https://www.slicer.org/w/api.php?action=feedcontributions&user=Prastawa&feedformat=atomSlicer Wiki - User contributions [en]2024-03-28T10:40:34ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=43072Documentation/4.4/Modules/ABC2015-10-21T23:09:50Z<p>Prastawa: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
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Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
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Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
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ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy human brain MRIs, and can be adapted to other applications that involve multi-channel MR images and a pre-defined atlas. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
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<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered or skull-stripped beforehand. All images are assumed to have the correct metadata for spatial orientation, voxel spacing, and image origin.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|480px|'''Example Parameters.''' Typical execution using default parameters.]]<br />
|[[Image:abc_panels_marked.png|thumb|480px|'''Basic Extension Panels.''' Panels with the minimal number of parameters that need to be specified for executing the software.]]<br />
|}<br />
<br />
The input images are specified in the first panel. The ''choice of the first image in the list is crucial'', as the outputs are generated in the space of the first image. All other image channels and the atlas are registered to the first image during processing.<br />
<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
{|<br />
|[[Image:abc_output.png|thumb|620px|'''Example Output.''' Brain MRI segmented using ABC]]<br />
|}<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
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[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
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* Automated model-based tissue classification of MR images of the brain. K Van Leemput, F Maes, D Vandermeulen, P Suetens. Medical Imaging, IEEE Transactions on 18 (10), 897-908.<br />
* Automated model-based bias field correction of MR images of the brain. K Van Leemput, F Maes, D Vandermeulen, P Suetens. Medical Imaging, IEEE Transactions on 18 (10), 885-896.<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
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Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
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<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42753Documentation/4.4/Modules/ABC2015-09-18T18:29:03Z<p>Prastawa: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
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<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered or skull-stripped beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|480px|'''Example Parameters.''' Typical execution using default parameters.]]<br />
|[[Image:abc_panels_marked.png|thumb|480px|'''Basic Extension Panels.''' Panels with the minimal number of parameters that need to be specified for executing the software.]]<br />
|}<br />
<br />
The input images are specified in the first panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
{|<br />
|[[Image:abc_output.png|thumb|620px|'''Example Output.''' Brain MRI segmented using ABC]]<br />
|}<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
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[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
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Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
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<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42752Documentation/4.4/Modules/ABC2015-09-18T18:27:59Z<p>Prastawa: </p>
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
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<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|480px|'''Example Parameters.''' Typical execution using default parameters.]]<br />
|[[Image:abc_panels_marked.png|thumb|480px|'''Basic Extension Panels.''' Panels with the minimal number of parameters that need to be specified for executing the software.]]<br />
|}<br />
<br />
The input images are specified in the first panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
{|<br />
|[[Image:abc_output.png|thumb|620px|'''Example Output.''' Brain MRI segmented using ABC]]<br />
|}<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
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Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42751Documentation/4.4/Modules/ABC2015-09-18T17:30:01Z<p>Prastawa: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|480px|'''Extension Panels.''']]<br />
|[[Image:abc_panels_marked.png|thumb|480px|'''Annotated Extension Panels.''']]<br />
|}<br />
<br />
The input images are specified in the first panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
{|<br />
|[[Image:abc_output.png|thumb|620px|'''Example Output.''' Brain MRI segmented using ABC]]<br />
|}<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=File:Abc_output.png&diff=42750File:Abc output.png2015-09-18T17:28:31Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42749Documentation/4.4/Modules/ABC2015-09-18T17:28:17Z<p>Prastawa: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|480px|'''Extension Panels.''']]<br />
|[[Image:abc_panels_marked.png|thumb|480px|'''Annotated Extension Panels.''']]<br />
|}<br />
<br />
The input images are specified in the first panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
[[Image:abc_output.png|thumb|620px|'''Example Output.''' Brain MRI segmented using ABC]]<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42748Documentation/4.4/Modules/ABC2015-09-18T17:08:20Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|480px|'''Extension Panels.''']]<br />
|[[Image:abc_panels_marked.png|thumb|480px|'''Annotated Extension Panels.''']]<br />
|}<br />
<br />
The input images are specified in the first panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42747Documentation/4.4/Modules/ABC2015-09-18T17:00:11Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|480px|'''Extension Panels.''']]<br />
|[[Image:abc_panels_marked.png|thumb|480px|'''Annotated Extension Panels.''']]<br />
|}<br />
<br />
The input images are specified in the first panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=File:Abc_panels_marked.png&diff=42746File:Abc panels marked.png2015-09-18T16:59:22Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=File:Abc_panels.png&diff=42745File:Abc panels.png2015-09-18T16:58:55Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42744Documentation/4.4/Modules/ABC2015-09-18T16:57:56Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
{|<br />
|[[Image:abc_panels.png|thumb|280px|'''Extension Panels.''']]<br />
|[[Image:abc_panels_marked.png|thumb|280px|'''Annotated Extension Panels.''']]<br />
|}<br />
<br />
The input images are specified in the first panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
The atlas can be specified through the second panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas is available through NITRC for adult brains: [https://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Adult Brain Atlas], which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The output images are specified in the third panel. Users can create and specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the '''Apply''' button.<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the '''Speed''' panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the '''Advanced''' panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the '''Speed''' panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42743Documentation/4.4/Modules/ABC2015-09-18T15:22:27Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult). Initiating the pipeline requires the specification of an atlas (which contains a template image and prior probability images) and at least one image modality for a subject. The module can accommodate up to five modalities, which need not be registered beforehand. All images are assumed to have the correct metadata for spatial orientation.<br />
<br />
The atlas can be specified through the first panel. The module assumes that it is stored in a directory where the template image (e.g., a T1 image) is specified as template.mha and that the prior images are stored in sequence (1.mha, 2.mha, ...). An example atlas can be found at , which needs to be uncompressed and stored in a local path before running the module.<br />
<br />
The input images are specified in the second panel. The choice of the first image in the list is crucial, as the outputs are generated in the space of the first image. All other modality images and the atlas are registered to the first image during processing.<br />
<br />
The output images are specified in the third panel. Users can specify the target volumes for the segmentation labels as well as the bias corrected images for each modality. The bias corrected output images do not need to be specified if they are of no interest.<br />
<br />
Once all input parameters have been specified, execution can be initiated by clicking the Apply button.<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the Speed panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the Advanced panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the Speed panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42648Documentation/4.4/Modules/ABC2015-09-09T20:46:24Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the Speed panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the Advanced panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the Speed panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-footer}} --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42647Documentation/4.4/Modules/ABC2015-09-09T20:42:02Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the Speed panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the Advanced panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the Speed panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegmenter]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}</div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42637Documentation/4.4/Modules/ABC2015-09-08T20:13:20Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the Speed panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the Advanced panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the Speed panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
EMSegmenter<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Source code can be found at http://www.nitrc.org/plugins/scmsvn/viewcvs.php/?root=abc<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}</div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42636Documentation/4.4/Modules/ABC2015-09-08T20:12:23Z<p>Prastawa: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
Author: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
<br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module can take up to five minutes for a typical MR image, using the default setting that was chosen to generate coarser results. Speed-ups are possible by increasing the number of threads (specified in the Speed panel). Results with higher accuracy can be obtained by increasing the maximum polynomial degree of the bias field (in the Advanced panel), increasing the number of pre-filtering iterations (in the Advanced panel), and switching to finer sampling for image registration (in the Speed panel).<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
EMSegmenter<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
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[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br />
<!-- ---------------------------- --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/ModulesMetadata&diff=42635Documentation/4.4/ModulesMetadata2015-09-08T20:10:27Z<p>Prastawa: </p>
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<includeonly><br />
Name, XMLDescriptionURL<br />
ABC, https://www.nitrc.org/plugins/scmsvn/viewcvs.php/trunk/Slicer4CommandLine/ABC.xml?view=co&root=abc<br />
ACPCTransform, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ACPCTransform/ACPCTransform.xml?revision=22697&view=co<br />
AddScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AddScalarVolumes/AddScalarVolumes.xml?revision=19194&view=co<br />
AffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AffineRegistration/AffineRegistration.xml?revision=19194&view=co<br />
Annotations, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Annotations/Documentation/Annotations.xml?revision=22424&view=co<br />
BRAINSDemonWarp, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSDemonWarp/BRAINSDemonWarp.xml<br />
BRAINSFit, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSFit/BRAINSFit.xml<br />
BRAINSResample, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSResample/BRAINSResample.xml<br />
BSplineDeformableRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineDeformableRegistration/BSplineDeformableRegistration.xml?revision=19194&view=co<br />
BSplineToDeformationField, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineToDeformationField/BSplineToDeformationField.xml?revision=19194&view=co<br />
Cameras, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/Cameras/Documentation/Cameras.xml?revision=19238&view=co<br />
CastScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CastScalarVolume/CastScalarVolume.xml?revision=19608&view=co<br />
CheckerBoardFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CheckerBoardFilter/CheckerBoardFilter.xml?revision=19170&view=co<br />
CLIModuleTemplate, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.xml?revision=22715&view=co<br />
CreateDICOMSeries, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CreateDICOMSeries/CreateDICOMSeries.xml?revision=19171&view=co<br />
CurvatureAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CurvatureAnisotropicDiffusion/CurvatureAnisotropicDiffusion.xml?revision=18864&view=co<br />
Data, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Data/Documentation/Data.xml?revision=22613&view=co<br />
DICOM, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/DICOM.xml?revision=19903&view=co<br />
DicomToNrrdConverter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/DicomToNrrdConverter.xml?revision=19089&view=co<br />
DiffusionTensorScalarMeasurements, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionTensorScalarMeasurements/DiffusionTensorScalarMeasurements.xml?revision=19172&view=co<br />
DiffusionWeightedVolumeMasking, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionWeightedVolumeMasking/DiffusionWeightedVolumeMasking.xml?revision=19194&view=co<br />
DTIExport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIexport.xml?revision=19928&view=co<br />
DTIImport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIimport.xml?revision=19928&view=co<br />
DWICompare, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/ExtendedTesting/DWICompare.xml?revision=18864&view=co<br />
DWIConverter, https://raw.githubusercontent.com/BRAINSia/BRAINSTools/487208d64667a95ece1a4e4a6aa1f19273108d18/DWIConvert/DWIConvert.xml<br />
DWIJointRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIJointRicianLMMSEFilter/DWIJointRicianLMMSEFilter.xml?revision=19197&view=co<br />
DWIRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIRicianLMMSEFilter/DWIRicianLMMSEFilter.xml?revision=19197&view=co<br />
DWIToDTIEstimation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIToDTIEstimation/DWIToDTIEstimation.xml?revision=19201&view=co<br />
DWIUnbiasedNonLocalMeansFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIUnbiasedNonLocalMeansFilter/DWIUnbiasedNonLocalMeansFilter.xml?revision=19197&view=co<br />
EMSegment_Command-line, http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co<br />
Endoscopy, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/Endoscopy.xml?revision=18864&view=co<br />
EventBroker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/EventBroker/Documentation/EventBroker.xml?revision=19045&view=co<br />
ExecutionModelTour, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExecutionModelTour/ExecutionModelTour.xml?revision=19194&view=co<br />
ExpertAutomatedRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExpertAutomatedRegistration/ExpertAutomatedRegistration.xml?revision=19173&view=co<br />
ExtractSkeleton, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExtractSkeleton/ExtractSkeleton.xml?revision=18864&view=co<br />
FiducialRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FiducialRegistration/FiducialRegistration.xml?revision=19173&view=co<br />
ForegroundMasking, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSROIAuto/BRAINSROIAuto.xml<br />
FreesurferSurfaceSectionExtraction, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FreesurferSurfaceSectionExtraction/FreesurferSurfaceSectionExtraction.xml?revision=18864&view=co<br />
GaussianBlurImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GaussianBlurImageFilter/GaussianBlurImageFilter.xml?revision=19194&view=co<br />
GradientAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GradientAnisotropicDiffusion/GradientAnisotropicDiffusion.xml?revision=18864&view=co<br />
GrayscaleFillHoleImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleFillHoleImageFilter/GrayscaleFillHoleImageFilter.xml?revision=19194&view=co<br />
GrayscaleGrindPeakImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleGrindPeakImageFilter/GrayscaleGrindPeakImageFilter.xml?revision=19194&view=co<br />
GrayscaleModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.xml?revision=18864&view=co<br />
HistogramMatching, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/HistogramMatching/HistogramMatching.xml?revision=18864&view=co<br />
ImageLabelCombine, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ImageLabelCombine/ImageLabelCombine.xml?revision=18864&view=co<br />
LabelMapSmoothing, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LabelMapSmoothing/LabelMapSmoothing.xml?revision=18864&view=co<br />
LinearRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LinearRegistration/LinearRegistration.xml?revision=19194&view=co<br />
Markups, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Markups/Documentation/Markups.xml?revision=22608&view=co<br />
MaskScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MaskScalarVolume/MaskScalarVolume.xml?revision=19608&view=co<br />
MatlabCommander, https://www.assembla.com/code/slicerrt/subversion/node/blob/trunk/MatlabBridge/src/MatlabCommander/MatlabCommander.xml?raw=1&rev=957<br />
MedianImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MedianImageFilter/MedianImageFilter.xml?revision=19194&view=co<br />
MergeModels, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MergeModels/MergeModels.xml?revision=22697&view=co<br />
MeshContourSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MeshContourSegmentation/MeshContourSegmentation.xml?revision=19175&view=co<br />
ModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelMaker/ModelMaker.xml?revision=22697&view=co<br />
Models, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Models/Documentation/Models.xml?revision=22705&view=co<br />
ModelToLabelMap, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml?revision=22697&view=co<br />
MRIBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MRIBiasFieldCorrection/MRIBiasFieldCorrection.xml?revision=18864&view=co<br />
MultiplyScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiplyScalarVolumes/MultiplyScalarVolumes.xml?revision=19194&view=co<br />
MultiResolutionAffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiResolutionAffineRegistration/MultiResolutionAffineRegistration.xml?revision=19194&view=co<br />
N4ITKBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/N4ITKBiasFieldCorrection/N4ITKBiasFieldCorrection.xml?revision=22688&view=co<br />
OrientScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OrientScalarVolume/OrientScalarVolume.xml?revision=19193&view=co<br />
OtsuThresholdImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdImageFilter/OtsuThresholdImageFilter.xml?revision=19194&view=co<br />
OtsuThresholdSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdSegmentation/OtsuThresholdSegmentation.xml?revision=18864&view=co<br />
PETStandardUptakeValueComputation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/PETStandardUptakeValueComputation/PETStandardUptakeValueComputation.xml?revision=19608&view=co<br />
ProbeVolumeWithModel, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ProbeVolumeWithModel/ProbeVolumeWithModel.xml?revision=19194&view=co<br />
Reformat, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Reformat/Documentation/Reformat.xml?revision=19165&view=co<br />
ResampleDTIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleDTIVolume/ResampleDTIVolume.xml?revision=19197&view=co<br />
ResampleScalarVectorDWIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVectorDWIVolume/ResampleScalarVectorDWIVolume.xml?revision=19186&view=co<br />
ResampleScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVolume/ResampleScalarVolume.xml?revision=19185&view=co<br />
RigidRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RigidRegistration/RigidRegistration.xml?revision=19194&view=co<br />
RobustStatisticsSegmenter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RobustStatisticsSegmenter/RobustStatisticsSegmenter.xml?revision=19198&view=co<br />
SceneViews, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/SceneViews/Documentation/SceneViews.xml?revision=19608&view=co<br />
SimpleRegionGrowingSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SimpleRegionGrowingSegmentation/SimpleRegionGrowingSegmentation.xml?revision=22482&view=co<br />
SubtractScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SubtractScalarVolumes/SubtractScalarVolumes.xml?revision=19194&view=co<br />
ThresholdScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.xml?revision=22407&view=co<br />
TractographyLabelMapSeeding, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.xml?revision=19194&view=co<br />
Transforms, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Transforms/Documentation/Transforms.xml?revision=19899&view=co<br />
ViewControllers, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/ViewControllers/Documentation/ViewControllers.xml?revision=18864&view=co<br />
VolumeRendering, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/VolumeRendering/Documentation/VolumeRendering.xml?revision=22805&view=co<br />
Volumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Volumes/Documentation/Volumes.xml?revision=18864&view=co<br />
VotingBinaryHoleFillingImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/VotingBinaryHoleFillingImageFilter/VotingBinaryHoleFillingImageFilter.xml?revision=19194&view=co<br />
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</noinclude></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/Modules/ABC&diff=42634Documentation/4.4/Modules/ABC2015-09-08T19:36:08Z<p>Prastawa: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'</p>
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ABC (Atlas Based Classification) is a full segmentation pipeline designed and developed for healthy brain MRIs. The processing pipeline includes image registration, filtering, inhomogeneity correction, and skull stripping.<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/ABC|ABC: Atlas Based Classification]]<br><br />
Acknowledgments: This project was supported by NIH grant U54 EB005149. <br><br />
<br />
Contributor: Marcel Prastawa <br><br />
Contact: Marcel Prastawa, <email>marcel.prastawa@gmail.com</email><br><br />
Website: http://www.nitrc.org/projects/abc<br><br />
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[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br />
<!-- ---------------------------- --></div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/4.4/ModuleExtensionListing&diff=42633Documentation/4.4/ModuleExtensionListing2015-09-08T19:23:54Z<p>Prastawa: /* Segmentation */</p>
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<div>__NOTOC__<br />
<noinclude>{{:Documentation/4.4/ModuleExtensionListing/TOC}}</noinclude><br />
= Modules by category =<br />
36 categories:<br />
* [[#Modules_by_category_BRAINS|BRAINS]]<br />
** [[#Modules_by_category_BRAINS_LabelStatistics|Label Statistics]]<br />
* [[#Modules_by_category_Cardiac_MRI_Toolkit|Cardiac MRI Toolkit]]<br />
* [[#Modules_by_category_CMF_Registration|CMF Registration]]<br />
** [[#Modules_by_category_CMF_Registration_Voxelbase_Registration|Voxelbase Registration]]<br />
* [[#Modules_by_category_Converters|Converters]]<br />
* [[#Modules_by_category_Developer_Tools|Developer Tools]]<br />
** [[#Modules_by_category_Developer_Tools_DICOM_Plugins|DICOM Plugins]]<br />
** [[#Modules_by_category_Developer_Tools_Editor_Extensions|Editor Extensions]]<br />
** [[#Modules_by_category_Developer_Tools_Matlab|Matlab]]<br />
* [[#Modules_by_category_Diffusion|Diffusion]]<br />
** [[#Modules_by_category_Diffusion_Diffusion_Data_Conversion|Diffusion Data Conversion]]<br />
** [[#Modules_by_category_Diffusion_Diffusion_Tensor_Images|Diffusion Tensor Images]]<br />
** [[#Modules_by_category_Diffusion_Diffusion_Weighted_Images|Diffusion Weighted Images]]<br />
** [[#Modules_by_category_Diffusion_FiberAnalysis|Fiber Analysis]]<br />
** [[#Modules_by_category_Diffusion_Tractography|Tractography]]<br />
* [[#Modules_by_category_Editor_Effects|Editor Effects]]<br />
* [[#Modules_by_category_EditorEffect|Editor Effect]]<br />
* [[#Modules_by_category_Endoscopy|Endoscopy]]<br />
* [[#Modules_by_category_Examples|Examples]]<br />
* [[#Modules_by_category_Exporter|Exporter]]<br />
* [[#Modules_by_category_File|File]]<br />
* [[#Modules_by_category_Filtering|Filtering]]<br />
** [[#Modules_by_category_Filtering_Arithmetic|Arithmetic]]<br />
** [[#Modules_by_category_Filtering_Denoising|Denoising]]<br />
** [[#Modules_by_category_Filtering_Morphology|Morphology]]<br />
* [[#Modules_by_category_IGT|IGT]]<br />
* [[#Modules_by_category_Informatics|Informatics]]<br />
* [[#Modules_by_category_Legacy|Legacy]]<br />
** [[#Modules_by_category_Legacy_Converters|Converters]]<br />
** [[#Modules_by_category_Legacy_Diffusion|Diffusion]]<br />
*** [[#Modules_by_category_Diffusion_Denoising|Denoising]]<br />
*** [[#Modules_by_category_Diffusion_Diffusion_Data_Conversion|Diffusion Data Conversion]]<br />
** [[#Modules_by_category_Legacy_Filtering|Filtering]]<br />
** [[#Modules_by_category_Legacy_Registration|Registration]]<br />
** [[#Modules_by_category_Legacy_Work_in_Progress|Work in Progress]]<br />
*** [[#Modules_by_category_Work_in_Progress_Diffusion_Tensor|Diffusion Tensor]]<br />
**** [[#Modules_by_category_Diffusion_Tensor_Test|Test]]<br />
* [[#Modules_by_category_Mesh_Generation|Mesh Generation]]<br />
* [[#Modules_by_category_MeshGeneration|Mesh Generation]]<br />
* [[#Modules_by_category_Microscopy|Microscopy]]<br />
* [[#Modules_by_category_Multidimensional_data|Multidimensional data]]<br />
* [[#Modules_by_category_MultiVolume_Support|Multi Volume Support]]<br />
* [[#Modules_by_category_Perk_Tutor|Perk Tutor]]<br />
* [[#Modules_by_category_Plastimatch|Plastimatch]]<br />
** [[#Modules_by_category_Plastimatch_Registration|Registration]]<br />
** [[#Modules_by_category_Plastimatch_Utilities|Utilities]]<br />
* [[#Modules_by_category_Quantification|Quantification]]<br />
** [[#Modules_by_category_Quantification_ChangeQuantification|Change Quantification]]<br />
* [[#Modules_by_category_Radiotherapy|Radiotherapy]]<br />
* [[#Modules_by_category_Registration|Registration]]<br />
** [[#Modules_by_category_Registration_Specialized|Specialized]]<br />
* [[#Modules_by_category_Segmentation|Segmentation]]<br />
** [[#Modules_by_category_Segmentation_Specialized|Specialized]]<br />
* [[#Modules_by_category_Shape_Analysis|Shape Analysis]]<br />
* [[#Modules_by_category_Slicelets|Slicelets]]<br />
* [[#Modules_by_category_Surface_Models|Surface Models]]<br />
* [[#Modules_by_category_Testing|Testing]]<br />
** [[#Modules_by_category_Testing_IGT_Tests|IGT Tests]]<br />
** [[#Modules_by_category_Testing_SlicerRT_Tests|Slicer RT Tests]]<br />
** [[#Modules_by_category_Testing_TestCases|Test Cases]]<br />
* [[#Modules_by_category_Unspecified|Unspecified]]<br />
* [[#Modules_by_category_Utilities|Utilities]]<br />
** [[#Modules_by_category_Utilities_BRAINS|BRAINS]]<br />
* [[#Modules_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]<br />
* [[#Modules_by_category_Wizards|Wizards]]<br />
* [[#Modules_by_category_Work_in_Progress|Work in Progress]]<br />
** [[#Modules_by_category_Work_in_Progress_Converters|Converters]]<br />
** [[#Modules_by_category_Work_in_Progress_Informatics|Informatics]]<br />
*** [[#Modules_by_category_Informatics_TestCases|Test Cases]]<br />
<span id='Modules_by_category_BRAINS'></span><br />
== BRAINS ==<br />
<span id='Modules_by_category_BRAINS_LabelStatistics'></span><br />
=== LabelStatistics ===<br />
* BRAINSLabel Stats <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Cardiac_MRI_Toolkit'></span><br />
== Cardiac MRI Toolkit ==<br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Connected Threshold Filter] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Isolated Connected Filter] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Wizard] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Axial Dilate] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Inhomogeneity Correction] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit PVAntrum Cut] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [[Documentation/4.4/Modules/ScarVisualization|Scar Visualization]] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Boolean REMOVEFilter] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [[Documentation/4.4/Modules/LASegmentationWorkflow|LASegmentation Workflow]] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Automatic Left Atrial Scar] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration BRAINSFit] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
<span id='Modules_by_category_CMF_Registration'></span><br />
== CMF Registration ==<br />
* [[Documentation/4.4/Extensions/CMFreg|Apply Matrix]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/LandmarkRegistration|Landmark Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Extensions/CMFreg|Surface Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/LabelExtraction|Label Extraction]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/LabelAddition|Label Addition]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/Downsize|Downsize]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
<span id='Modules_by_category_CMF_Registration_Voxelbase_Registration'></span><br />
=== Voxelbase Registration ===<br />
* [[Documentation/4.4/Modules/MaskCreation|Mask Creation]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/NonGrowing|Non Growing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/Growing|Growing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
<span id='Modules_by_category_Converters'></span><br />
== Converters ==<br />
* [[Documentation/4.4/Modules/VectorToScalarVolume|Vector To Scalar Volume]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/CropVolume|Crop Volume]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/CreateDICOMSeries|Create DICOMSeries]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/OrientScalarVolume|Orient Scalar Volume]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Developer_Tools'></span><br />
== Developer Tools ==<br />
* [[Documentation/4.4/Modules/EventBroker|Event Broker]]<br />
* [[Documentation/4.4/Modules/ExecutionModelTour|Execution Model Tour]] <small>(cli, built-in)</small><br />
* Double Arrays <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Extensions/PyDevRemoteDebug|Py Dev Remote Debug]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PyDevRemoteDebug|Py Dev Remote Debug]] extension)</small><br />
* [[Documentation/4.4/Modules/Cameras|Cameras]] <small>(loadable, built-in)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DeveloperToolsForExtensions Extension Stats] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DeveloperToolsForExtensions Developer Tools For Extensions] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DeveloperToolsForExtensions Developer Tools For Extensions] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DeveloperToolsForExtensions Developer Tools For Extensions] extension)</small><br />
* [[Documentation/4.4/Modules/ExtensionWizard|Extension Wizard]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Extensions/ImageMaker|Image Maker]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ImageMaker|Image Maker]] extension)</small><br />
<span id='Modules_by_category_Developer_Tools_DICOM_Plugins'></span><br />
=== DICOM Plugins ===<br />
* DICOMLongitudinal PETCTPlugin<br />
* [[Documentation/4.4/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]<br />
* Multi Volume Importer Plugin<br />
* [[Documentation/4.4/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]<br />
* Dicom Rt Import Plugin<br />
* DICOMDiffusion Volume Plugin<br />
* DICOMSegmentation Plugin<br />
* Dicom Sro Import Plugin<br />
* DICOMScalar Volume Plugin<br />
* DICOMSlicer Data Bundle Plugin<br />
<span id='Modules_by_category_Developer_Tools_Editor_Extensions'></span><br />
=== Editor Extensions ===<br />
* [[Documentation/4.4/Extensions/IASEM|Binary Watershed Effect]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|Double Threshold Effect]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Modules/PETTumorSegmentationEffect|PETTumor Segmentation Effect]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PETTumorSegmentation|PETTumor Segmentation]] extension)</small><br />
<span id='Modules_by_category_Developer_Tools_Matlab'></span><br />
=== Matlab ===<br />
* [[Documentation/4.4/Modules/MatlabCommander|Matlab Commander]] <small>(cli, bundled in [[Documentation/4.4/Extensions/MatlabBridge|Matlab Bridge]] extension)</small><br />
* [[Documentation/4.4/Modules/MatlabModuleGenerator|Matlab Module Generator]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/MatlabBridge|Matlab Bridge]] extension)</small><br />
<span id='Modules_by_category_Diffusion'></span><br />
== Diffusion ==<br />
* DICOM2Full Brain Tractography <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/TractographyDisplay|Tractography Display]] <small>(loadable, built-in)</small><br />
<span id='Modules_by_category_Diffusion_Diffusion_Data_Conversion'></span><br />
=== Diffusion Data Conversion ===<br />
* DWIConvert <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Diffusion_Diffusion_Tensor_Images'></span><br />
=== Diffusion Tensor Images ===<br />
* [[Documentation/4.4/Modules/ResampleDTIVolume|Resample DTIVolume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] <small>(cli, built-in)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/ResampleDTIlogEuclidean Resample DTIlog Euclidean] <small>(cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/ResampleDTIlogEuclidean Resample DTIlog Euclidean] extension)</small><br />
* [[Documentation/4.4/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] <small>(cli, built-in)</small><br />
* Tractography Interactive Seeding <small>(loadable, built-in)</small><br />
<span id='Modules_by_category_Diffusion_Diffusion_Weighted_Images'></span><br />
=== Diffusion Weighted Images ===<br />
* [[Documentation/4.4/Modules/DWIRicianLMMSEFilter|DWIRician LMMSEFilter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWIVolume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/DWIToDTIEstimation|DWITo DTIEstimation]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/FinslerBacktracing|Finsler Backtracing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/FinslerTractography|Finsler Tractography]] extension)</small><br />
* [[Documentation/4.4/Modules/DWIJointRicianLMMSEFilter|DWIJoint Rician LMMSEFilter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/FinslerTractography|Finsler Tractography]] <small>(cli, bundled in [[Documentation/4.4/Extensions/FinslerTractography|Finsler Tractography]] extension)</small><br />
* [[Documentation/4.4/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Diffusion_FiberAnalysis'></span><br />
=== FiberAnalysis ===<br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|Fiber Compare]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|Merge Stat With Fiber]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|dtitractstat]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
<span id='Modules_by_category_Diffusion_Tractography'></span><br />
=== Tractography ===<br />
* [[Documentation/4.4/Modules/FiberBundleToLabelMap|Fiber Bundle To Label Map]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/UKFTractography|UKFTractography]] <small>(cli, bundled in [[Documentation/4.4/Extensions/UKFTractography|UKFTractography]] extension)</small><br />
* Fiber Bundle Label Select <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Editor_Effects'></span><br />
== Editor Effects ==<br />
* [[Documentation/4.4/Extensions/WindowLevelEffect|Window Level Effect]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/WindowLevelEffect|Window Level Effect]] extension)</small><br />
<span id='Modules_by_category_EditorEffect'></span><br />
== EditorEffect ==<br />
* [[Documentation/4.4/Extensions/PETTumorSegmentation|PETTumor Segmentation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PETTumorSegmentation|PETTumor Segmentation]] extension)</small><br />
<span id='Modules_by_category_Endoscopy'></span><br />
== Endoscopy ==<br />
* [[Documentation/4.4/Modules/Endoscopy|Endoscopy]] <small>(scripted, built-in)</small><br />
<span id='Modules_by_category_Examples'></span><br />
== Examples ==<br />
* [[Documentation/4.4/Modules/FastGrowCut|Fast Grow Cut]] <small>(loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect] extension)</small><br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Fast Grow Cut Segmenter] <small>(loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)</small><br />
* [[Documentation/4.4/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] <small>(cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SegmentationAidedRegistration Segmentation Aided Registration] extension)</small><br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] <small>(loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)</small><br />
<span id='Modules_by_category_Exporter'></span><br />
== Exporter ==<br />
* [[Documentation/4.4/Modules/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] extension)</small><br />
<span id='Modules_by_category_File'></span><br />
== File ==<br />
* [[Documentation/4.4/Extensions/UKFTractography|Convert VTK]] <small>(cli, bundled in [[Documentation/4.4/Extensions/UKFTractography|UKFTractography]] extension)</small><br />
<span id='Modules_by_category_Filtering'></span><br />
== Filtering ==<br />
* [[Documentation/4.4/Modules/ExtractSkeleton|Extract Skeleton]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/N4ITKBiasFieldCorrection|N4ITKBias Field Correction]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/SimpleFilters|Simple Filters]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/ImageLabelCombine|Image Label Combine]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/HistogramMatching|Histogram Matching]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/CheckerBoardFilter|Checker Board Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Filtering_Arithmetic'></span><br />
=== Arithmetic ===<br />
* [[Documentation/4.4/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/AddScalarVolumes|Add Scalar Volumes]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/CastScalarVolume|Cast Scalar Volume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/MaskScalarVolume|Mask Scalar Volume]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Filtering_Denoising'></span><br />
=== Denoising ===<br />
* [[Documentation/4.4/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/MedianImageFilter|Median Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Filtering_Morphology'></span><br />
=== Morphology ===<br />
* [[Documentation/4.4/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/ErodeDilateLabel|Erode Label]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ErodeDilateLabel|Erode Dilate Label]] extension)</small><br />
* [[Documentation/4.4/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/ErodeDilateLabel|Dilate Label]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ErodeDilateLabel|Erode Dilate Label]] extension)</small><br />
<span id='Modules_by_category_IGT'></span><br />
== IGT ==<br />
* [[Documentation/4.4/Modules/ResectionVolume|Resection Volume]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/ResectionPlanner|Resection Planner]] extension)</small><br />
* [[Documentation/4.4/Modules/VolumeResliceDriver|Volume Reslice Driver]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/CollectFiducials|Collect Fiducials]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Fiducials To Model Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Create Models]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/PortPlacement|Port Placement]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PortPlacement|Port Placement]] extension)</small><br />
* [[Documentation/4.4/Modules/OpenIGTLinkIF|Open IGTLink IF]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/TrackerStabilizer|Tracker Stabilizer]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/TrackerStabilizer|Tracker Stabilizer]] extension)</small><br />
* [[Documentation/4.4/Modules/PathExplorer|Path Explorer]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Ultrasound Snapshots]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Transform Fusion]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Breach Warning]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/GyroGuide|Gyro Guide]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/GyroGuide|Gyro Guide]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Fiducial Registration Wizard]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Watchdog]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/OpenIGTLinkRemote|Open IGTLink Remote]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/PlusRemote|Plus Remote]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/iGyne|i Gyne]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/iGyne|i Gyne]] extension)</small><br />
* [[Documentation/4.4/Extensions/NeedleFinder|Needle Finder]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/NeedleFinder|Needle Finder]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Model Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Pivot Calibration]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/CornerAnnotation|Corner Annotation]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CornerAnnotation|Corner Annotation]] extension)</small><br />
<span id='Modules_by_category_Informatics'></span><br />
== Informatics ==<br />
* [[Documentation/4.4/Modules/Annotations|Annotations]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/Markups|Markups]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/Units|Units]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/DICOM|DICOM]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/SampleData|Sample Data]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/SubjectHierarchy|Subject Hierarchy]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/Data|Data]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/Colors|Colors]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Extensions/CurveMaker|Curve Maker]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CurveMaker|Curve Maker]] extension)</small><br />
* [[Documentation/4.4/Extensions/TCIABrowser|TCIABrowser]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/TCIABrowser|TCIABrowser]] extension)</small><br />
<span id='Modules_by_category_Legacy'></span><br />
== Legacy ==<br />
<span id='Modules_by_category_Legacy_Converters'></span><br />
=== Converters ===<br />
* [[Documentation/4.4/Modules/BSplineToDeformationField|BSpline To Deformation Field]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Legacy_Diffusion'></span><br />
=== Diffusion ===<br />
<span id='Modules_by_category_Diffusion_Denoising'></span><br />
==== Denoising ====<br />
* [[Documentation/4.4/Modules/DWIUnbiasedNonLocalMeansFilter|DWIUnbiased Non Local Means Filter]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Diffusion_Diffusion_Data_Conversion'></span><br />
==== Diffusion Data Conversion ====<br />
* DTIimport <small>(cli, built-in)</small><br />
* DTIexport <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Legacy_Filtering'></span><br />
=== Filtering ===<br />
* [[Documentation/4.4/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/ResampleScalarVolume|Resample Scalar Volume]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Legacy_Registration'></span><br />
=== Registration ===<br />
* Test Grid Transform Registration <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Legacy_Work_in_Progress'></span><br />
=== Work in Progress ===<br />
<span id='Modules_by_category_Work_in_Progress_Diffusion_Tensor'></span><br />
==== Diffusion Tensor ====<br />
<span id='Modules_by_category_Diffusion_Tensor_Test'></span><br />
===== Test =====<br />
* Diffusion Tensor Test <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Mesh_Generation'></span><br />
== Mesh Generation ==<br />
* [[Documentation/4.4/Extensions/CleaverExtension|Cleaver CLI]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CleaverExtension|Cleaver Extension]] extension)</small><br />
<span id='Modules_by_category_MeshGeneration'></span><br />
== MeshGeneration ==<br />
* [[Documentation/4.4/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)</small><br />
* [[Documentation/4.4/Modules/MeshCompression|Mesh Compression]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)</small><br />
<span id='Modules_by_category_Microscopy'></span><br />
== Microscopy ==<br />
* [[Documentation/4.4/Extensions/IASEM|Bin Shrink]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|Label Object Statistics]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|Spacing Aware Curvature Diffusion]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|IASEMImport Series]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|IASEMImport]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
<span id='Modules_by_category_Multidimensional_data'></span><br />
== Multidimensional data ==<br />
* [[Documentation/4.4/Extensions/MultidimData|Metafile Importer]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/MultidimData|Multidim Data]] extension)</small><br />
* [[Documentation/4.4/Extensions/MultidimData|Sequence Browser]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/MultidimData|Multidim Data]] extension)</small><br />
* [[Documentation/4.4/Extensions/MultidimData|Sequences]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/MultidimData|Multidim Data]] extension)</small><br />
<span id='Modules_by_category_MultiVolume_Support'></span><br />
== MultiVolume Support ==<br />
* [[Documentation/4.4/Modules/MultiVolumeExplorer|Multi Volume Explorer]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/MultiVolumeImporter|Multi Volume Importer]] <small>(scripted, built-in)</small><br />
<span id='Modules_by_category_Perk_Tutor'></span><br />
== Perk Tutor ==<br />
* [[Documentation/4.4/Extensions/PerkTutor|Python Metrics Calculator]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small><br />
* [[Documentation/4.4/Modules/WorkflowSegmentation|Workflow Segmentation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small><br />
* [[Documentation/4.4/Modules/TransformRecorder|Transform Recorder]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small><br />
* [[Documentation/4.4/Modules/PerkEvaluator|Perk Evaluator]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small><br />
<span id='Modules_by_category_Plastimatch'></span><br />
== Plastimatch ==<br />
* [[Documentation/4.4/Modules/DicomSroExport|Dicom Sro Export]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Plm Register]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
<span id='Modules_by_category_Plastimatch_Registration'></span><br />
=== Registration ===<br />
* [[Documentation/4.4/Extensions/SlicerRT|plastimatch slicer bspline]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|plastimatch slicer landwarp]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
<span id='Modules_by_category_Plastimatch_Utilities'></span><br />
=== Utilities ===<br />
* [[Documentation/4.4/Extensions/SlicerRT|Plastimatch Py]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
<span id='Modules_by_category_Quantification'></span><br />
== Quantification ==<br />
* [[Documentation/4.4/Modules/dPetBrainQuantification|d Pet Brain Quantification]] <small>(scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis] extension)</small><br />
* [[Documentation/4.4/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]] <small>(cli, bundled in [[Documentation/4.4/Extensions/PET-IndiC|PET-Indi C]] extension)</small><br />
* [[Documentation/4.4/Modules/PETStandardUptakeValueComputation|PETStandard Uptake Value Computation]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/SUVFactorCalculator|SUVFactor Calculator]] <small>(cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)</small><br />
* [[Documentation/4.4/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/Scoliosis|Scoliosis]] extension)</small><br />
* [[Documentation/4.4/Extensions/PET-IndiC|PETIndi C]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PET-IndiC|PET-Indi C]] extension)</small><br />
* [[Documentation/4.4/Modules/PkModeling|Pk Modeling]] <small>(cli, bundled in [[Documentation/4.4/Extensions/PkModeling|Pk Modeling]] extension)</small><br />
* [[Documentation/4.4/Extensions/PET-IndiC|Quantitative Indices Tool]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PET-IndiC|PET-Indi C]] extension)</small><br />
* [[Documentation/4.4/Modules/HeterogeneityCAD|Heterogeneity CAD]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/OpenCAD|Open CAD]] extension)</small><br />
* [[Documentation/4.4/Extensions/LongitudinalPETCT|PETSUVImage Maker]] <small>(cli, bundled in [[Documentation/4.4/Extensions/LongitudinalPETCT|Longitudinal PETCT]] extension)</small><br />
* [[Documentation/4.4/Modules/DiceComputation|Dice Computation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/DiceComputation|Dice Computation]] extension)</small><br />
* [[Documentation/4.4/Modules/DataProbe|Data Probe]] <small>(scripted, built-in)</small><br />
<span id='Modules_by_category_Quantification_ChangeQuantification'></span><br />
=== ChangeQuantification ===<br />
* [[Documentation/4.4/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ChangeTracker|Change Tracker]] extension)</small><br />
<span id='Modules_by_category_Radiotherapy'></span><br />
== Radiotherapy ==<br />
* [[Documentation/4.4/Modules/ContourComparison|Contour Comparison]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DicomRtImport|Dicom Rt Import]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Beams]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Dvh Comparison]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/Isodose|Isodose]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/Contours|Contours]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DoseAccumulation|Dose Accumulation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DicomRtExport|Dicom Rt Export]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DoseComparison|Dose Comparison]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/ContourMorphology|Contour Morphology]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DicomSroImport|Dicom Sro Import]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DoseVolumeHistogram|Dose Volume Histogram]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Planar Image]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
<span id='Modules_by_category_Registration'></span><br />
== Registration ==<br />
* [[Documentation/4.4/Modules/BRAINSResample|BRAINSResample]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/Transforms|Transforms]] <small>(loadable, built-in)</small><br />
* BRAINSResize <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/BRAINSFit|BRAINSFit]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/PBNRR|PBNRR]] <small>(cli, bundled in [[Documentation/4.4/Extensions/PBNRR|PBNRR]] extension)</small><br />
* Perform Metric Test <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Registration_Specialized'></span><br />
=== Specialized ===<br />
* [[Documentation/4.4/Modules/ACPCTransform|ACPCTransform]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/FiducialRegistration|Fiducial Registration]] <small>(cli, built-in)</small><br />
* VBRAINSDemon Warp <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/BRAINSDemonWarp|BRAINSDemon Warp]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/Reformat|Reformat]] <small>(loadable, built-in)</small><br />
<span id='Modules_by_category_Segmentation'></span><br />
== Segmentation ==<br />
* [[Documentation/4.4/Modules/AirwaySegmentation|Airway Segmentation]] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation] extension)</small><br />
* [[Documentation/4.4/Extensions/MABMIS|IGR3D MABMIS Training]] <small>(cli, bundled in [[Documentation/4.4/Extensions/MABMIS|MABMIS]] extension)</small><br />
* [[Documentation/4.4/Modules/ABC|ABC]] <small>(cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)</small><br />
* EMSegment Quick <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/EMSegment|EMSegment]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Extensions/VolumeClip|Volume Clip With Roi]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/VolumeClip|Volume Clip]] extension)</small><br />
* [[Documentation/4.4/Modules/SegmentCAD|Segment CAD]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/OpenCAD|Open CAD]] extension)</small><br />
* [[Documentation/4.4/Modules/SwissSkullStripper|Swiss Skull Stripper]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SwissSkullStripper|Swiss Skull Stripper]] extension)</small><br />
* [[Documentation/4.4/Extensions/AirwaySegmentation|Airway Segmentation CLI]] <small>(cli, bundled in [[Documentation/4.4/Extensions/AirwaySegmentation|Airway Segmentation]] extension)</small><br />
* [[Documentation/4.4/Modules/LAScarSegmenter|LAScar Segmenter]] <small>(cli, bundled in [[Documentation/4.4/Extensions/LAScarSegmenter|LAScar Segmenter]] extension)</small><br />
* [[Documentation/4.4/Modules/SobolevSegmenter|Sobolev Segmenter]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SobolevSegmenter|Sobolev Segmenter]] extension)</small><br />
* [[Documentation/4.4/Extensions/VolumeClip|Volume Clip With Model]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/VolumeClip|Volume Clip]] extension)</small><br />
* [[Documentation/4.4/Extensions/MABMIS|IGR3D MABMIS Testing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/MABMIS|MABMIS]] extension)</small><br />
* [[Documentation/4.4/Extensions/IntensitySegmenter|Intensity Segmenter]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IntensitySegmenter|Intensity Segmenter]] extension)</small><br />
<span id='Modules_by_category_Segmentation_Specialized'></span><br />
=== Specialized ===<br />
* EMSegment Command Line <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] <small>(cli, built-in)</small><br />
* BRAINSROIAuto <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Shape_Analysis'></span><br />
<br />
== Shape Analysis ==<br />
* [[Documentation/4.4/Extensions/MeshToLabelMap|Mesh To Label Map]] <small>(cli, bundled in [[Documentation/4.4/Extensions/MeshToLabelMap|Mesh To Label Map]] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension] extension)</small><br />
* [[Documentation/4.4/Extensions/ModelToModelDistance|Model To Model Distance]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ModelToModelDistance|Model To Model Distance]] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics Mesh Statistics] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics Mesh Statistics Extension] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/EasyClip Easy Clip] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/EasyClip Easy Clip] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Q3DC Q3DC] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Q3DC Q3DC] extension)</small><br />
<span id='Modules_by_category_Slicelets'></span><br />
== Slicelets ==<br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis Algo] <small>(loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)</small><br />
<span id='Modules_by_category_Surface_Models'></span><br />
== Surface Models ==<br />
* [[Documentation/4.4/Modules/ModelToLabelMap|Model To Label Map]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/MergeModels|Merge Models]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/SurfaceToolbox|Surface Toolbox]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/ProbeVolumeWithModel|Probe Volume With Model]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/ModelMaker|Model Maker]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/GrayscaleModelMaker|Grayscale Model Maker]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/LabelMapSmoothing|Label Map Smoothing]] <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Testing'></span><br />
== Testing ==<br />
* Self Tests<br />
* CLIROITest <small>(cli, built-in)</small><br />
* CLI4Test<br />
* Threshold Threading Test<br />
* [[Documentation/4.4/Extensions/Scoliosis|Scoliosis Monitoring]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/Scoliosis|Scoliosis]] extension)</small><br />
* Performance Tests<br />
* Slicer MRBTest<br />
<span id='Modules_by_category_Testing_IGT_Tests'></span><br />
=== IGT Tests ===<br />
* Breach Warning Self Test<br />
* Watchdog Self Test<br />
<span id='Modules_by_category_Testing_SlicerRT_Tests'></span><br />
=== SlicerRT Tests ===<br />
* NAMIC Tutorial 2013June Self Test<br />
* Dicom Rt Import Self Test<br />
* [[Documentation/4.4/Extensions/SlicerRT|Batch Contour Conversion]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
<span id='Modules_by_category_Testing_TestCases'></span><br />
=== TestCases ===<br />
* Slice Link Logic <small>(scripted, built-in)</small><br />
* Atlas Tests<br />
* RSNAQuant Tutorial<br />
* Volume Rendering Scene Close <small>(scripted, built-in)</small><br />
* test tractography display<br />
* slicer Close Crash Bug2590<br />
* Subject Hierarchy Generic Self Test<br />
* Charting <small>(scripted, built-in)</small><br />
* Scene Performance <small>(scripted, built-in)</small><br />
* Neurosurgical Planning Tutorial Markups Self Test<br />
* Markups In Compare Viewers Self Test<br />
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures] <small>(scripted, bundled in [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures] extension)</small><br />
* fiber visibility crash2438<br />
* scene Import2428<br />
* RSNAVis Tutorial<br />
* JRC2013Vis<br />
* RSNA2012Prostate Demo<br />
* Add Many Markups Fiducial Test<br />
* Colors Scalar Bar Self Test<br />
* Markups In Views Self Test<br />
* Subject Hierarchy Core Plugins Self Test<br />
* Change Tracker Self Test<br />
* Fiducial Layout Switch Bug1914<br />
* View Controllers Slice Interpolation Bug1926<br />
* Slicer4Minute <small>(scripted, built-in)</small><br />
* label Toggle Bug2049<br />
<span id='Modules_by_category_Unspecified'></span><br />
== Unspecified ==<br />
* BRAINSDWICleanup <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Utilities'></span><br />
== Utilities ==<br />
* [[Documentation/4.4/Modules/ThingiverseBrowser|Thingiverse Browser]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/ThingiverseBrowser|Thingiverse Browser]] extension)</small><br />
* BRAINSStrip Rotation <small>(cli, built-in)</small><br />
* EMSegment Transform To New Format <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/DataStore|Data Store]] <small>(loadable, built-in)</small><br />
<span id='Modules_by_category_Utilities_BRAINS'></span><br />
=== BRAINS ===<br />
* BRAINSTransform Convert <small>(cli, built-in)</small><br />
<span id='Modules_by_category_Vascular_Modeling_Toolkit'></span><br />
== Vascular Modeling Toolkit ==<br />
* [http://slicer.vmtk.org/ Vesselness Filtering] <small>(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)</small><br />
* [http://slicer.vmtk.org/ Centerline Computation] <small>(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)</small><br />
* [http://slicer.vmtk.org/ Level Set Segmentation] <small>(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)</small><br />
<span id='Modules_by_category_Wizards'></span><br />
== Wizards ==<br />
* [[Documentation/4.4/Modules/CompareVolumes|Compare Volumes]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/ChangeTracker|Change Tracker]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/ChangeTracker|Change Tracker]] extension)</small><br />
<span id='Modules_by_category_Work_in_Progress'></span><br />
== Work in Progress ==<br />
* [[Documentation/4.4/Extensions/LongitudinalPETCT|Longitudinal PETCT]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/LongitudinalPETCT|Longitudinal PETCT]] extension)</small><br />
<span id='Modules_by_category_Work_in_Progress_Converters'></span><br />
=== Converters ===<br />
* [[Documentation/4.4/Extensions/Reporting|Label To DICOMSEGConverter]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/Reporting|Reporting]] extension)</small><br />
<span id='Modules_by_category_Work_in_Progress_Informatics'></span><br />
=== Informatics ===<br />
* [[Documentation/4.4/Extensions/Reporting|Reporting]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/Reporting|Reporting]] extension)</small><br />
<span id='Modules_by_category_Informatics_TestCases'></span><br />
==== TestCases ====<br />
* Reporting Self Test<br />
* Label To DICOMSEGConverter Self Test<br />
= Modules by name =<br />
226 modules:<br />
* [http://www.nitrc.org/projects/abc ABC] <small>(cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)</small><br />
* [[Documentation/4.4/Modules/ACPCTransform|ACPCTransform]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/AddScalarVolumes|Add Scalar Volumes]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/AirwaySegmentation|Airway Segmentation]] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation] extension)</small><br />
* [[Documentation/4.4/Extensions/AirwaySegmentation|Airway Segmentation CLI]] <small>(cli, bundled in [[Documentation/4.4/Extensions/AirwaySegmentation|Airway Segmentation]] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension] extension)</small><br />
* [[Documentation/4.4/Modules/Annotations|Annotations]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Extensions/CMFreg|Apply Matrix]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Beams]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|Bin Shrink]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)</small><br />
* [[Documentation/4.4/Modules/BRAINSDemonWarp|BRAINSDemon Warp]] <small>(cli, built-in)</small><br />
* BRAINSDWICleanup <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/BRAINSFit|BRAINSFit]] <small>(cli, built-in)</small><br />
* BRAINSLabel Stats <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/BRAINSResample|BRAINSResample]] <small>(cli, built-in)</small><br />
* BRAINSResize <small>(cli, built-in)</small><br />
* BRAINSROIAuto <small>(cli, built-in)</small><br />
* BRAINSStrip Rotation <small>(cli, built-in)</small><br />
* BRAINSTransform Convert <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Breach Warning]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] <small>(loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)</small><br />
* [[Documentation/4.4/Modules/CastScalarVolume|Cast Scalar Volume]] <small>(cli, built-in)</small><br />
* [http://slicer.vmtk.org/ Centerline Computation] <small>(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)</small><br />
* [[Documentation/4.4/Modules/ChangeTracker|Change Tracker]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/ChangeTracker|Change Tracker]] extension)</small><br />
* [[Documentation/4.4/Modules/CheckerBoardFilter|Checker Board Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/CleaverExtension|Cleaver CLI]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CleaverExtension|Cleaver Extension]] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Automatic Left Atrial Scar] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Axial Dilate] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Boolean REMOVEFilter] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Connected Threshold Filter] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Inhomogeneity Correction] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Isolated Connected Filter] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit PVAntrum Cut] <small>(cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Registration BRAINSFit] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkit Wizard] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [[Documentation/4.4/Modules/CollectFiducials|Collect Fiducials]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/Colors|Colors]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/CompareVolumes|Compare Volumes]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/ContourComparison|Contour Comparison]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/ContourMorphology|Contour Morphology]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/Contours|Contours]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/UKFTractography|Convert VTK]] <small>(cli, bundled in [[Documentation/4.4/Extensions/UKFTractography|UKFTractography]] extension)</small><br />
* [[Documentation/4.4/Modules/CornerAnnotation|Corner Annotation]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CornerAnnotation|Corner Annotation]] extension)</small><br />
* [[Documentation/4.4/Modules/CreateDICOMSeries|Create DICOMSeries]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Create Models]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/CropVolume|Crop Volume]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/CurveMaker|Curve Maker]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CurveMaker|Curve Maker]] extension)</small><br />
* [[Documentation/4.4/Modules/Data|Data]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/DataProbe|Data Probe]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/DataStore|Data Store]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/DiceComputation|Dice Computation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/DiceComputation|Dice Computation]] extension)</small><br />
* [[Documentation/4.4/Modules/DICOM|DICOM]] <small>(scripted, built-in)</small><br />
* DICOM2Full Brain Tractography <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/DicomRtExport|Dicom Rt Export]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DicomRtImport|Dicom Rt Import]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DicomSroExport|Dicom Sro Export]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DicomSroImport|Dicom Sro Import]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/ErodeDilateLabel|Dilate Label]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ErodeDilateLabel|Erode Dilate Label]] extension)</small><br />
* [[Documentation/4.4/Modules/DoseAccumulation|Dose Accumulation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DoseComparison|Dose Comparison]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/DoseVolumeHistogram|Dose Volume Histogram]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/Downsize|Downsize]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/dPetBrainQuantification|d Pet Brain Quantification]] <small>(scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis] extension)</small><br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|dtitractstat]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Dvh Comparison]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* DWIConvert <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/DWIJointRicianLMMSEFilter|DWIJoint Rician LMMSEFilter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/DWIRicianLMMSEFilter|DWIRician LMMSEFilter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/DWIToDTIEstimation|DWITo DTIEstimation]] <small>(cli, built-in)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/EasyClip Easy Clip] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/EasyClip Easy Clip] extension)</small><br />
* [[Documentation/4.4/Modules/EMSegment|EMSegment]] <small>(loadable, built-in)</small><br />
* EMSegment Command Line <small>(cli, built-in)</small><br />
* EMSegment Quick <small>(loadable, built-in)</small><br />
* EMSegment Transform To New Format <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/Endoscopy|Endoscopy]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Extensions/ErodeDilateLabel|Erode Label]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ErodeDilateLabel|Erode Dilate Label]] extension)</small><br />
* [[Documentation/4.4/Modules/ExtractSkeleton|Extract Skeleton]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/FastGrowCut|Fast Grow Cut]] <small>(loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect] extension)</small><br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Fast Grow Cut Segmenter] <small>(loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)</small><br />
* Fiber Bundle Label Select <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/FiberBundleToLabelMap|Fiber Bundle To Label Map]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|Fiber Compare]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
* [[Documentation/4.4/Modules/FiducialRegistration|Fiducial Registration]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Fiducial Registration Wizard]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Fiducials To Model Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/FinslerBacktracing|Finsler Backtracing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/FinslerTractography|Finsler Tractography]] extension)</small><br />
* [[Documentation/4.4/Modules/FinslerTractography|Finsler Tractography]] <small>(cli, bundled in [[Documentation/4.4/Extensions/FinslerTractography|Finsler Tractography]] extension)</small><br />
* [[Documentation/4.4/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] <small>(cli, built-in)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis Algo] <small>(loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis] extension)</small><br />
* [[Documentation/4.4/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Diffusion]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/GrayscaleModelMaker|Grayscale Model Maker]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/Growing|Growing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/GyroGuide|Gyro Guide]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/GyroGuide|Gyro Guide]] extension)</small><br />
* [[Documentation/4.4/Modules/HeterogeneityCAD|Heterogeneity CAD]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/OpenCAD|Open CAD]] extension)</small><br />
* [[Documentation/4.4/Modules/HistogramMatching|Histogram Matching]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/IASEM|IASEMImport]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|IASEMImport Series]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/MABMIS|IGR3D MABMIS Testing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/MABMIS|MABMIS]] extension)</small><br />
* [[Documentation/4.4/Extensions/MABMIS|IGR3D MABMIS Training]] <small>(cli, bundled in [[Documentation/4.4/Extensions/MABMIS|MABMIS]] extension)</small><br />
* [[Documentation/4.4/Extensions/iGyne|i Gyne]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/iGyne|i Gyne]] extension)</small><br />
* [[Documentation/4.4/Modules/ImageLabelCombine|Image Label Combine]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ChangeTracker|Change Tracker]] extension)</small><br />
* [[Documentation/4.4/Extensions/IntensitySegmenter|Intensity Segmenter]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IntensitySegmenter|Intensity Segmenter]] extension)</small><br />
* [[Documentation/4.4/Modules/Isodose|Isodose]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter KUtil] <small>(scripted, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice] extension)</small><br />
* [[Documentation/4.4/Modules/LabelAddition|Label Addition]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/LabelExtraction|Label Extraction]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/LabelMapSmoothing|Label Map Smoothing]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/IASEM|Label Object Statistics]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Extensions/Reporting|Label To DICOMSEGConverter]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/Reporting|Reporting]] extension)</small><br />
* [[Documentation/4.4/Modules/LandmarkRegistration|Landmark Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/LAScarSegmenter|LAScar Segmenter]] <small>(cli, bundled in [[Documentation/4.4/Extensions/LAScarSegmenter|LAScar Segmenter]] extension)</small><br />
* [[Documentation/4.4/Modules/LASegmentationWorkflow|LASegmentation Workflow]] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [http://slicer.vmtk.org/ Level Set Segmentation] <small>(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)</small><br />
* [[Documentation/4.4/Extensions/LongitudinalPETCT|Longitudinal PETCT]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/LongitudinalPETCT|Longitudinal PETCT]] extension)</small><br />
* [[Documentation/4.4/Modules/Markups|Markups]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/MaskCreation|Mask Creation]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/MaskScalarVolume|Mask Scalar Volume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/MedianImageFilter|Median Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/MergeModels|Merge Models]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|Merge Stat With Fiber]] <small>(cli, bundled in [[Documentation/4.4/Extensions/DTIAtlasFiberAnalyzer|DTIAtlas Fiber Analyzer]] extension)</small><br />
* [[Documentation/4.4/Modules/MeshCompression|Mesh Compression]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics Mesh Statistics] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics Mesh Statistics Extension] extension)</small><br />
* [[Documentation/4.4/Extensions/MeshToLabelMap|Mesh To Label Map]] <small>(cli, bundled in [[Documentation/4.4/Extensions/MeshToLabelMap|Mesh To Label Map]] extension)</small><br />
* [[Documentation/4.4/Extensions/MultidimData|Metafile Importer]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/MultidimData|Multidim Data]] extension)</small><br />
* [[Documentation/4.4/Modules/ModelMaker|Model Maker]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Model Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/Models|Models]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/ModelToLabelMap|Model To Label Map]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/ModelToModelDistance|Model To Model Distance]] <small>(cli, bundled in [[Documentation/4.4/Extensions/ModelToModelDistance|Model To Model Distance]] extension)</small><br />
* [[Documentation/4.4/Modules/MultiplyScalarVolumes|Multiply Scalar Volumes]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/MultiVolumeExplorer|Multi Volume Explorer]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/MultiVolumeImporter|Multi Volume Importer]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/N4ITKBiasFieldCorrection|N4ITKBias Field Correction]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/NeedleFinder|Needle Finder]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/NeedleFinder|Needle Finder]] extension)</small><br />
* [[Documentation/4.4/Modules/NonGrowing|Non Growing]] <small>(cli, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/OpenIGTLinkIF|Open IGTLink IF]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/OpenIGTLinkRemote|Open IGTLink Remote]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/OrientScalarVolume|Orient Scalar Volume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/PathExplorer|Path Explorer]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Extensions/PBNRR|PBNRR]] <small>(cli, bundled in [[Documentation/4.4/Extensions/PBNRR|PBNRR]] extension)</small><br />
* [[Documentation/4.4/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] extension)</small><br />
* Perform Metric Test <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/PerkEvaluator|Perk Evaluator]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small><br />
* [[Documentation/4.4/Extensions/PET-IndiC|PETIndi C]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PET-IndiC|PET-Indi C]] extension)</small><br />
* [[Documentation/4.4/Modules/PETStandardUptakeValueComputation|PETStandard Uptake Value Computation]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/LongitudinalPETCT|PETSUVImage Maker]] <small>(cli, bundled in [[Documentation/4.4/Extensions/LongitudinalPETCT|Longitudinal PETCT]] extension)</small><br />
* [[Documentation/4.4/Extensions/PETTumorSegmentation|PETTumor Segmentation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PETTumorSegmentation|PETTumor Segmentation]] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Pivot Calibration]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/PkModeling|Pk Modeling]] <small>(cli, bundled in [[Documentation/4.4/Extensions/PkModeling|Pk Modeling]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Planar Image]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|plastimatch slicer bspline]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|plastimatch slicer landwarp]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Plastimatch Py]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Plm Register]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/PlusRemote|Plus Remote]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/PortPlacement|Port Placement]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PortPlacement|Port Placement]] extension)</small><br />
* [[Documentation/4.4/Modules/ProbeVolumeWithModel|Probe Volume With Model]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/PerkTutor|Python Metrics Calculator]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Q3DC Q3DC] <small>(scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Q3DC Q3DC] extension)</small><br />
* [[Documentation/4.4/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]] <small>(cli, bundled in [[Documentation/4.4/Extensions/PET-IndiC|PET-Indi C]] extension)</small><br />
* [[Documentation/4.4/Extensions/PET-IndiC|Quantitative Indices Tool]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/PET-IndiC|PET-Indi C]] extension)</small><br />
* [[Documentation/4.4/Modules/Reformat|Reformat]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Extensions/Reporting|Reporting]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/Reporting|Reporting]] extension)</small><br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/ResampleDTIlogEuclidean Resample DTIlog Euclidean] <small>(cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/ResampleDTIlogEuclidean Resample DTIlog Euclidean] extension)</small><br />
* [[Documentation/4.4/Modules/ResampleDTIVolume|Resample DTIVolume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/ResampleScalarVectorDWIVolume|Resample Scalar Vector DWIVolume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/ResectionVolume|Resection Volume]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/ResectionPlanner|Resection Planner]] extension)</small><br />
* [[Documentation/4.4/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/SampleData|Sample Data]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/ScarVisualization|Scar Visualization]] <small>(scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit] extension)</small><br />
* [[Documentation/4.4/Modules/SceneViews|Scene Views]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] <small>(cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SegmentationAidedRegistration Segmentation Aided Registration] extension)</small><br />
* [[Documentation/4.4/Modules/SegmentCAD|Segment CAD]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/OpenCAD|Open CAD]] extension)</small><br />
* [[Documentation/4.4/Extensions/MultidimData|Sequence Browser]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/MultidimData|Multidim Data]] extension)</small><br />
* [[Documentation/4.4/Extensions/MultidimData|Sequences]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/MultidimData|Multidim Data]] extension)</small><br />
* [[Documentation/4.4/Modules/SimpleFilters|Simple Filters]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] extension)</small><br />
* [[Documentation/4.4/Modules/SobolevSegmenter|Sobolev Segmenter]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SobolevSegmenter|Sobolev Segmenter]] extension)</small><br />
* [[Documentation/4.4/Extensions/IASEM|Spacing Aware Curvature Diffusion]] <small>(cli, bundled in [[Documentation/4.4/Extensions/IASEM|IASEM]] extension)</small><br />
* [[Documentation/4.4/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/Scoliosis|Scoliosis]] extension)</small><br />
* [[Documentation/4.4/Modules/SubjectHierarchy|Subject Hierarchy]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/SubtractScalarVolumes|Subtract Scalar Volumes]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/CMFreg|Surface Registration]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/CMFreg|CMFreg]] extension)</small><br />
* [[Documentation/4.4/Modules/SurfaceToolbox|Surface Toolbox]] <small>(scripted, built-in)</small><br />
* [[Documentation/4.4/Modules/SUVFactorCalculator|SUVFactor Calculator]] <small>(cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)</small><br />
* [[Documentation/4.4/Modules/SwissSkullStripper|Swiss Skull Stripper]] <small>(cli, bundled in [[Documentation/4.4/Extensions/SwissSkullStripper|Swiss Skull Stripper]] extension)</small><br />
* [[Documentation/4.4/Extensions/TCIABrowser|TCIABrowser]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/TCIABrowser|TCIABrowser]] extension)</small><br />
* [[Documentation/4.4/Modules/ThingiverseBrowser|Thingiverse Browser]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/ThingiverseBrowser|Thingiverse Browser]] extension)</small><br />
* [[Documentation/4.4/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/TrackerStabilizer|Tracker Stabilizer]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/TrackerStabilizer|Tracker Stabilizer]] extension)</small><br />
* [[Documentation/4.4/Modules/TractographyDisplay|Tractography Display]] <small>(loadable, built-in)</small><br />
* Tractography Interactive Seeding <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Transform Fusion]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/TransformRecorder|Transform Recorder]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small><br />
* [[Documentation/4.4/Modules/Transforms|Transforms]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/UKFTractography|UKFTractography]] <small>(cli, bundled in [[Documentation/4.4/Extensions/UKFTractography|UKFTractography]] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Ultrasound Snapshots]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/Units|Units]] <small>(loadable, built-in)</small><br />
* VBRAINSDemon Warp <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Modules/VectorToScalarVolume|Vector To Scalar Volume]] <small>(scripted, built-in)</small><br />
* [http://slicer.vmtk.org/ Vesselness Filtering] <small>(scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)</small><br />
* [[Documentation/4.4/Extensions/SlicerRT|Vff File Reader]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerRT|Slicer RT]] extension)</small><br />
* [[Documentation/4.4/Modules/ViewControllers|View Controllers]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Extensions/VolumeClip|Volume Clip With Model]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/VolumeClip|Volume Clip]] extension)</small><br />
* [[Documentation/4.4/Extensions/VolumeClip|Volume Clip With Roi]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/VolumeClip|Volume Clip]] extension)</small><br />
* [[Documentation/4.4/Modules/VolumeRendering|Volume Rendering]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/VolumeResliceDriver|Volume Reslice Driver]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/Volumes|Volumes]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] <small>(cli, built-in)</small><br />
* [[Documentation/4.4/Extensions/SlicerIGT|Watchdog]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/SlicerIGT|Slicer IGT]] extension)</small><br />
* [[Documentation/4.4/Modules/Welcome|Welcome]] <small>(loadable, built-in)</small><br />
* [[Documentation/4.4/Extensions/WindowLevelEffect|Window Level Effect]] <small>(scripted, bundled in [[Documentation/4.4/Extensions/WindowLevelEffect|Window Level Effect]] extension)</small><br />
* [[Documentation/4.4/Modules/WorkflowSegmentation|Workflow Segmentation]] <small>(loadable, bundled in [[Documentation/4.4/Extensions/PerkTutor|Perk Tutor]] extension)</small></div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12554Modules:ABC-Documentation-3.52010-03-18T21:11:15Z<p>Prastawa: </p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
<br />
{|<br />
|[[Image:ABC_Slicer3.png|thumb|280px|Interface in Slicer 3]]<br />
|[[Image:ABC_out3d.png|thumb|280px|3D visualization of the result]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module is not designed for interactive use. It may take up to 30 minutes to 1 hour for processing a dataset. Speed-ups are possible by modifying the advanced parameters and disabling the bias correction and deformable registration of the atlas.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
{|<br />
|-<br />
|* '''Input Panel'''<br />
Specify the input images representing the different modalities of the same subject (up to five). First image in the list is the reference image space. All other images are registered to first image. Intra-subject registration can be disabled in the advanced setting by choosing the identity transform type.<br />
|[[Image:abc-slicer-inputs.png|thumb|350px|Input panel]]<br />
<br />
|-<br />
|* '''Atlas Panel'''<br />
Specify the atlas information. The atlas is represented as a directory that contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha)<br />
The atlas orientation specifies the code for the different axes ([R]ight-[L]eft, [A]nterior-[P]osterior, [I]nferior-[S]uperior): RAI, ASR, LPS, etc. If the image orientation matrix is embedded in the image, you can simply specify "file" as the orientation code.<br />
The prior weight can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers. You must specify the same amount of numbers as the amount of priors in the atlas directory.<br />
|[[Image:abc-slicer-atlas.png|thumb|350px|Atlas information panel]]<br />
<br />
|-<br />
|* '''Output Panel'''<br />
Specify where to store the output files (optional), this includes the segmentation label image, and bias corrected images.<br />
|[[Image:abc-slicer-outputs.png|thumb|350px|Output panel]]<br />
<br />
|-<br />
|* '''Advanced Panel'''<br />
Advanced parameters for registration and bias correction. You can adjust the type of linear transformation for the alignment of the intra-subject modalities and the subject-template. Bias correction polynomial degree adjust the severity of the bias field in your images, and this part can be disabled by setting it to zero. The amount of deformation of the atlas is controlled by the number of iterations in the fluid flow, and setting it to zero will disable the atlas deformation component.<br />
|[[Image:abc-slicer-advanced.png|thumb|350px|Advanced panel]]<br />
<br />
<br />
|}<br />
<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
[http://www.itk.org ITK]<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://www.nitrc.org/tracker/?group_id=297 link] to the bug tracker at NITRC. <br />
<br />
<br />
===Source code & documentation===<br />
<br />
Available at [http://www.nitrc.org/projects/abc NITRC]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
<br />
<br />
===References===</div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12186Modules:ABC-Documentation-3.52010-02-09T18:07:22Z<p>Prastawa: </p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
(Documentation in progress)<br />
<br />
{|<br />
|[[Image:ABC_Slicer3.png|thumb|280px|Interface in Slicer 3]]<br />
|[[Image:ABC_out3d.png|thumb|280px|3D visualization of the result]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module is not designed for interactive use. It may take up to 30 minutes to 1 hour for processing a dataset. Speed-ups are possible by modifying the advanced parameters and disabling the bias correction and deformable registration of the atlas.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
{|<br />
|-<br />
|* '''Input Panel'''<br />
Specify the input images representing the different modalities of the same subject (up to five). First image in the list is the reference image space. All other images are registered to first image.<br />
|[[Image:abc-slicer-inputs.png|thumb|350px|Input panel]]<br />
<br />
|-<br />
|* '''Atlas Panel'''<br />
Specify the atlas information. The atlas is represented as a directory that contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha)<br />
The atlas orientation specifies the code for the different axes ([R]ight-[L]eft, [A]nterior-[P]osterior, [I]nferior-[S]uperior): RAI, ASR, LPS, etc. If the image orientation matrix is embedded in the image, you can simply specify "file" as the orientation code.<br />
The prior weight can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers. You must specify the same amount of numbers as the amount of priors in the atlas directory.<br />
|[[Image:abc-slicer-atlas.png|thumb|350px|Atlas information panel]]<br />
<br />
|-<br />
|* '''Output Panel'''<br />
Specify where to store the output files (optional), this includes the segmentation label image, and bias corrected images.<br />
|[[Image:abc-slicer-outputs.png|thumb|350px|Output panel]]<br />
<br />
|-<br />
|* '''Advanced Panel'''<br />
Advanced parameters for registration and bias correction. You can adjust the type of linear transformation for the alignment of the intra-subject modalities and the subject-template. Bias correction polynomial degree adjust the severity of the bias field in your images, and this part can be disabled by setting it to zero. The amount of deformation of the atlas is controlled by the number of iterations in the fluid flow, and setting it to zero will disable the atlas deformation component.<br />
|[[Image:abc-slicer-advanced.png|thumb|350px|Advanced panel]]<br />
<br />
<br />
|}<br />
<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
None<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://www.nitrc.org/tracker/?group_id=297 link] to the bug tracker at NITRC. <br />
<br />
<br />
===Source code & documentation===<br />
<br />
Available at [http://www.nitrc.org/projects/abc NITRC]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
<br />
<br />
===References===</div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12185Modules:ABC-Documentation-3.52010-02-09T18:06:07Z<p>Prastawa: </p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
(Documentation in progress)<br />
<br />
{|<br />
|[[Image:ABC_Slicer3.png|thumb|280px|Interface in Slicer 3]]<br />
|[[Image:ABC_out3d.png|thumb|280px|3D visualization of the result]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module is not designed for interactive use. It may take up to 30 minutes to 1 hour for processing a dataset. Speed-ups are possible by modifying the advanced parameters and disabling the bias correction and deformable registration of the atlas.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
{|<br />
|-<br />
|* '''Input Panel'''<br />
Specify the input images representing the different modalities of the same subject (up to five). First image in the list is the reference image space. All other images are registered to first image.<br />
|[[Image:abc-slicer-inputs.png|thumb|250px|Input panel]]<br />
<br />
|-<br />
|* '''Atlas Panel'''<br />
Specify the atlas information. The atlas is represented as a directory that contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha)<br />
The atlas orientation specifies the code for the different axes ([R]ight-[L]eft, [A]nterior-[P]osterior, [I]nferior-[S]uperior): RAI, ASR, LPS, etc. If the image orientation matrix is embedded in the image, you can simply specify "file" as the orientation code.<br />
The prior weight can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers. You must specify the same amount of numbers as the amount of priors in the atlas directory.<br />
|[[Image:abc-slicer-atlas.png|thumb|250px|Atlas information panel]]<br />
<br />
|-<br />
|* '''Output Panel'''<br />
Specify where to store the output files (optional), this includes the segmentation label image, and bias corrected images.<br />
|[[Image:abc-slicer-outputs.png|thumb|250px|Output panel]]<br />
<br />
|-<br />
|* '''Advanced Panel'''<br />
Advanced parameters for registration and bias correction. You can adjust the type of linear transformation for the alignment of the intra-subject modalities and the subject-template. Bias correction polynomial degree adjust the severity of the bias field in your images, and this part can be disabled by setting it to zero. The amount of deformation of the atlas is controlled by the number of iterations in the fluid flow, and setting it to zero will disable the atlas deformation component.<br />
|[[Image:abc-slicer-advanced.png|thumb|250px|Advanced panel]]<br />
<br />
<br />
|}<br />
<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
None<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://www.nitrc.org/tracker/?group_id=297 link] to the bug tracker at NITRC. <br />
<br />
<br />
===Source code & documentation===<br />
<br />
Available at [http://www.nitrc.org/projects/abc NITRC]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
<br />
<br />
===References===</div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12184Modules:ABC-Documentation-3.52010-02-09T18:03:46Z<p>Prastawa: </p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
(Documentation in progress)<br />
<br />
{|<br />
|[[Image:ABC_Slicer3.png|thumb|280px|Interface in Slicer 3]]<br />
|[[Image:ABC_out3d.png|thumb|280px|3D visualization of the result]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
The software is designed and tested for healthy brain MRI (pediatric - adult).<br />
<br />
The processing involved in the module is not designed for interactive use. It may take up to 30 minutes to 1 hour for processing a dataset. Speed-ups are possible by modifying the advanced parameters and disabling the bias correction and deformable registration of the atlas.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
{|<br />
|-<br />
|* '''Input Panel'''<br />
Specify the input images representing the different modalities of the same subject (up to five). First image in the list is the reference image space. All other images are registered to first image.<br />
|[[Image:abc-slicer-inputs.png|thumb|250px|Input panel]]<br />
<br />
|-<br />
|* '''Atlas Panel'''<br />
Specify the atlas information. The atlas is represented as a directory that contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha)<br />
The atlas orientation specifies the code for the different axes ([R]ight-[L]eft, [A]nterior-[P]osterior, [I]nferior-[S]uperior): RAI, ASR, LPS, etc. If the image orientation matrix is embedded in the image, you can simply specify "file" as the orientation code.<br />
The prior weight can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through space separated numbers. You must specify the same amount of numbers as the amount of priors in the atlas directory.<br />
|[[Image:abc-slicer-atlas.png|thumb|250px|Atlas information panel]]<br />
<br />
|-<br />
|* '''Output Panel'''<br />
Specify where to store the output files (optional), this includes the segmentation label image, and bias corrected images.<br />
|[[Image:abc-slicer-outputs.png|thumb|250px|Output panel]]<br />
<br />
|-<br />
|* '''Advanced Panel'''<br />
Advanced parameters for registration and bias correction. You can adjust the type of linear transformation for the alignment of the intra-subject modalities and the subject-template. Bias correction polynomial degree adjust the severity of the bias field in your images, and can this part can be disabled by setting it to zero. The amount of deformation of the atlas is controlled by the number of iterations in the fluid flow, and setting it to zero will disable the atlas deformation component.<br />
|[[Image:abc-slicer-advanced.png|thumb|250px|Advanced panel]]<br />
<br />
<br />
|}<br />
<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
None<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://www.nitrc.org/tracker/?group_id=297 link] to the bug tracker at NITRC. <br />
<br />
<br />
===Source code & documentation===<br />
<br />
Available at [http://www.nitrc.org/projects/abc]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
<br />
<br />
===References===</div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12183Modules:ABC-Documentation-3.52010-02-09T17:54:15Z<p>Prastawa: </p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
(Documentation in progress)<br />
<br />
{|<br />
|[[Image:ABC_Slicer3.png|thumb|280px|Interface in Slicer 3]]<br />
|[[Image:ABC_out3d.png|thumb|280px|3D visualization of the result]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|<br />
|-<br />
|* '''Input Panel'''<br />
Input images. First image in the list is the reference image space. All other images are registered to first image.<br />
|[[Image:abc-slicer-inputs.png|thumb|250px|Input panel]]<br />
<br />
|-<br />
|* '''Atlas Panel'''<br />
Atlas information.<br />
Atlas directory contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha)<br />
Orientation: RAI, ASR, LPS, etc<br />
Prior weight adjustments: space separated numbers, must be the same number as number of priors.<br />
|[[Image:abc-slicer-atlas.png|thumb|250px|Atlas information panel]]<br />
<br />
|-<br />
|* '''Output Panel'''<br />
Specify where to store output files (optional). Segmentation label image, and bias corrected image.<br />
|[[Image:abc-slicer-outputs.png|thumb|250px|Output panel]]<br />
<br />
|-<br />
|* '''Advanced Panel'''<br />
Advanced parameters<br />
|[[Image:abc-slicer-advanced.png|thumb|250px|Advanced panel]]<br />
<br />
<br />
|}<br />
<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
None<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://www.nitrc.org/tracker/?group_id=297 link] to the bug tracker at NITRC. <br />
<br />
<br />
===Source code & documentation===<br />
<br />
Available at [http://www.nitrc.org/projects/abc]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
<br />
<br />
===References===</div>Prastawahttps://www.slicer.org/w/index.php?title=File:ABC_out3d.png&diff=12182File:ABC out3d.png2010-02-09T17:51:41Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12181Modules:ABC-Documentation-3.52010-02-09T17:42:42Z<p>Prastawa: </p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
{|<br />
|[[Image:ABC_Slicer3.png|thumb|280px|Interface in Slicer 3]]<br />
|[[Image:ABC_out3d.png|thumb|280px|3D visualization of the result]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|<br />
|-<br />
* '''Input Panel'''<br />
Input images. First image in the list is the reference image space. All other images are registered to first image.<br />
|-<br />
[[Image:abc-slicer-inputs.png|thumb|250px|Input panel]]<br />
|}<br />
<br />
{|<br />
|-<br />
* '''Atlas Panel'''<br />
Atlas information.<br />
Atlas directory contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha)<br />
Orientation: RAI, ASR, LPS, etc<br />
Prior weight adjustments: space separated numbers, must be the same number as number of priors.<br />
|-<br />
[[Image:abc-slicer-atlas.png|thumb|250px|Atlas information panel]]<br />
|}<br />
<br />
{|<br />
|-<br />
* '''Output Panel'''<br />
Specify where to store output files (optional). Segmentation label image, and bias corrected image.<br />
|-<br />
[[Image:abc-slicer-outputs.png|thumb|250px|Output panel]]<br />
|}<br />
<br />
[[Image:abc-slicer-advanced.png|thumb|250px|Advanced panel]]<br />
<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
None<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://www.nitrc.org/tracker/?group_id=297 link] to the bug tracker at NITRC. <br />
<br />
<br />
===Source code & documentation===<br />
<br />
Available at [http://www.nitrc.org/projects/abc]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
<br />
<br />
===References===</div>Prastawahttps://www.slicer.org/w/index.php?title=File:Abc-slicer-advanced.png&diff=12180File:Abc-slicer-advanced.png2010-02-09T17:18:47Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=File:Abc-slicer-outputs.png&diff=12179File:Abc-slicer-outputs.png2010-02-09T17:18:24Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=File:Abc-slicer-atlas.png&diff=12178File:Abc-slicer-atlas.png2010-02-09T17:17:53Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=File:Abc-slicer-inputs.png&diff=12177File:Abc-slicer-inputs.png2010-02-09T17:17:32Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=File:ABC_Slicer3.png&diff=12176File:ABC Slicer3.png2010-02-09T17:15:03Z<p>Prastawa: </p>
<hr />
<div></div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12175Modules:ABC-Documentation-3.52010-02-09T17:14:37Z<p>Prastawa: </p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
{|<br />
|[[Image:ABC_Slicer3.png|thumb|280px|Interface in Slicer 3]]<br />
|[[Image:ABC_out3d.png|thumb|280px|3D visualization of the result]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
[[Image:abc-slicer-inputs.png|thumb|250px|Input panel]]<br />
<br />
[[Image:abc-slicer-atlas.png|thumb|250px|Atlas information panel]]<br />
<br />
[[Image:abc-slicer-outputs.png|thumb|250px|Output panel]]<br />
<br />
[[Image:abc-slicer-advanced.png|thumb|250px|Advanced panel]]<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following links for your module:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Prastawahttps://www.slicer.org/w/index.php?title=Modules:ABC-Documentation-3.5&diff=12174Modules:ABC-Documentation-3.52010-02-09T17:06:15Z<p>Prastawa: Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Atlas Based Classification=== Atlas Based C…'</p>
<hr />
<div>[[Documentation-3.5|Return to Slicer 3.5 Documentation]]<br />
<br />
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Atlas Based Classification===<br />
Atlas Based Classification<br />
<br />
{|<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Marcel Prastawa, Utah<br />
* Guido Gerig, Utah<br />
* Contact: Marcel Prastawa, prastawa@sci.utah.edu<br />
<br />
===Module Description===<br />
ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following links for your module:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Prastawahttps://www.slicer.org/w/index.php?title=Documentation/3.5&diff=12173Documentation/3.52010-02-09T17:00:35Z<p>Prastawa: /* Listing of available plug-ins */</p>
<hr />
<div>=Main GUI=<br />
<br />
==Main GUI==<br />
*[[Modules:MainApplicationGUI-Documentation-3.5| Main Application GUI]] <br />
*[[Modules:EventBindings-3.5| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.5| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.5| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.5| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.5| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.5| Extensions Management Wizard]] (Terry G.)<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]]<br />
*See [[Documentation-3.5#Requirements for Modules|below]] for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)<br />
<br />
= Requirements for Modules =<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. <br />
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.<br />
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. <br />
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)<br />
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Rons rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules new to 3.5=<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume)<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda)<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda)<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov)<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev)<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov)<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin)<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett)<br />
<br />
=List of pre-existing Modules=<br />
===Core===<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre)<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.5|Register Images Revised]] (Casey Goodlett, Stephen Aylward)<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett)<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek)<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal)<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja Fernandez)<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal)<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal)<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal)<br />
*[[Modules:ROISelect-Documentation-3.5|ROI Select]] (Lauren O'Donnell)<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) <br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin)<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] ( )<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) <br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)<br />
*Grayscale Model Maker (Bill Lorensen)<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.<br />
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of available plug-ins===<br />
* VMTK (Daniel Haehn)<br />
**You need to install the [[Modules:VMTKSlicerModule|VmtkSlicerModule]] to run any of the other three.<br />
**[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface<br />
**[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms<br />
**[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] - providing vessel enhancement filters to highlight vasculature or tubular structures<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EM DTI Clustering]] (Mahnaz Maddah)<br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|Label Diameter Estimation]] (Andriy Fedorov)<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] (Marcel Prastawa)<br />
<br />
===Extensions Contact List===<br />
This is a first pass list of extension authors; more to come!<br />
<br />
*EMFiberClusteringModule Mahnaz Maddah maddah @nospam@ ge.com<br />
*BRAINSROIAuto Greg Harris gregory-harris @nospam@ uiowa.edu<br />
*Bubble Maker Carlos Mendoza carlos.sanchez.medoza @nospam@ gmail.com<br />
*Hammer Registration Dinggang Shen dgshen @nospam@ med.unc.edu<br />
*Lupus Lesion Mark Scully mscully @nospam@ mrn.org<br />
*VmtkSlicerModule Daniel Haehn haehn @nospam@ bwh.harvard.edu<br />
*Vmtkin3DSlicer Daniel Haehn<br />
*BRAINSFit Eun Young Kim eunyoung-kim @nospam@ uiowa.edu<br />
*ARCTIC Cedric Mathieu ced.mathieu @nospam@ gmail.com</div>Prastawa