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	<id>https://www.na-mic.org/w/index.php?action=history&amp;feed=atom&amp;title=Projects%3ASlicerFAQ%3ARegistrationRerun</id>
	<title>Projects:SlicerFAQ:RegistrationRerun - Revision history</title>
	<link rel="self" type="application/atom+xml" href="https://www.na-mic.org/w/index.php?action=history&amp;feed=atom&amp;title=Projects%3ASlicerFAQ%3ARegistrationRerun"/>
	<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;action=history"/>
	<updated>2026-05-19T06:30:16Z</updated>
	<subtitle>Revision history for this page on the wiki</subtitle>
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	<entry>
		<id>https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=97060&amp;oldid=prev</id>
		<title>Grundlett: Text replacement - &quot;http://www.slicer.org/slicerWiki/index.php/&quot; to &quot;https://www.slicer.org/wiki/&quot;</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=97060&amp;oldid=prev"/>
		<updated>2017-07-10T17:01:52Z</updated>

		<summary type="html">&lt;p&gt;Text replacement - &amp;quot;http://www.slicer.org/slicerWiki/index.php/&amp;quot; to &amp;quot;https://www.slicer.org/wiki/&amp;quot;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
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				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 17:01, 10 July 2017&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l5&quot; &gt;Line 5:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 5:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Fix:'''  Your first try however should be to obtain a better automated registration by changing some of to re-run the automated registration, while changing either initial position, initialization method, parameters or the method/module used. Most helpful to determine a good secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the remedies:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Fix:'''  Your first try however should be to obtain a better automated registration by changing some of to re-run the automated registration, while changing either initial position, initialization method, parameters or the method/module used. Most helpful to determine a good secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the remedies:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too much initial misalignment:''' particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:BRAINSFit BRAINSfit] or [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too much initial misalignment:''' particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:BRAINSFit BRAINSfit] or [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''insufficient detail:''' consider increasing the number of sample points used for the registration, depending on time/speed constraints, increase to 5-10% of image size.  &lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''insufficient detail:''' consider increasing the number of sample points used for the registration, depending on time/speed constraints, increase to 5-10% of image size.  &lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''insufficient contrast:''' consider adjusting the ''Histogram Bins'' (where avail.) to tune the algorithm to weigh small intensity variations more or less heavily&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''insufficient contrast:''' consider adjusting the ''Histogram Bins'' (where avail.) to tune the algorithm to weigh small intensity variations more or less heavily&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''strong anisotropy:''' if one or both of the images have strong voxel anisotropy of ratios 5 or more, rotational alignment may become increasingly difficult for an automated method. Consider increasing the sample points and reducing the ''Histogram Bins''.  In extreme cases you may need to switch to a manual or fiducial-based approach&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''strong anisotropy:''' if one or both of the images have strong voxel anisotropy of ratios 5 or more, rotational alignment may become increasingly difficult for an automated method. Consider increasing the sample points and reducing the ''Histogram Bins''.  In extreme cases you may need to switch to a manual or fiducial-based approach&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''distracting image content:''' pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:BRAINSFit BRAINSFit], [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''distracting image content:''' pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:BRAINSFit BRAINSFit], [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too many/too few DOF''': the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:BRAINSFit BRAINSfit] and [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too many/too few DOF''': the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:BRAINSFit BRAINSfit] and [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''inappropriate algorithm:''' there are many different registration methods available in Slicer. Have a look at the [&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;http&lt;/del&gt;://www.slicer.org/&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;slicerWiki/index.php&lt;/del&gt;/Slicer3:Registration '''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''inappropriate algorithm:''' there are many different registration methods available in Slicer. Have a look at the [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;https&lt;/ins&gt;://www.slicer.org/&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;wiki&lt;/ins&gt;/Slicer3:Registration '''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust|here]].&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust|here]].&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Grundlett</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60780&amp;oldid=prev</id>
		<title>Meier at 20:23, 11 November 2010</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60780&amp;oldid=prev"/>
		<updated>2010-11-11T20:23:49Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
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				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 20:23, 11 November 2010&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l12&quot; &gt;Line 12:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 12:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too many/too few DOF''': the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too many/too few DOF''': the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''inappropriate algorithm:''' there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration '''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''inappropriate algorithm:''' there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration '''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust here]].&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;|&lt;/ins&gt;here]].&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Meier</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60779&amp;oldid=prev</id>
		<title>Meier: /* Automated Registration Result is Insufficient */</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60779&amp;oldid=prev"/>
		<updated>2010-11-11T20:23:23Z</updated>

		<summary type="html">&lt;p&gt;&lt;span dir=&quot;auto&quot;&gt;&lt;span class=&quot;autocomment&quot;&gt;Automated Registration Result is Insufficient&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 20:23, 11 November 2010&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l11&quot; &gt;Line 11:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 11:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''distracting image content:''' pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''distracting image content:''' pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too many/too few DOF''': the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''too many/too few DOF''': the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''inappropriate algorithm:''' there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''inappropriate algorithm:''' there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration &lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'&lt;/ins&gt;''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust here]].&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust here]].&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Meier</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60778&amp;oldid=prev</id>
		<title>Meier: /* Automated Registration Result is Insufficient */</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60778&amp;oldid=prev"/>
		<updated>2010-11-11T20:22:55Z</updated>

		<summary type="html">&lt;p&gt;&lt;span dir=&quot;auto&quot;&gt;&lt;span class=&quot;autocomment&quot;&gt;Automated Registration Result is Insufficient&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 20:22, 11 November 2010&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l4&quot; &gt;Line 4:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 4:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Problem:''' automated registration provides an alignment that is insufficient, possibly worse than the initial position&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Problem:''' automated registration provides an alignment that is insufficient, possibly worse than the initial position&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Fix:'''  Your first try however should be to obtain a better automated registration by changing some of to re-run the automated registration, while changing either initial position, initialization method, parameters or the method/module used. &lt;del class=&quot;diffchange diffchange-inline&quot;&gt;Some guidelines for modification:&lt;/del&gt;&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Fix:'''  Your first try however should be to obtain a better automated registration by changing some of to re-run the automated registration, while changing either initial position, initialization method, parameters or the method/module used. &lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;Most &lt;/ins&gt;helpful to determine &lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;a good &lt;/ins&gt;secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the &lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;remedies&lt;/ins&gt;:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;**most &lt;/del&gt;helpful to determine &lt;del class=&quot;diffchange diffchange-inline&quot;&gt;the &lt;/del&gt;secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the &lt;del class=&quot;diffchange diffchange-inline&quot;&gt;remedy&lt;/del&gt;:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''&lt;/ins&gt;too much initial misalignment:&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;''' &lt;/ins&gt;particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**too much initial misalignment: particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''&lt;/ins&gt;insufficient detail:&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;''' &lt;/ins&gt;consider increasing the number of sample points used for the registration, depending on time/speed constraints, increase to 5-10% of image size.  &lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**insufficient detail: consider increasing the number of sample points used for the registration, depending on time/speed constraints, increase to 5-10% of image size.  &lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''&lt;/ins&gt;insufficient contrast:&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;''' &lt;/ins&gt;consider adjusting the ''Histogram Bins'' (where avail.) to tune the algorithm to weigh small intensity variations more or less heavily&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**insufficient contrast: consider adjusting the ''Histogram Bins'' (where avail.) to tune the algorithm to weigh small intensity variations more or less heavily&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''&lt;/ins&gt;strong anisotropy:&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;''' &lt;/ins&gt;if one or both of the images have strong voxel anisotropy of ratios 5 or more, rotational alignment may become increasingly difficult for an automated method. Consider increasing the sample points and reducing the ''Histogram Bins''.  In extreme cases you may need to switch to a manual or fiducial-based approach&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**strong anisotropy: if one or both of the images have strong voxel anisotropy of ratios 5 or more, rotational alignment may become increasingly difficult for an automated method. Consider increasing the sample points and reducing the ''Histogram Bins''.  In extreme cases you may need to switch to a manual or fiducial-based approach&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''&lt;/ins&gt;distracting image content:&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;''' &lt;/ins&gt;pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**distracting image content: pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''&lt;/ins&gt;too many/too few DOF&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''&lt;/ins&gt;: the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**too many/too few DOF: the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;'''inappropriate &lt;/ins&gt;algorithm:&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;''' &lt;/ins&gt;there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;inapropriate &lt;/del&gt;algorithm: there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust here]].&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust here]].&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Meier</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60775&amp;oldid=prev</id>
		<title>Meier at 20:21, 11 November 2010</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60775&amp;oldid=prev"/>
		<updated>2010-11-11T20:21:25Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
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				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 20:21, 11 November 2010&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l4&quot; &gt;Line 4:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 4:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Problem:''' automated registration provides an alignment that is insufficient, possibly worse than the initial position&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Problem:''' automated registration provides an alignment that is insufficient, possibly worse than the initial position&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Fix:'''  Your first try however should be to obtain a better automated registration by changing some of &lt;del class=&quot;diffchange diffchange-inline&quot;&gt;t**'''Rerun Automated Registration'''&lt;/del&gt;:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;*'''Fix:'''  Your first try however should be to obtain a better automated registration by changing some of &lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;to re-run the automated registration, while changing either initial position, initialization method, parameters or the method/module used. Some guidelines for modification&lt;/ins&gt;:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**most helpful to determine the secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the remedy:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**most helpful to determine the secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the remedy:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**too much initial misalignment: particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**too much initial misalignment: particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**insufficient detail: consider increasing the number of sample points used for the registration, depending on time/speed constraints, increase to 5-10% of image size.  &lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**insufficient detail: consider increasing the number of sample points used for the registration, depending on time/speed constraints, increase to 5-10% of image size.  &lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**insufficient contrast: consider adjusting the ''Histogram Bins'' (where avail.) to tune the algorithm to weigh small intensity variations more or less heavily&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**insufficient contrast: consider adjusting the ''Histogram Bins'' (where avail.) to tune the algorithm to weigh small intensity variations more or less heavily&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**strong anisotropy: if one or both of the images have strong voxel anisotropy of ratios 5 or more, rotational alignment may become increasingly difficult for an automated method. Consider increasing the sample points and reducing the ''Histogram Bins''.  In extreme cases you may need to switch to a manual or fiducial-based approach&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**strong anisotropy: if one or both of the images have strong voxel anisotropy of ratios 5 or more, rotational alignment may become increasingly difficult for an automated method. Consider increasing the sample points and reducing the ''Histogram Bins''.  In extreme cases you may need to switch to a manual or fiducial-based approach&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**distracting image content: pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**distracting image content: pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**too many/too few DOF: the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**too many/too few DOF: the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**inapropriate algorithm: there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**inapropriate algorithm: there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/del&gt;**you can adjust/correct an obtained registration manually, within limits&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;. As &lt;/del&gt;outlined [here].&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**you can adjust/correct an obtained registration manually, within limits&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;, as &lt;/ins&gt;outlined [&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;[Projects:SlicerFAQ:RegistrationAdjust &lt;/ins&gt;here&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;]&lt;/ins&gt;].&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Meier</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60774&amp;oldid=prev</id>
		<title>Meier at 20:19, 11 November 2010</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60774&amp;oldid=prev"/>
		<updated>2010-11-11T20:19:22Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 20:19, 11 November 2010&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l1&quot; &gt;Line 1:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 1:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;**'''Rerun Automated Registration''':&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*[[Projects:SlicerFAQ|back to Slicer FAQ]]&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt; &lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;= Automated Registration Result is Insufficient  = &lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*'''Problem:''' automated registration provides an alignment that is insufficient, possibly worse than the initial position&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*'''Fix:'''  Your first try however should be to obtain a better automated registration by changing some of t&lt;/ins&gt;**'''Rerun Automated Registration''':&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***most helpful to determine the secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the remedy:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***most helpful to determine the secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the remedy:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***too much initial misalignment: particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***too much initial misalignment: particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l8&quot; &gt;Line 8:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 13:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***too many/too few DOF: the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***too many/too few DOF: the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***inapropriate algorithm: there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;***inapropriate algorithm: there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;***you can adjust/correct an obtained registration manually, within limits. As outlined [here].&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Meier</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60773&amp;oldid=prev</id>
		<title>Meier: Created page with '**'''Rerun Automated Registration''': ***most helpful to determine the secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and th…'</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=Projects:SlicerFAQ:RegistrationRerun&amp;diff=60773&amp;oldid=prev"/>
		<updated>2010-11-11T20:16:42Z</updated>

		<summary type="html">&lt;p&gt;Created page with &amp;#039;**&amp;#039;&amp;#039;&amp;#039;Rerun Automated Registration&amp;#039;&amp;#039;&amp;#039;: ***most helpful to determine the secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and th…&amp;#039;&lt;/p&gt;
&lt;p&gt;&lt;b&gt;New page&lt;/b&gt;&lt;/p&gt;&lt;div&gt;**'''Rerun Automated Registration''':&lt;br /&gt;
***most helpful to determine the secondary approach is to know why the first one was likely to fail. Below a list of possible reasons and the remedy:&lt;br /&gt;
***too much initial misalignment: particularly rotation can be difficult for automated registration to capture. If the two images have strong rotational misalignment, consider A) one of the initialization options (e.g. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated]), B) a manual initial alignment using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and then use this as initialization input&lt;br /&gt;
***insufficient detail: consider increasing the number of sample points used for the registration, depending on time/speed constraints, increase to 5-10% of image size. &lt;br /&gt;
***insufficient contrast: consider adjusting the ''Histogram Bins'' (where avail.) to tune the algorithm to weigh small intensity variations more or less heavily&lt;br /&gt;
***strong anisotropy: if one or both of the images have strong voxel anisotropy of ratios 5 or more, rotational alignment may become increasingly difficult for an automated method. Consider increasing the sample points and reducing the ''Histogram Bins''.  In extreme cases you may need to switch to a manual or fiducial-based approach&lt;br /&gt;
***distracting image content: pathology, strong edges, clipped FOV with image content at the border of the image can easily dominate the cost function driving the registration algorithm. '''Masking''' is a powerful remedy for this problem: create a mask (binary labelmap/segmentation) that excludes the distracting parts and includes only those areas of the image where matching content exists. This requires one of the modules that supports masking input, such as: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 ExpertAutomated], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Multi Resolution]. Next best thing to use with modules that do not support masking is to mask the image manually and create a temporary masked image where the excluded content is set to 0 intensity; the ''Mask Volume'' module performs this task&lt;br /&gt;
***too many/too few DOF: the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.&lt;br /&gt;
***inapropriate algorithm: there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration ''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.&lt;/div&gt;</summary>
		<author><name>Meier</name></author>
		
	</entry>
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