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Documentation.Visualization History
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The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two scripts: tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate vtk outputs with different attributes. In fact, they rely on the meshcluster and the meshglm functions of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]], respectively.
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The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two scripts: tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Documentation/tsa_stats_glm|tsa_stats_glm]]. These two scripts generate vtk outputs with different attributes. In fact, they rely on the meshcluster and the meshglm functions of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]], respectively.
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Another way of displaying the tract is to use this script. To do so, [[http://www.imagemagick.org/Imagemagick]] as well as [[http://www.vtk.org/vtk]] must be installed on your computed.
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Another way of displaying the tract is to use these two scripts:
# [[http://dti-tk.sourceforge.net/pmwiki/uploads/Documentation/display_allmesh/picstmap_v2.py| picstmap_v2.py]]
#[[http://dti-tk.sourceforge.net/pmwiki/uploads/Documentation/display_allmesh/tsafig.bash| tsafig.bash]]
which are combined here
[[http://dti-tk.sourceforge.net/pmwiki/uploads/Documentation/display_allmesh/make_sshots.sh| make_sshots.sh]]
To do so, [[http://www.imagemagick.org/|Imagemagick]], [[http://www.vtk.org/|vtk]] and [[http://www.python.org/|python]] must be installed on your computer.
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!! Displaying all the tracts
Another way of displaying the tract is to use this script. To do so, [[http://www.imagemagick.org/|Imagemagick]] as well as [[http://www.vtk.org/|vtk]] must be installed on your computed.
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These results can be simply visualized with [[http://www.paraview.org/|paraview]], as it is the case below:
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%center% Results obtained from a study comparing an adult male population to an adult female population. Here, the right CST is represented using paraview. The scale shows values from the t-test
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%center% Difference in FA between men and women in the right corticospinal tract. T-values are displayed showing increased FA values in the inferior part of the CST. The significant region is represented in black (result obtained with meshcluster, left) and outlined in black (results obtained with meshglm, right)
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%center%%width=550px%Attach:display_meshglm_meshcluster.jpg to:
%center%%width=750px%Attach:display_meshglm_meshcluster.jpg
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%center%%width=550px%Attach:display_meshglm_meshcluster.jpeg to:
%center%%width=550px%Attach:display_meshglm_meshcluster.jpg
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%center%%width=550px%Attach:right_cst_meshcluster.png to:
%center%%width=550px%Attach:display_meshglm_meshcluster.jpeg
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* [type] is mean or maxFA (see [[Documentation.TsaCasual|Sampling values over all the subjects]] to:
* [type] is mean or maxFA (see [[Documentation.TsaCasual|Sampling values over all the subjects]]) Deleted line 20:
!!Comprehensive representation
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The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two scripts: tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate outputs of different format, as they rely on the meshcluster and the meshglm functions of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]], respectively.
#from tsa_stats. For each of the tracts, there are two main outputs: [file_name].med.maxFA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_pos.FA.vtk (or [file_name].med.maxFA.clusters.ttst.[threshold]_neg.FA.vtk if you chose the
#from group_tsa_stats: Two main outputs will result from the analysis: [file_name].med.maxFA.vtk and [file_name]_edges.med.maxFA.clusters.[feature]_[threshold].vtk
to:
The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two scripts: tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate vtk outputs with different attributes. In fact, they rely on the meshcluster and the meshglm functions of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]], respectively.
#outputs obtained with tsa_stats. For each of the tracts, there are two outputs: [file_name].med.[type].vtk and [file_name].med.[type].clusters.ttst.[threshold]_pos.[feature].vtk (or [file_name].med.[type].clusters.ttst.[threshold]_neg.[feature].vtk)
#outputs obtained with group_tsa_stats: Two main outputs will result from the analysis: [file_name].med.[type].vtk and [file_name]_edges.med.[type].clusters.[feature]_[threshold].vtk
where:
* [type] is mean or maxFA (see [[Documentation.TsaCasual|Sampling values over all the subjects]]
* [threshold] is the p-value threshold use in the statistical analysis
* [feature] is the feature analyzed (FA, ADC, for example)
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#from tsa_stats. For each of the tracts, there are two main outputs: [file_name].med.maxFA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_pos.FA.vtk (or [file_name].med.maxFA.clusters.ttst.[threshold]_neg.FA.vtk. [file_name].med.maxFA.vtk to:
#from tsa_stats. For each of the tracts, there are two main outputs: [file_name].med.maxFA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_pos.FA.vtk (or [file_name].med.maxFA.clusters.ttst.[threshold]_neg.FA.vtk if you chose the
Changed lines 5-7 from:
The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two scripts: tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate outputs of different format, as one of them rely on the meshcluster or the meshglm function of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
#from tsa_stats. For each of the tracts, there are three main outputs: [file_name].med.maxFA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_pos.FA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_neg.FA.vtk. [file_name].med.maxFA.vtk to:
The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two scripts: tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate outputs of different format, as they rely on the meshcluster and the meshglm functions of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]], respectively.
#from tsa_stats. For each of the tracts, there are two main outputs: [file_name].med.maxFA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_pos.FA.vtk (or [file_name].med.maxFA.clusters.ttst.[threshold]_neg.FA.vtk. [file_name].med.maxFA.vtk
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The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate outputs of different format, as one of them rely on the meshcluster or the meshglm function of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
to:
The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two scripts: tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate outputs of different format, as one of them rely on the meshcluster or the meshglm function of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
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After a successful statistical analysis of your dataset, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from 1/ tsa_stats (contained in earlier version of DTI-TK) or 2/ the [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] script.
Hence, there are two kinds of outputs:
to:
The TSA [[Documentation.TsaCasual|statistical analysis]] can be run using two tsa_stats (from earlier versions of DTI-TK) or [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]]. These two scripts generate outputs of different format, as one of them rely on the meshcluster or the meshglm function of [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
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#from group_tsa_stats:
%center%%width=750px%Attach:right_cst_meshcluster.png
%center% ''Left'': Results obtained from a study comparing an adult male population to an adult female population. Here, the right CST is represented using paraview.
to:
#from group_tsa_stats: Two main outputs will result from the analysis: [file_name].med.maxFA.vtk and [file_name]_edges.med.maxFA.clusters.[feature]_[threshold].vtk
%center%%width=550px%Attach:right_cst_meshcluster.png
%center% Results obtained from a study comparing an adult male population to an adult female population. Here, the right CST is represented using paraview. The scale shows values from the t-test
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After a successful statistical analysis of your dataset, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from the [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] script.
There are two kinds of files:
#the ones resulting the use of an early version of tsa_stat, using the meshcluster function from [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
#the ones resulting from [http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] (see [[Documentation.TsaCasual|here]]), which uses the newer meshglm function also contained in [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
to:
After a successful statistical analysis of your dataset, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from 1/ tsa_stats (contained in earlier version of DTI-TK) or 2/ the [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] script.
Hence, there are two kinds of outputs:
#from tsa_stats. For each of the tracts, there are three main outputs: [file_name].med.maxFA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_pos.FA.vtk and [file_name].med.maxFA.clusters.ttst.[threshold]_neg.FA.vtk. [file_name].med.maxFA.vtk
#from group_tsa_stats:
%center%%width=750px%Attach:right_cst_meshcluster.png
%center% ''Left'': Results obtained from a study comparing an adult male population to an adult female population. Here, the right CST is represented using paraview.
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After a successful statistical analysis, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from the [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] script.
to:
After a successful statistical analysis of your dataset, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from the [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] script.
There are two kinds of files:
#the ones resulting the use of an early version of tsa_stat, using the meshcluster function from [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
#the ones resulting from [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] (see [[Documentation.TsaCasual|here]]), which uses the newer meshglm function also contained in [[http://www.itksnap.org/pmwiki/pmwiki.php?n=CMREP.Documentation|cmrep]]
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After a successful statistical analysis, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from the meshcluster or the meshglm analysis.
to:
After a successful statistical analysis, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from the [[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/group_tsa_stats.sh|group_tsa_stats]] script.
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After a successful statistical analysis, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]])
to:
After a successful statistical analysis, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]]), the result of your study are consigned in the output files obtained from the meshcluster or the meshglm analysis.
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(:noleft:) (:notitle:)(:title Displaying TSA Results:)
! Displaying TSA results
!!Outputs of the statistical analysis
After a successful statistical analysis, (see paragraph "Statistical Analysis", [[Documentation.TsaCasual|here]])
!!Comprehensive representation
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