolume);
myHelper->StartRegistration();
currentGenericTransform=myHelper->GetCurrentGenericTransform();
MovingVolumeType::ConstPointer preprocessedMovingVolume = myHelper->GetPreprocessedMovingVolume();

/* Optional member functions that can also be set */
myHelper->SetHistogramMatch(histogramMatch);
myHelper->SetNumberOfMatchPoints(numberOfMatchPoints);
myHelper->SetFixedBinaryVolume(fixedMask);
myHelper->SetMovingBinaryVolume(movingMask);
myHelper->SetPermitParameterVariation(permitParameterVariation);
myHelper->SetNumberOfSamples(numberOfSamples);
myHelper->SetNumberOfHistogramBins(numberOfHistogramBins);
myHelper->SetNumberOfIterations(numberOfIterations);
myHelper->SetMaximumStepLength(maximumStepSize);
myHelper->SetMinimumStepLength(minimumStepSize);
myHelper->SetRelaxationFactor(relaxationFactor);
myHelper->SetTranslationScale(translationScale);
myHelper->SetReproportionScale(reproportionScale);
myHelper->SetSkewScale(skewScale);
myHelper->SetUseExplicitPDFDerivativesMode(useExplicitPDFDerivativesMode);
myHelper->SetUseCachingOfBSplineWeightsMode(useCachingOfBSplineWeightsMode);
myHelper->SetBackgroundFillValue(backgroundFillValue);
myHelper->SetInitializeTransformMode(localInitializeTransformMode);
myHelper->SetMaskInferiorCutOffFromCenter(maskInferiorCutOffFromCenter);
myHelper->SetCurrentGenericTransform(currentGenericTransform);
myHelper->SetSplineGridSize(splineGridSize);
myHelper->SetCostFunctionConvergenceFactor(costFunctionConvergenceFactor);
myHelper->SetProjectedGradientTolerance(projectedGradientTolerance);
myHelper->SetMaxBSplineDisplacement(maxBSplineDisplacement);
myHelper->SetDisplayDeformedImage(UseDebugImageViewer);
myHelper->SetPromptUserAfterDisplay(PromptAfterImageSend);
myHelper->SetDebugLevel(debugLevel);
if(debugLevel > 7 )
{
myHelper->PrintCommandLine(true,"BF");
}

</pre>

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
BRAINSFit depends on the BRAINSCommonLib library

===Tests===

Nightly testing of the development head can be found at: http://testing.psychiatry.uiowa.edu/CDash

===Known bugs===

Links to known bugs and feature requests are listed at:
* http://www.nitrc.org/projects/multimodereg/

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://www.nitrc.org/projects/multimodereg/|Hosted by NITRC ]

== More Information ==

===Acknowledgment===

This research was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.

===References===
* [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.

Modules:BRAINSFit

2010-12-29T22:28:22Z

Mscully: /* Use Cases, Examples */

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

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

__NOTOC__
===Module Name===
BRAINSFit

{|
| [[Image:Before.png|thumb|280px|Before registration]]
|-
| [[Image:After.png|thumb|280px|AfterRegistration]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===

Author: Hans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu

Contributors: Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3); Andriy Fedorov(5), fedorov -at- bwh.harvard.edu (Slicer integration); (1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard)

===Module Description===

{| style="color:green" border="1"
|Program title || BRAINSFit
|-
|Program description || Uses the Mattes Mutual Registration algorithm to register a three-dimensional volume to a reference volume. Described in BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007. http://hdl.handle.net/1926/1291
|-
|Program version || 3.0.0
|-
|Program documentation-url || http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit
|-

|}

Insight/Examples/Registration/ImageRegistration8.cxx
This program is the most functional example of multi-modal 3D rigid image registration provided with ITK. ImageRegistration8 is in the Examples directory, and also sec. 8.5.3 in the ITK manual. We have modified and extended this example in several ways:

*defined a new ITK Transform class, based on itkScaleSkewVersor3DTransform which has 3 dimensions of scale but no skew aspect.
*implemented a set of functions to convert between Versor Transforms and the general itk::AffineTransform and deferred converting from specific to more general representations to preserve transform information specificity as long as possible. Our Rigid transform is the narrowest, a Versor rotation plus separate translation.
*Added a template class itkMultiModal3DMutualRegistrationHelper which is templated over the type of ITK transform generated, and the optimizer used.
*Added image masks as an optional input to the Registration algorithm, limiting the volume considered during registration to voxels within the brain.
*Added image mask generation as an optional input to the Registration algorithm when meaningful masks such as for whole brain are not available, allowing the fit to at least be focused on whole head tissue.
*Added the ability to use one transform result, such as the Rigid transform, to initialize a more adaptive transform
*Defined the command line parameters using tools from the Slicer [ 3] program, in order to conform to the Slicer3 Execution model.
Added the ability to write output images in any ITK-supported scalar image format.
*Extensive testing as part of the BRAINS2 application suite, determined reasonable defaults for registration algorithm parameters. http://testing.psychiatry.uiowa.edu/CDash/

== Usage ==
The BRAINSFit distribution contains a directory named TestData, which contains two example images. The first, test.nii.gz is a NIfTI format image volume, which is used the input for the CTest-managed regression test program. The program makexfrmedImage.cxx, included in the BRAINSFit distribution was used to generate test2.nii.gz, by scaling, rotating and translating test.nii.gz. You can see representative Sagittal slices of test.nii.gz (in this case, the fixed image, test2.nii.gz (the moving image), and the two images ’checkerboarded’ together to the right. To register test2.nii.gz to test.nii.gz, you can use the following command:

BRAINSFit --fixedVolume test.nii.gz \
--movingVolume test2.nii.gz \
--outputVolume registered.nii.gz \
--transformType Affine
A representative slice of the registered results image registered.nii.gz is to the right. You can see from the Checkerboard of the Fixed and Registered images that the fit is quite good with Affine transform-based registration. The blurring of the registered images is a consequence of the initial scaling used in generating the moving image from the fixed image, compounded by the interpolation necessitated by the transform operation.

You can see the differences in results if you re-run BRAINSFit using Rigid, ScaleVersor3D, or ScaleSkewVersor3D as the ----transformType parameter. In this case, the authors judged Affine the best method for registering these particular two images; in the BRAINS2 automated processing pipeline, Rigid usually works well for registering research scans.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: Same Subject: Longitudinal

For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later. The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT1Longitudinal.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
</pre>
Since these are the same subject and very little has likely changed in the last year we'll use a Rigid registration. If the registration is poor or there are reasons to expect anatomical changes then additional transforms may be needed, in which case they can be added in a comma separated list, such as "Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline".
<pre>
--transformType Rigid \
</pre>
The scans are the same modality so we'll use --histogramMatch to match the intensity profiles as this tends to help registration. If there are lesions or tumors that vary between images this may not be a good idea, as it will make it harder to detect differences between the images.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHead, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHead \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT1Longitudinal.nii.gz \
--outputVolume testT1LongRegFixed.nii.gz \
--outputTransform longToBase.xform \
--transformType Rigid \
--histogramMatch \
--initializeTransformMode useCenterOfHead \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:LongitudinalCheckerboardPreReg.png|thumb|180px|Longitudinal Checkerboard Before registration]]
| [[Image:LogitudinalCheckerboardPostReg.png|thumb|180px|Longitudinal Checkerboard After registration]]
|}

* Use Case 2: Same Subject: MultiModal

For this use case we're registering a T1 scan with a T2 scan collected in the same sesson. The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT2.nii.gz

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
</pre>
Since these are the same subject, same session we'll use a Rigid registration.
<pre>
--transformType Rigid \
</pre>
The scans are different modalities so we absolutely DO NOT want to use --histogramMatch to match the intensity profiles as this would try to map the T2 intensities into T1 intensities, resulting in an image that was neither, and hence useless.

To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHead, which detects the center of head even with varying amounts of neck or shoulders present.
<pre>
--initializeTransformMode useCenterOfHead \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
The registration generally performs better if we include some background in the mask that way the tissue boundary is very clear. The parameter that expands the mask outside the brain is ROIAutoDilateSize (under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value is 3.
<pre>
--ROIAutoDilateSize 3 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume testT1.nii.gz \
--movingVolume testT2.nii.gz \
--outputVolume testT2RegT1.nii.gz \
--outputTransform T2ToT1.xform \
--transformType Rigid \
--initializeTransformMode useCenterOfHead \
--maskProcessingMode ROIAUTO \
--ROIAutoDilateSize 3 \
--interpolationMode Linear
</pre>

{|
| [[Image:T1T2PreRegCheckerboard.png|thumb|180px|Multimodal Checkerboard Before registration]]
| [[Image:T1T2RegCheckerboard.png|thumb|180px|Multimodal Checkerboard After registration]]
|}

* Use Case 3: Mouse Registration

Here we'll register brains from two different mice together. The fixed and moving mouse brains used in this example are available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory.

First we set the fixed and moving volumes as well as the output transform and output volume names.
<pre>
--fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
</pre>
Since the subjects are different we are going to use transforms all the way through BSpline. Again, building up transforms one type at a time can't hurt and might help, so we're including all transforms from Rigid through BSpline in the transformType parameter.
<pre>
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
</pre>
The scans are the same modality so we'll use --histogramMatch.
<pre>
--histogramMatch \
</pre>
To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHead. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
<pre>
--initializeTransformMode useMomentsAlign \
</pre>
ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
<pre>
--maskProcessingMode ROIAUTO \
</pre>
Since the mouse brains are much smaller than human brains there are a few advanced parameters we'll need to tweak, ROIAutoClosingSize and ROIAutoDilateSize (both under Registration Debugging Parameters if using the GUI). These values are in millimeters so a good starting value for mice is 0.9.
<pre>
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
</pre>
Last we set the interpolation mode to be Linear, which is a decent tradeoff between quality and speed. If the best possible interpolation is needed regardless of processing time, select WindowedSync instead of linear.
<pre>
--interpolationMode Linear
</pre>

The full command is:
<pre>
BRAINSFit --fixedVolume mouseFixed.nii.gz \
--movingVolume mouseMoving.nii.gz \
--outputVolume movingRegFixed.nii.gz \
--outputTransform movingToFixed.xform \
--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline \
--histogramMatch \
--initializeTransformMode useMomentsAlign \
--maskProcessingMode ROIAUTO \
--ROIAutoClosingSize 0.9 \
--ROIAutoDilateSize 0.9 \
--interpolationMode Linear
</pre>

{|
| [[Image:MouseCheckerboardPreRegistration.png|thumb|180px|Mouse Checkerboard Before registration]]
| [[Image:MouseCheckerboardPostRegistration.png|thumb|180px|Mouse Checkerboard After registration]]
|}



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

This section was partially generated with a [http://svn.slicer.org/Slicer4/trunk/Scripts/SEMToMediaWiki.py python script to convert Slicer Execution Model xml files into MediaWiki compatible documentation]

{|
|
* '''''Input Parameters''''':
** '''Fixed Image Volume''' [--fixedVolume] : The fixed image for registration by mutual information optimization.
** '''Moving Image Volume''' [--movingVolume] : The moving image for registration by mutual information optimization.

* '''''Registration phases to use''''': Parameters that define which registration steps to use.
** '''Initialize with previously generated transform''' [--initialTransform] : Filename of transform used to initialize the registration. This CAN NOT be used with either CenterOfHeadLAlign, MomentsAlign, GeometryAlign, or initialTransform file.
** '''Intitialze Transform Mode''' [--initializeTransformMode] : Determine how to initialize the transform center. GeometryAlign on assumes that the center of the voxel lattice of the images represent similar structures. MomentsAlign assumes that the center of mass of the images represent similar structures. useCenterOfHeadAlign attempts to use the top of head and shape of neck to drive a center of mass estimate. Off assumes that the physical space of the images are close, and that centering in terms of the image Origins is a good starting point. This flag is mutually exclusive with the initialTransform flag. ''Default value: Off''
** '''Include Rigid registration phase''' [--useRigid] : Perform a rigid registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include ScaleVersor3D registration phase''' [--useScaleVersor3D] : Perform a ScaleVersor3D registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include ScaleSkewVersor3D registration phase''' [--useScaleSkewVersor3D] : Perform a ScaleSkewVersor3D registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include Affine registration phase''' [--useAffine] : Perform an Affine registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** '''Include BSpline registration phase''' [--useBSpline] : Perform a BSpline registration as part of the sequential registration steps. This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
* '''''Output Settings (At least one output must be specified.)''''':
** '''Slicer BSpline Transform''' [--bsplineTransform] : (optional) Filename to which save the estimated transform. NOTE: You must set at least one output object (either a deformed image or a transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS BSpline
** '''Slicer Linear Transform''' [--linearTransform] : (optional) Filename to which save the estimated transform. NOTE: You must set at least one output object (either a deformed image or a transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS ---NOT--- BSpline
** '''Output Transform''' [--outputTransform] : (optional) Filename to which save the (optional) estimated transform. NOTE: You must select either the outputTransform or the outputVolume option.
** '''Output Image Volume''' [--outputVolume] : (optional) Output image for registration. NOTE: You must select either the outputTransform or the outputVolume option.
** '''Output Image Pixel Type''' [--outputVolumePixelType] : The output image Pixel Type is the scalar datatype for representation of the Output Volume. ''Default value: float''
* '''''Registration Parameters''''':
** '''Transform Type''' [--transformType] : Specifies a list of registration types to be used. The valid types are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline. Specifiying more than one in a comma separated list will initialize the next stage with the previous results. If registrationClass flag is used, it overrides this parameter setting.
** '''Number Of Iterations''' [--numberOfIterations] : The maximum number of iterations to try before failing to converge. Use an explicit limit like 500 or 1000 to manage risk of divergence ''Default value: 1500''
** '''Number Of Samples''' [--numberOfSamples] : The number of voxels sampled for mutual information computation. Increase this for a slower, more careful fit. You can also limit the sampling focus with ROI masks and ROIAUTO mask generation. ''Default value: 100000''
** '''Minimum Step Length''' [--minimumStepLength] : Each step in the optimization takes steps at least this big. When none are possible, registration is complete. ''Default value: 0.005''
** '''Transform Scale''' [--translationScale] : How much to scale up changes in position compared to unit rotational changes in radians -- decrease this to put more rotation in the search pattern. ''Default value: 1000.0''
** '''Reproportion Scale''' [--reproportionScale] : ScaleVersor3D 'Scale' compensation factor. Increase this to put more rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern. 1.0 works well with a translationScale of 1000.0 ''Default value: 1.0''
** '''Skew Scale''' [--skewScale] : ScaleSkewVersor3D Skew compensation factor. Increase this to put more skew in a ScaleSkewVersor3D search pattern. 1.0 works well with a translationScale of 1000.0 ''Default value: 1.0''
** '''Number Of Grid Subdivisions''' [--splineGridSize] : The number of subdivisions of the BSpline Grid to be centered on the image space. Each dimension must have at least 3 subdivisions for the BSpline to be correctly computed. ''Default value: 14,10,12''
** '''Maximum B-Spline Displacement''' [--maxBSplineDisplacement] : Sets the maximum allowed displacements in image physical coordinates for BSpline control grid along each axis. A value of 0.0 indicates that the problem should be unbounded. NOTE: This only constrains the BSpline portion, and does not limit the displacement from the associated bulk transform. This can lead to a substantial reduction in computation time in the BSpline optimizer. ''Default value: 0.0''
* '''''Advanced Output Settings''''':
** '''Stripped Output Transform''' [--strippedOutputTransform] : File name for the rigid component of the estimated affine transform. Can be used to rigidly register the moving image to the fixed image. NOTE: This value is overwritten if either bsplineTransform or linearTransform is set.
** '''Background Fill Value''' [--backgroundFillValue] : Background fill value for output image. ''Default value: 0.0''
** '''Inferior Cut Off From Center''' [--maskInferiorCutOffFromCenter] : For use with --useCenterOfHeadAlign (and --maskProcessingMode ROIAUTO): the cut-off below the image centers, in millimeters, ''Default value: 1000.0''
** '''Scale Output Values''' [--scaleOutputValues] : If true, and the voxel values do not fit within the minimum and maximum values of the desired outputVolumePixelType, then linearly scale the min/max output image voxel values to fit within the min/max range of the outputVolumePixelType. ''Default value: false''
** '''Interpolation Mode''' [--interpolationMode] : Type of interpolation to be used when applying transform to moving volume. Options are Linear, NearestNeighbor, BSpline, WindowedSinc, or RigidInPlace. The RigidInPlace option will create an image with the same discrete voxel values and will adjust the origin and direction of the physical space interpretation. ''Default value: Linear''
* '''''Control of Mask Processing''''':
** '''Mask Processing Mode''' [--maskProcessingMode] : What mode to use for using the masks. If ROIAUTO is choosen, then the mask is implicitly defined using a otsu forground and hole filling algorithm. The Region Of Interest mode (choose ROI) uses the masks to define what parts of the image should be used for computing the transform. ''Default value: NOMASK''
** '''Output Fixed Mask (ROIAUTO only)''' [--outputFixedVolumeROI] : The ROI automatically found in fixed image.
** '''Output Moving Mask (ROIAUTO only)''' [--outputMovingVolumeROI] : The ROI automatically found in moving image.
** '''Input Fixed Mask (ROI only)''' [--fixedBinaryVolume] : Fixed Image binary mask volume.
** '''Input Moving Mask (ROI only)''' [--movingBinaryVolume] : Moving Image binary mask volume.

* '''''Special Input Image Parameters''''':
** '''Fixed Image Time Index''' [--fixedVolumeTimeIndex] : The index in the time series for the 3D fixed image to fit, if 4-dimensional. ''Default value: 0''
** '''Moving Image Time Index''' [--movingVolumeTimeIndex] : The index in the time series for the 3D moving image to fit, if 4-dimensional. ''Default value: 0''
** '''Median Filter Size''' [--medianFilterSize] : The radius for the optional MedianImageFilter preprocessing in all 3 directions. ''Default value: 0,0,0''
** '''Histogram Match''' [--histogramMatch] [-e]: Histogram Match the input images. This is suitable for images of the same modality that may have different absolute scales, but the same overall intensity profile. Do NOT use if registering images from different modailties. ''Default value: false''
** '''Number of Histogram Bins''' [--numberOfHistogramBins] : The number of histogram levels ''Default value: 50''
** '''Number of Match Points''' [--numberOfMatchPoints] : the number of match points ''Default value: 10''
* '''''Registration Debugging Parameters''''':
** '''Caching BSpline Weights Mode''' [--useCachingOfBSplineWeightsMode] : This is a 5x speed advantage at the expense of requiring much more memory. Only relevant when transformType is BSpline. ''Default value: ON''
** '''Explicit PDF Derivatives Mode''' [--useExplicitPDFDerivativesMode] : Using mode AUTO means OFF for BSplineDeformableTransforms and ON for the linear transforms. The ON alternative uses more memory to sometimes do a better job. ''Default value: AUTO''
** ''' ROIAuto Dilate Size''' [--ROIAutoDilateSize] : This flag is only relavent when using ROIAUTO mode for initializing masks. It defines the final dilation size to capture a bit of background outside the tissue region. At setting of 10mm has been shown to help regularize a BSpline registration type so that there is some background constraints to match the edges of the head better. ''Default value: 0.0''
** ''' ROIAuto Closing Size''' [--ROIAutoClosingSize] : This flag is only relavent when using ROIAUTO mode for initializing masks. It defines the hole closing size in mm. It is rounded up to the nearest whole pixel size in each direction. The default is to use a closing size of 9mm. For mouse data this value may need to be reset to 0.9 or smaller. ''Default value: 9.0''
** '''Relaxation Factor''' [--relaxationFactor] : Internal debugging parameter, and should probably never be used from the command line. This will be removed in the future. ''Default value: 0.5''
** '''Maximum Step Length''' [--maximumStepLength] : Internal debugging parameter, and should probably never be used from the command line. This will be removed in the future. ''Default value: 0.2''
** '''Failure Exit Code''' [--failureExitCode] : If the fit fails, exit with this status code. (It can be used to force a successfult exit status of (0) if the registration fails due to reaching the maximum number of iterations. ''Default value: -1''
** '''Write Transform On Failure''' [--writeTransformOnFailure] : Flag to save the final transform even if the numberOfIterations are reached without convergence. (Intended for use when --failureExitCode 0 ) ''Default value: 0''
** '''debugNumberOfThreads''' [--debugNumberOfThreads] : Explicitly specify the maximum number of threads to use. ''Default value: -1''
** '''Debug option''' [--debugLevel] : Display debug messages, and produce debug intermediate results. 0=OFF, 1=Minimal, 10=Maximum debugging. ''Default value: 0''
* '''''Risky Expert-only Parameters''''':
** '''DO NOT USE''' [--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00] : DO NOT USE THIS FLAG ''Default value: false''
** '''DO NOT USE''' [--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01] : DO NOT USE THIS FLAG ''Default value: false''
** '''DO NOT USE''' [--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02] : DO NOT USE THIS FLAG ''Default value: false''
** '''Selective Permission for Transform Parameters to Vary''' [--permitParameterVariation] : A bit vector to permit linear transform parameters to vary under optimization. The vector order corresponds with transform parameters, and beyond the end ones fill in as a default. For instance, you can choose to rotate only in x (pitch) with 1,0,0; this is mostly for expert use in turning on and off individual degrees of freedom in rotation, translation or scaling without multiplying the number of transform representations; this trick is probably meaningless when tried with the general affine transform.=
** '''Cost Metric''' [--costMetric] : The cost metric to be used during fitting. Defaults to MMI. Options are MMI (Mattes Mutual Information), MSE (Mean Square Error), NC (Normalized Correlation), MC (Match Cardinality for binary images) ''Default value: MMI''

||[[Image:BRAINSFitUI_part1.png|thumb|280px|User Interface]] [[Image:BRAINSFitUI_part2.png|thumb|280px|User Interface]]
|}

== Development ==

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

This is a thin wrapper program around the BRAINSFitHelper class in BRAINSCommonLib. The BRAINSFitHelper class
is intended to allow all the functionality of BRAINSFit to be easily incorporated into another program by including a single header file, linking against the BRAINSCommonLib library, and adding code similar to the following to your application:
<pre>

typedef itk::BRAINSFitHelper HelperType;
HelperType::Pointer myHelper=HelperType::New();
myHelper->SetTransformType(localTransformType);
myHelper->SetFixedVolume(extractFixedVolume);
myHelper->SetMovingVolume(extractMovingVolume);
myHelper->StartRegistration();
currentGenericTransform=myHelper->GetCurrentGenericTransform();
MovingVolumeType::ConstPointer preprocessedMovingVolume = myHelper->GetPreprocessedMovingVolume();

/* Optional member functions that can also be set */
myHelper->SetHistogramMatch(histogramMatch);
myHelper->SetNumberOfMatchPoints(numberOfMatchPoints);
myHelper->SetFixedBinaryVolume(fixedMask);
myHelper->SetMovingBinaryVolume(movingMask);
myHelper->SetPermitParameterVariation(permitParameterVariation);
myHelper->SetNumberOfSamples(numberOfSamples);
myHelper->SetNumberOfHistogramBins(numberOfHistogramBins);
myHelper->SetNumberOfIterations(numberOfIterations);
myHelper->SetMaximumStepLength(maximumStepSize);
myHelper->SetMinimumStepLength(minimumStepSize);
myHelper->SetRelaxationFactor(relaxationFactor);
myHelper->SetTranslationScale(translationScale);
myHelper->SetReproportionScale(reproportionScale);
myHelper->SetSkewScale(skewScale);
myHelper->SetUseExplicitPDFDerivativesMode(useExplicitPDFDerivativesMode);
myHelper->SetUseCachingOfBSplineWeightsMode(useCachingOfBSplineWeightsMode);
myHelper->SetBackgroundFillValue(backgroundFillValue);
myHelper->SetInitializeTransformMode(localInitializeTransformMode);
myHelper->SetMaskInferiorCutOffFromCenter(maskInferiorCutOffFromCenter);
myHelper->SetCurrentGenericTransform(currentGenericTransform);
myHelper->SetSplineGridSize(splineGridSize);
myHelper->SetCostFunctionConvergenceFactor(costFunctionConvergenceFactor);
myHelper->SetProjectedGradientTolerance(projectedGradientTolerance);
myHelper->SetMaxBSplineDisplacement(maxBSplineDisplacement);
myHelper->SetDisplayDeformedImage(UseDebugImageViewer);
myHelper->SetPromptUserAfterDisplay(PromptAfterImageSend);
myHelper->SetDebugLevel(debugLevel);
if(debugLevel > 7 )
{
myHelper->PrintCommandLine(true,"BF");
}

</pre>

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
BRAINSFit depends on the BRAINSCommonLib library

===Tests===

Nightly testing of the development head can be found at: http://testing.psychiatry.uiowa.edu/CDash

===Known bugs===

Links to known bugs and feature requests are listed at:
* http://www.nitrc.org/projects/multimodereg/

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://www.nitrc.org/projects/multimodereg/|Hosted by NITRC ]

== More Information ==

===Acknowledgment===

This research was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.

===References===
* [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.

File:T1T2PreRegCheckerboard.png

2010-12-29T22:25:11Z

Mscully: Checkerboard of T1 and T2 image before T2 image has been registered to the T1 (intensities in the T1 have been increased in order to make the image more visible)

Checkerboard of T1 and T2 image before T2 image has been registered to the T1 (intensities in the T1 have been increased in order to make the image more visible)

File:T1T2RegCheckerboard.png

2010-12-29T22:25:02Z

Mscully: Checkerboard of T1 and T2 image after T2 image has been registered to the T1 (intensities in the T1 have been increased in order to make the image more visible)

Checkerboard of T1 and T2 image after T2 image has been registered to the T1 (intensities in the T1 have been increased in order to make the image more visible)