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!!!Tract-Based Spatial Statistics - TBSS (:showhide init=hide div=tbss:)
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*'''[[Documentation.TBSS| TBSS Integration]]'''
>><<
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!!!Getting Started (:showhide init=hide div=getting_started:)
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!!! Basic Processing and Visualization to:
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!!! Basic Processing and Visualization (:showhide init=hide div=basic:)
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!!!Spatial Normalization and Atlas Construction to:
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!!!Spatial Normalization and Atlas Construction (:showhide init=hide div=spatial_normalization:)
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!!!Tract Specific Analysis - TSA to:
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!!!Tract Specific Analysis - TSA (:showhide init=hide div=tsa:)
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!!!Visualization of the Statistical Analysis - TSA
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>><<
!!!Video Tutorials (:showhide init=hide div=video:)
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*'''[[http://www.dailymotion.com/video/xjzxat_ismrm-2011-tutorial-group-analysis-atlases_tech|Video Tutorial on Group Analysis of Diffusion Data]]'''
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!!!Video Tutorials
*'''[[http://www.dailymotion.com/video/xjzxat_ismrm-2011-tutorial-group-analysis-atlases_tech|A Tutorial on Group Analysis of Diffusion Data]]'''
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*'''[http://www.dailymotion.com/video/xjzxat_ismrm-2011-tutorial-group-analysis-atlases_tech|Video Tutorial on Group Analysis of Diffusion Data]]'''
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*'''[[http://www.dailymotion.com/video/xjzxat_ismrm-2011-tutorial-group-analysis-atlases_tech|Video Tutorial on Group Analysis of Diffusion Data]]'''
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*'''[http://www.dailymotion.com/video/xjzxat_ismrm-2011-tutorial-group-analysis-atlases_tech|Video Tutorial on Group Analysis of Diffusion Data]]'''
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*'''[[Documentation.matrix_generator|Contrast & Design Matrices Generator]]'"
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*'''[[Documentation.matrix_generator|Contrast & Design Matrices Generator]]'''
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*'''[[http://dti-tk.sourceforge.net/pmwiki/uploads/testing/config_file_generator.html|Contrast & Design Matrices Generator]]'''
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*'''[[Documentation.matrix_generator|Contrast & Design Matrices Generator]]'"
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*'''[[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/config_file_generator.html|Contrast & Design Matrices Generator]]'''
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*'''[[http://dti-tk.sourceforge.net/pmwiki/uploads/testing/config_file_generator.html|Contrast & Design Matrices Generator]]'''
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*'''[[Documentation.visualization| Showing your results]]'''
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*'''[[Documentation.visualization| Presentation of the results]]'''
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!!!Visualization of the Statistical Analysis - TSA
*'''[[Documentation.visualization| Showing your results]]'''
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*'''[[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TsaCasual|Contrast & Design Matrices Generator]]'''
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*'''[[http://dti-tk.sourceforge.net/pmwiki/uploads/Applet/config_file_generator.html|Contrast & Design Matrices Generator]]'''
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*'''[[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TsaCasual|Contrast & Design Matrices Generator]]'''
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!!!About the orientation of the images: to:
!!!Note about the orientation of the images:
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'''ABOUT THE ORIENTATION OF THE IMAGES''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image. This orientation is consistent with the one of the pre-designed atlases and specific tracts.
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!!!About the orientation of the images:
DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image. This orientation is consistent with the one of the pre-designed atlases and specific tracts.
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'''Warning''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image. This orientation is consistent with the one of the pre-designed atlases and specific tracts.
to:
'''ABOUT THE ORIENTATION OF THE IMAGES''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image. This orientation is consistent with the one of the pre-designed atlases and specific tracts.
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'''Warning''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image.
to:
'''Warning''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image. This orientation is consistent with the one of the pre-designed atlases and specific tracts.
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'''Warning''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image.
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'''Warning''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image.
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'''Warning''': DTI-TK unifies the orientation of the images. As a consequence, all the tools turn an image with any orientation into an LPI oriented image.
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(:noleft:) (:notitle:)(:title Tutorial:) to:
(:noleft:) (:notitle:)(:title DTI-TK Documentation: Tutorials:) Changed line 39 from:
!!!Next Section: [[ManualPage.ManualPage|List of Commands]] to:
!!!Next Section: [[ManualPage.ManualPage|List of Tools]]
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!!! Basic DTI Volume Processing and Visualization to:
!!! Basic Processing and Visualization
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!!! Basic DTI Volume Processing and Visualization Added lines 22-23:
!!!Spatial Normalization and Atlas Construction Changed lines 32-33 from:
*'''[[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]'''
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*'''[[Documentation.Quality|Visualization of Spatial Transformations]]'''
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*'''[[Documentation.tsa_advanced| Building your own TSA template]]''' to:
*'''[[Documentation.tsa_advanced| Building your own TSA template]]'''
!!!Next Section: [[ManualPage.ManualPage|List of Commands]]
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!!Tract Specific Analysis - TSA to:
!!!Tract Specific Analysis - TSA
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*'''[[Documentation.diffusivity|Important Information About Unit of Diffusivity]]'''
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*'''[[Documentation.diffusivity|Using the Correct Unit of Diffusivity]]'''
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*''[[Documentation.tsa_advanced| Building your own TSA template]]''' to:
*'''[[Documentation.tsa_advanced| Building your own TSA template]]'''
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!!Tract Specific Analysis to:
!!Tract Specific Analysis - TSA
*'''[[Documentation.tsa_casual| TSA using existing templates]]'''
*''[[Documentation.tsa_advanced| Building your own TSA template]]'''
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*'''[[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]''' to:
*'''[[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]'''
!!Tract Specific Analysis
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!![[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]
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*'''[[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]'''
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*'''[[Documentation.FirstRegistration|First Registration with DTI-TK]]'''
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*'''[[Documentation.FirstRegistration|First Registration with DTI-TK: example]]'''
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*'''[[Documentation.FirstRegistration|First Registration with DTI-TK]]'''
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*'''[[Documentation.FirstRegistration|First Registration with DTI-TK]]'''
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(:noleft:) (:notitle:)(:title DTI-TK Documentation:)
! DTI-TK Documentation
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(:noleft:) (:notitle:)(:title Tutorial:)
! Tutorial
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*[[Downloads.Downloads|Downloads]]
*[[Documentation.install|Instructions for Installation]]
*[[Documentation.FirstRegistration|First Registration with DTI-TK]]
*[[Documentation.Format|Data Format (DWI vs DTI)]]
*[[Documentation.diffusivity|Important Information About Unit of Diffusivity]]
to:
*'''[[Downloads.Downloads|Downloads]]'''
*'''[[Documentation.install|Instructions for Installation]]'''
*'''[[Documentation.FirstRegistration|First Registration with DTI-TK]]'''
*'''[[Documentation.Format|Data Format (DWI vs DTI)]]'''
*'''[[Documentation.diffusivity|Important Information About Unit of Diffusivity]]'''
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'''*[[Downloads.Downloads|Downloads]]
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*[[Downloads.Downloads|Downloads]]
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'''*[[Documentation.Interoperability|Interoperability with Major DTI Tools]]'''
'''*[[Documentation.computation|Computing Rotation-Invariant Scalar Indices]]'''
'''*[[Documentation.VisualizationTool|Visualization of DTI Volumes]]'''
'''*[[Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]'''
'''*[[Documentation.Registration|Registration & Spatial Normalization of DTI Volumes]]'''
'''*[[Documentation.OptionspostReg|Image Mapping Options after Registration]]'''
'''*[[Documentation.StdSpace|Image Mapping to Standard Space]]'''
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*'''[[Documentation.Interoperability|Interoperability with Major DTI Tools]]'''
*'''[[Documentation.computation|Computing Rotation-Invariant Scalar Indices]]'''
*'''[[Documentation.VisualizationTool|Visualization of DTI Volumes]]'''
*'''[[Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]'''
*'''[[Documentation.Registration|Registration & Spatial Normalization of DTI Volumes]]'''
*'''[[Documentation.OptionspostReg|Image Mapping Options after Registration]]'''
*'''[[Documentation.StdSpace|Image Mapping to Standard Space]]'''
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*[[Documentation.Interoperability|Interoperability with Major DTI Tools]]
*[[Documentation.computation|Computing Rotation-Invariant Scalar Indices]]
*[[Documentation.VisualizationTool|Visualization of DTI Volumes]]
*[[Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]
*[[Documentation.Registration|Registration & Spatial Normalization of DTI Volumes]]
*[[Documentation.OptionspostReg|Image Mapping Options after Registration]]
*[[Documentation.StdSpace|Image Mapping to Standard Space]]'''
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'''*[[Documentation.Interoperability|Interoperability with Major DTI Tools]]'''
'''*[[Documentation.computation|Computing Rotation-Invariant Scalar Indices]]'''
'''*[[Documentation.VisualizationTool|Visualization of DTI Volumes]]'''
'''*[[Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]'''
'''*[[Documentation.Registration|Registration & Spatial Normalization of DTI Volumes]]'''
'''*[[Documentation.OptionspostReg|Image Mapping Options after Registration]]'''
'''*[[Documentation.StdSpace|Image Mapping to Standard Space]]'''
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*[[Downloads.Downloads|Downloads]]
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'''*[[Downloads.Downloads|Downloads]]
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*[[Documentation.StdSpace|Image Mapping to Standard Space]]
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*[[Documentation.StdSpace|Image Mapping to Standard Space]]'''
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*[[Main.Interoperability|Interoperability with Major DTI Tools]]
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*[[Documentation.Interoperability|Interoperability with Major DTI Tools]]
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*[[Main.Interoperability |Interoperability with Major DTI Tools]]
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*[[Main.Interoperability|Interoperability with Major DTI Tools]]
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#[[Downloads.Downloads|Downloads]]
#[[Documentation.install|Instructions for Installation]]
#[[Documentation.FirstRegistration|First Registration with DTI-TK]]
#[[Documentation.Format|Data Format (DWI vs DTI)]]
#[[Documentation.diffusivity|Important Information About Unit of Diffusivity]]
to:
*[[Downloads.Downloads|Downloads]]
*[[Documentation.install|Instructions for Installation]]
*[[Documentation.FirstRegistration|First Registration with DTI-TK]]
*[[Documentation.Format|Data Format (DWI vs DTI)]]
*[[Documentation.diffusivity|Important Information About Unit of Diffusivity]]
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!!! [[Main.Interoperability |Interoperability with Major DTI Tools]]
!!![[Documentation.computation|Computing
!!![[Documentation.VisualizationTool|Visualization
!!![[Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]
!!![[Documentation.Registration|Registration & Spatial Normalization of DTI Volumes]]
!!![[Documentation.OptionspostReg|Image Mapping Options after Registration]]
!!![[Documentation.StdSpace|Image Mapping to Standard Space]]
to:
*[[Main.Interoperability |Interoperability with Major DTI Tools]]
*[[Documentation.computation|Computing Rotation-Invariant Scalar Indices]]
*[[Documentation.VisualizationTool|Visualization of DTI Volumes]]
*[[Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]
*[[Documentation.Registration|Registration & Spatial Normalization of DTI Volumes]]
*[[Documentation.OptionspostReg|Image Mapping Options after Registration]]
*[[Documentation.StdSpace|Image Mapping to Standard Space]]
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!!!Installation and Downloads
Refer to [[Downloads.Downloads|this page]] to download the toolkit. Then, follow [[Documentation.install|these instructions]] carefully.
!!![[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.FirstRegistration|First Registration with DTI-TK]]
!!![[Documentation.Format|Data Format (DWI vs DTI)]]
!!! [[Documentation.diffusivity|Important Information About Unit of Diffusivity]]
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#[[Downloads.Downloads|Downloads]]
#[[Documentation.install|Instructions for Installation]]
#[[Documentation.FirstRegistration|First Registration with DTI-TK]]
#[[Documentation.Format|Data Format (DWI vs DTI)]]
#[[Documentation.diffusivity|Important Information About Unit of Diffusivity]]
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!!! [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability |Interoperability with Major DTI Tools]]
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!!! [[Main.Interoperability |Interoperability with Major DTI Tools]]
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!![[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]
!! Documentation for specific tools
:: [[Documentation.SingleTensorFT | SingleTensorFT]]: A command that generates white matter tractography corresponding to a specific mask defined by the user.
:: [[Documentation.TractTool | TractTool]]: Using TractTool allows you to limit the tractography to tracts of interest defined by ROIs.
:: [[Documentation.TVtool | TVtool]]: A tool for many common tensorial volume processing.
:: [[Documentation.TVglyphView | TVglyphView]]: Tool that allows to visualize tensor images as 3D ellipsoids
:: [[Documentation.Volumeinfo |VolumeInfo]]: A command that displays the specifics of your image (voxel size, dimension, origin) to:
!![[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]
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!!Quality Control - Visualization of Spatial Transformations
Visualizing spatial transformations is an important quality assurance step. [[Documentation.Quality|This tutorial]] describes how to create uniform grid images and how to visualize a spatial transformation by viewing the warped grid images.
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!![[Documentation.Quality|Quality Control - Visualization of Spatial Transformations]]
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!!!Image Mapping to Standard Space
Image mapping to standard space is often required in reporting results from voxel-based analysis. [[Documentation.StdSpace|This tutorial]] outlines the steps necessary to accomplish this task. I assume you have gone through [[Documentation.Registration|the image registration]] and [[Documentation.OptionspostReg|the image mapping]] tutorials and are familiar with the concepts and commands introduced in those tutorials.
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!!![[Documentation.StdSpace|Image Mapping to Standard Space]]
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!!!Image Mapping Options after Registration
After the registration/spatial normalization step, DTI-TK outputs, for each subject, two transformations that together defines the mapping from the subject to the template space:
# the affine transformation stored in a text file with suffix ''aff'', which minimizes the global difference between the subject and the template, and
# the displacement field stored in a NIfTI formatted vector volume with suffix ''df.nii.gz'', which minimizes the residual local difference between the subject and the template.
Two common needs arise here:
# to warp the subject data in its native space to the template space with a single interpolation operation;
# to warp the template to the native space of a particular subject with a single interpolation operation. Meeting these needs require the ability to combine the affine transformation and the displacement field into one single displacement field, as well as the ability to invert this single displacement field. [[Documentation.OptionspostReg |This tutorial]] will describe the procedure to accomplish these goals.
In addition, we will describe how to warp images with the affine transform only.
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!!![[Documentation.OptionspostReg|Image Mapping Options after Registration]]
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!!![Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]
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!!![[Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]
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!!!Preprocessing of DTI Volumes Before Registration
A few preprocessing operations are required before any further image registration. Check [[Documentation.beforeReg|this]] page!
!!!Registration & Spatial Normalization of DTI Volumes
[[Documentation.Registration|Here]], we describe how the core functionality, the spatial normalization pipeline, is supported by the toolkit. The spatial normalization pipeline includes the following five steps:
#Preprocessing of the input DTI volumes
#Bootstrapping the initial DTI template from the input DTI volumes
#Rigid alignment with template refinement
#Affine alignment with template refinement
#Deformable alignment with template refinement
On this page, we will first go through each of these steps in detail. A practical example with illustrations is given at the very end of it. Be sure to check that out!
to:
!!![Documentation.beforeReg|Preprocessing of DTI Volumes Before Registration]]
!!![[Documentation.Registration|Registration & Spatial Normalization of DTI Volumes]]
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!!!Visualization of DTI Volumes
Effective visualization of DTI volumes is critically important for processing and analyzing this type of data. For example, after reconstructing a DTI volume from the raw diffusion-weighted images (DWIs), it is imperative to examine if the tensors are properly oriented in space. For this purpose, neither the FA map nor the RGB map of the principal diffusion directions suffice. It is necessary to visualize the principal diffusion direction as 3D vectors or to visualize the tensors as 3D tensor glyphs. DTI-TK offers a simple tool for the latter, called [[Documentation.TVglyphView | TVglyphView]].
In the context of spatial normalization, visualization serves the purpose of qualitative quality control. For sanity checks, looking at the FA map is usually sufficient.
[[Documentation.VisualizationTool|Here]], we discuss three different approaches towards DTI volume visualization, from looking at rotation-invariant scalar indices to visualizing the full tensors.
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!!![[Documentation.VisualizationTool|Visualization of DTI Volumes]]
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!!!Computing Rotation-Invariant Scalar Indices
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!!![[Documentation.computation|Computing Rotation-Invariant Scalar Indices]]
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The number of dimensions of a DTI image may sometimes require to be reduced for statistical analyses or visual inspection purposes. Creating 1- scalar or 2-higher-order images, (such as 1- fractional anisotropy, trace or axial diffusivity or 2- principal component direction images can be achieved using [[Documentation.TVtool|TVTool]].
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!![[Documentation.Interoperability|Using the Toolkit]]
!!! Interoperability with Major DTI Tools
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!!Using the Toolkit
!!! [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability |Interoperability with Major DTI Tools]]
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!![[Documentation.Interoperability|Using the Toolkit]] Changed lines 17-23 from:
There are many excellent DTI tools including [[http://afni.nimh.nih.gov/afni | AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide | CAMINO]], [[https://www.mristudio.org/ | DTI Studio]], [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html | FSL]] to name a few, that provide important functions in most users' existing DTI analysis pipeline, such as tensor reconstruction. However, none of these programs currently output their DTI volumes in a common data format. An important contribution of DTI-TK is in providing necessary tools for users to
# convert the DTI volumes output from these popular packages into an open standard -- the NIfTI tensor format
# convert the NIfTI tensor format back to the DTI volumes in the native formats of these packages.
This makes it possible for users that have existing pipelines using any of these popular packages to take advantage of DTI-TK. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability | Here]], we describe the details of the tools that enable DTI-TK to work seamlessly with other DTI packages.
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!!!Important Information About Unit of Diffusivity
Since DTI volumes store values of physical quantities, diffusivity in this case, it is important to specify the particular physical unit used to store these values. Check [[Documentation.diffusivity|this]] to verify that your images are stored in the right unit and to modify it if ever it is not the case.
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!!! [[Documentation.diffusivity|Important Information About Unit of Diffusivity]]
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!!!Data Format (DWI vs DTI)
DTI-TK is designed to work with DTI volumes. It does not directly work with diffusion-weight image (DWI) volumes, which are the raw image data acquired from MRI scanners. The DTI volumes that DTI-TK takes as inputs are calculated from their corresponding DWI volumes in a process known as tensor reconstruction. As an example, in a typical diffusion imaging protocol, at least 6 DWI volumes together with 1 minimally diffusion-weighted volume, commonly known as the b=0 image, are acquired for a single subject. Then for this subject, a single DTI volume is then computed from these DWI volumes. The relationship between DWI and DTI is illustrated pictorially in these [[http://www.nitrc.org/frs/download.php/841/DTI-TK_NITRC_Grantee_Meeting_Talk.pdf|slides]].
This tensor reconstruction process can be accomplished by many excellent software packages including [[http://afni.nimh.nih.gov/afni|AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide|Camino]], [[https://www.mristudio.org/|DTIStudio]] and [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html|FSL]], to name a few. In this [[Documentation.Format|section]], we describe the DTI volume format that DTI-TK supports natively. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability|A separate page]] describing the tools for converting the DTI volumes reconstructed by most of the popular DTI tools can be found here.
to:
!!![[Documentation.Format|Data Format (DWI vs DTI)]]
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!!!First Registration with DTI-TK
[[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.FirstRegistration|This tutorial]] shows you how to register one DTI volume to another using DTI-TK. The goal is to demonstrate the registration performance of DTI-TK without you having to understand many intricacies of working with DTI volumes, discussed in depth in other tutorials. Hopefully, you will be satisfied with its performance and find it worthwhile to go on to understand how to properly prepare your dataset for use with DTI-TK!
to:
!!![[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.FirstRegistration|First Registration with DTI-TK]]
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Visualizing spatial transformations is an important quality assurance step. [[Documentation.Quality|This tutorial]] describes how to create uniform grid images and how to visualize a spatial transformation by viewing the warped grid images.
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Image mapping to standard space is often required in reporting results from voxel-based analysis. [[Documentation.StdSpace|This tutorial]] outlines the steps necessary to accomplish this task. I assume you have gone through [[Documentation.Registration|the image registration]] and [[Documentation.OptionspostReg|the image mapping]] tutorials and are familiar with the concepts and commands introduced in those tutorials.
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After the registration/spatial normalization step, DTI-TK outputs, for each subject, two transformations that together defines the mapping from the subject to the template space:
# the affine transformation stored in a text file with suffix ''aff'', which minimizes the global difference between the subject and the template, and
# the displacement field stored in a NIfTI formatted vector volume with suffix ''df.nii.gz'', which minimizes the residual local difference between the subject and the template.
Two common needs arise here:
# to warp the subject data in its native space to the template space with a single interpolation operation;
# to warp the template to the native space of a particular subject with a single interpolation operation. Meeting these needs require the ability to combine the affine transformation and the displacement field into one single displacement field, as well as the ability to invert this single displacement field. [[Documentation.OptionspostReg |This tutorial]] will describe the procedure to accomplish these goals.
In addition, we will describe how to warp images with the affine transform only.
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In this page, we will first go through each of these steps in detail. A practical example with illustrations is given at the very end of it. Be sure to check that out!
to:
On this page, we will first go through each of these steps in detail. A practical example with illustrations is given at the very end of it. Be sure to check that out!
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Refer to [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Downloads.Downloads|this page]] to download the toolkit. Then, follow [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.install|these instructions]] carefully.
to:
Refer to [[Downloads.Downloads|this page]] to download the toolkit. Then, follow [[Documentation.install|these instructions]] carefully.
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[[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.FirstRegistration|This tutorial]] shows you how to register a pair of DTI volumes using DTI-TK. The goal is to demonstrate the registration performance of DTI-TK without you having to understand many intricacies of working with DTI volumes, discussed in depth in other tutorials. Hopefully, you will be satisfied with its performance and find it worthwhile to go on to understand how to properly prepare your dataset for use with DTI-TK!
to:
[[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.FirstRegistration|This tutorial]] shows you how to register one DTI volume to another using DTI-TK. The goal is to demonstrate the registration performance of DTI-TK without you having to understand many intricacies of working with DTI volumes, discussed in depth in other tutorials. Hopefully, you will be satisfied with its performance and find it worthwhile to go on to understand how to properly prepare your dataset for use with DTI-TK!
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DTI-TK is designed to work with DTI volumes. It does not directly work with diffusion-weight image (DWI) volumes, which are the raw image data acquired from MRI scanners. The DTI volumes that DTI-TK takes as inputs are calculated from their corresponding DWI volumes in a process known as tensor reconstruction. As an example, in a typical diffusion imaging protocol, at least 6 DWI volumes together with 1 minimally diffusion-weighted volume, commonly known as the b=0 image, are acquired for a single subject. Then for this subject, a single DTI volume is then computed from these DWI volumes. This tensor reconstruction process can be accomplished by many excellent software packages including [[http://afni.nimh.nih.gov/afni|AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide|Camino]], [[https://www.mristudio.org/|DTIStudio]] and [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html|FSL]], to name a few. In this [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Format|section]], we describe the DTI volume format that DTI-TK supports natively. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability|A separate page]] describing the tools for converting the DTI volumes reconstructed by most of the popular DTI tools can be found here.
Update: The relationship between DWI and DTI is illustrated pictorially in these [[http://www.nitrc.org/frs/download.php/841/DTI-TK_NITRC_Grantee_Meeting_Talk.pdf|slides]].
to:
DTI-TK is designed to work with DTI volumes. It does not directly work with diffusion-weight image (DWI) volumes, which are the raw image data acquired from MRI scanners. The DTI volumes that DTI-TK takes as inputs are calculated from their corresponding DWI volumes in a process known as tensor reconstruction. As an example, in a typical diffusion imaging protocol, at least 6 DWI volumes together with 1 minimally diffusion-weighted volume, commonly known as the b=0 image, are acquired for a single subject. Then for this subject, a single DTI volume is then computed from these DWI volumes. The relationship between DWI and DTI is illustrated pictorially in these [[http://www.nitrc.org/frs/download.php/841/DTI-TK_NITRC_Grantee_Meeting_Talk.pdf|slides]].
This tensor reconstruction process can be accomplished by many excellent software packages including [[http://afni.nimh.nih.gov/afni|AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide|Camino]], [[https://www.mristudio.org/|DTIStudio]] and [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html|FSL]], to name a few. In this [[Documentation.Format|section]], we describe the DTI volume format that DTI-TK supports natively. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability|A separate page]] describing the tools for converting the DTI volumes reconstructed by most of the popular DTI tools can be found here.
Changed lines 17-18 from:
Since DTI volumes store values of physical quantities, diffusivity in this case, it is important to specify the particular physical unit used to store these values. Check [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.diffusivity|this]] to verify that your images are stored in the right unit and to modify it if ever it is not the case.
to:
Since DTI volumes store values of physical quantities, diffusivity in this case, it is important to specify the particular physical unit used to store these values. Check [[Documentation.diffusivity|this]] to verify that your images are stored in the right unit and to modify it if ever it is not the case.
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There are many excellent DTI tools including [[http://afni.nimh.nih.gov/afni | AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide | CAMINO]], [[https://www.mristudio.org/ | DTI Studio]], [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html | FSL]] to name a few, that provide important functions in most users' existing DTI analysis pipeline, such as tensor reconstruction. However, none of these programs currently output their DTI volumes in a common data format. An important contribution of DTI-TK is in providing necessary tools for users to
to:
There are many excellent DTI tools including [[http://afni.nimh.nih.gov/afni | AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide | CAMINO]], [[https://www.mristudio.org/ | DTI Studio]], [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html | FSL]] to name a few, that provide important functions in most users' existing DTI analysis pipeline, such as tensor reconstruction. However, none of these programs currently output their DTI volumes in a common data format. An important contribution of DTI-TK is in providing necessary tools for users to
Changed lines 26-27 from:
This makes it possible for users that have existing pipelines using any of these popular packages to take advantage of DTI-TK. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability | Here]], we describe the details of the tools that enable DTI-TK to work seamlessly with other DTI packages.
to:
This makes it possible for users that have existing pipelines using any of these popular packages to take advantage of DTI-TK. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability | Here]], we describe the details of the tools that enable DTI-TK to work seamlessly with other DTI packages.
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The number of dimensions of a DTI image may sometimes require to be reduced for statistical analyses or visual inspection purposes. Creating 1- scalar or 2-higher-order images, (such as 1- fractional anisotropy, trace or axial diffusivity or 2- principal component direction images can be achieved using [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TVtool|TVTool]].
to:
The number of dimensions of a DTI image may sometimes require to be reduced for statistical analyses or visual inspection purposes. Creating 1- scalar or 2-higher-order images, (such as 1- fractional anisotropy, trace or axial diffusivity or 2- principal component direction images can be achieved using [[Documentation.TVtool|TVTool]].
Changed lines 33-36 from:
Effective visualization of DTI volumes is critically important for processing and analyzing this type of data. For example, after reconstructing a DTI volume from the raw diffusion-weighted images (DWIs), it is imperative to examine if the tensors are properly oriented in space. For this purpose, neither the FA map nor the RGB map of the principal diffusion directions suffice. It is necessary to visualize the principal diffusion direction as 3D vectors or to visualize the tensors as 3D tensor glyphs. DTI-TK offers a simple tool for the latter, called [[Documentation.TVglyphView | TVglyphView]].
In the context of spatial normalization, visualization serves the purpose of qualitative quality control. For sanity checks, looking at the FA map is usually sufficient.
to:
Effective visualization of DTI volumes is critically important for processing and analyzing this type of data. For example, after reconstructing a DTI volume from the raw diffusion-weighted images (DWIs), it is imperative to examine if the tensors are properly oriented in space. For this purpose, neither the FA map nor the RGB map of the principal diffusion directions suffice. It is necessary to visualize the principal diffusion direction as 3D vectors or to visualize the tensors as 3D tensor glyphs. DTI-TK offers a simple tool for the latter, called [[Documentation.TVglyphView | TVglyphView]].
In the context of spatial normalization, visualization serves the purpose of qualitative quality control. For sanity checks, looking at the FA map is usually sufficient.
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A few preprocessing operations are required before any further image registration. Check]] this page!
to:
A few preprocessing operations are required before any further image registration. Check [[Documentation.beforeReg|this]] page!
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[[Documentation.Registration|text]]
to:
[[Documentation.Registration|Here]], we describe how the core functionality, the spatial normalization pipeline, is supported by the toolkit. The spatial normalization pipeline includes the following five steps:
#Preprocessing of the input DTI volumes
#Bootstrapping the initial DTI template from the input DTI volumes
#Rigid alignment with template refinement
#Affine alignment with template refinement
#Deformable alignment with template refinement
In this page, we will first go through each of these steps in detail. A practical example with illustrations is given at the very end of it. Be sure to check that out!
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[[Documentation.Registration|text]]
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!!!Preprocessing of DTI Volumes Before Registration to:
!!!Preprocessing of DTI Volumes Before Registration
A few preprocessing operations are required before any further image registration. [[Documentation.beforeReg|Check]] this page!
Changed lines 18-19 from:
Since DTI volumes store values of physical quantities, diffusivity in this case, it is important to specify the particular physical unit used to store these values. Check this important [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.diffusivity|information]] to know more about it.
to:
Since DTI volumes store values of physical quantities, diffusivity in this case, it is important to specify the particular physical unit used to store these values. Check [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.diffusivity|this]] to verify that your images are stored in the right unit and to modify it if ever it is not the case.
Deleted lines 16-17:
Changed lines 18-19 from:
to:
Since DTI volumes store values of physical quantities, diffusivity in this case, it is important to specify the particular physical unit used to store these values. Check this important [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.diffusivity|information]] to know more about it.
Changed lines 13-14 from:
DTI-TK is designed to work with DTI volumes. It does not directly work with diffusion-weight image (DWI) volumes, which are the raw image data acquired from MRI scanners. The DTI volumes that DTI-TK takes as inputs are calculated from their corresponding DWI volumes in a process known as tensor reconstruction. As an example, in a typical diffusion imaging protocol, at least 6 DWI volumes together with 1 minimally diffusion-weighted volume, commonly known as the b=0 image, are acquired for a single subject. Then for this subject, a single DTI volume is then computed from these DWI volumes. This tensor reconstruction process can be accomplished by many excellent software packages including [[http://afni.nimh.nih.gov/afni|AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide|Camino]], [[https://www.mristudio.org/|DTIStudio]] and [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html|FSL]], to name a few. In this [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Format|this page|section]], we describe the DTI volume format that DTI-TK supports natively. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability|A separate page]] describing the tools for converting the DTI volumes reconstructed by most of the popular DTI tools can be found here.
to:
DTI-TK is designed to work with DTI volumes. It does not directly work with diffusion-weight image (DWI) volumes, which are the raw image data acquired from MRI scanners. The DTI volumes that DTI-TK takes as inputs are calculated from their corresponding DWI volumes in a process known as tensor reconstruction. As an example, in a typical diffusion imaging protocol, at least 6 DWI volumes together with 1 minimally diffusion-weighted volume, commonly known as the b=0 image, are acquired for a single subject. Then for this subject, a single DTI volume is then computed from these DWI volumes. This tensor reconstruction process can be accomplished by many excellent software packages including [[http://afni.nimh.nih.gov/afni|AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide|Camino]], [[https://www.mristudio.org/|DTIStudio]] and [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html|FSL]], to name a few. In this [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Format|section]], we describe the DTI volume format that DTI-TK supports natively. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability|A separate page]] describing the tools for converting the DTI volumes reconstructed by most of the popular DTI tools can be found here.
Added lines 13-18:
DTI-TK is designed to work with DTI volumes. It does not directly work with diffusion-weight image (DWI) volumes, which are the raw image data acquired from MRI scanners. The DTI volumes that DTI-TK takes as inputs are calculated from their corresponding DWI volumes in a process known as tensor reconstruction. As an example, in a typical diffusion imaging protocol, at least 6 DWI volumes together with 1 minimally diffusion-weighted volume, commonly known as the b=0 image, are acquired for a single subject. Then for this subject, a single DTI volume is then computed from these DWI volumes. This tensor reconstruction process can be accomplished by many excellent software packages including [[http://afni.nimh.nih.gov/afni|AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide|Camino]], [[https://www.mristudio.org/|DTIStudio]] and [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html|FSL]], to name a few. In this [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Format|this page|section]], we describe the DTI volume format that DTI-TK supports natively. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability|A separate page]] describing the tools for converting the DTI volumes reconstructed by most of the popular DTI tools can be found here.
Update: The relationship between DWI and DTI is illustrated pictorially in these [[http://www.nitrc.org/frs/download.php/841/DTI-TK_NITRC_Grantee_Meeting_Talk.pdf|slides]].
Changed lines 50-52 from:
:: [[Documentation.TVglyphView | TVglyphView]]: Tool that allows to visualize tensor images as 3D ellipsoids to:
:: [[Documentation.TVglyphView | TVglyphView]]: Tool that allows to visualize tensor images as 3D ellipsoids
:: [[Documentation.Volumeinfo |VolumeInfo]]: A command that displays the specifics of your image (voxel size, dimension, origin)
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:: [[Documentation.TVglyphView | TVglyphView]]: Tool that allows to visualize tensor images to:
:: [[Documentation.TVglyphView | TVglyphView]]: Tool that allows to visualize tensor images as 3D ellipsoids
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[[Documentation.VisualizationTool | Visualization tools]]
to:
Effective visualization of DTI volumes is critically important for processing and analyzing this type of data. For example, after reconstructing a DTI volume from the raw diffusion-weighted images (DWIs), it is imperative to examine if the tensors are properly oriented in space. For this purpose, neither the FA map nor the RGB map of the principal diffusion directions suffice. It is necessary to visualize the principal diffusion direction as 3D vectors or to visualize the tensors as 3D tensor glyphs. DTI-TK offers a simple tool for the latter, called [[Documentation.TVglyphView | TVglyphView]].
In the context of spatial normalization, visualization serves the purpose of qualitative quality control. For sanity checks, looking at the FA map is usually sufficient.
[[Documentation.VisualizationTool|Here]], we discuss three different approaches towards DTI volume visualization, from looking at rotation-invariant scalar indices to visualizing the full tensors.
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[[Documentation.VisualizationTool | Visualization tools]]
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:: [[Documentation.VisualizationTool | Visualization tools]]: Commands to visualize the DTI images and their subcomponents to:
:: [[Documentation.TVglyphView | TVglyphView]]: Tool that allows to visualize tensor images
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The number of dimensions of a DTI image may sometimes required to be reduced for statistical analyses or visual inspection purposes. It is then possible to create scalar images, such as fractional anisotropy, trace or axial diffusivity images, or to create higher-order images, such as principal component direction images. Most of these features can be computed using [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TVtool|TVTool]].
to:
The number of dimensions of a DTI image may sometimes require to be reduced for statistical analyses or visual inspection purposes. Creating 1- scalar or 2-higher-order images, (such as 1- fractional anisotropy, trace or axial diffusivity or 2- principal component direction images can be achieved using [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TVtool|TVTool]].
Added lines 25-27:
The number of dimensions of a DTI image may sometimes required to be reduced for statistical analyses or visual inspection purposes. It is then possible to create scalar images, such as fractional anisotropy, trace or axial diffusivity images, or to create higher-order images, such as principal component direction images. Most of these features can be computed using [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TVtool|TVTool]].
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[[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.FirstRegistration|This tutorial]] shows you how to register a pair of DTI volumes using DTI-TK. The goal is to demonstrate the registration performance of DTI-TK without you having to understand many intricacies of working with DTI volumes, discussed in depth in other tutorials. Hopefully, you will be satisfied with its performance and find it worthwhile to go on to understand how to properly prepare your dataset for use with DTI-TK!
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Refer to [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Downloads.Downloads|this page]] to download the toolkit. Then, follow [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.install|these instructions]] carefully.
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!!!Installation
!!! to:
!!!Installation and Downloads
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!!Getting Started
!!!Installation
!!!Downloads
!!!First Registration with DTI-TK
!!!Data Format (DWI vs DTI)
!!!Important Information About Unit of Diffusivity
!!Using the Toolkit Changed lines 20-30 from:
!!! Documentation for specific tools to:
!!!Computing Rotation-Invariant Scalar Indices
!!!Visualization of DTI Volumes
!!!Preprocessing of DTI Volumes Before Registration
!!!Registration & Spatial Normalization of DTI Volumes
!!!Image Mapping Options after Registration
!!!Image Mapping to Standard Space
!!Quality Control - Visualization of Spatial Transformations
!! Documentation for specific tools
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:: [[Documentation.TVtool | TVtool]]: A tool for many common tensorial volume processing. to:
:: [[Documentation.TVtool | TVtool]]: A tool for many common tensorial volume processing.
:: [[Documentation.VisualizationTool | Visualization tools]]: Commands to visualize the DTI images and their subcomponents
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This makes it possible for users that have existing pipelines using any of these popular packages to take advantage of DTI-TK. Here, we describe the details of the tools that enable DTI-TK to work seamlessly with other DTI packages.
to:
This makes it possible for users that have existing pipelines using any of these popular packages to take advantage of DTI-TK. [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Interoperability | Here]], we describe the details of the tools that enable DTI-TK to work seamlessly with other DTI packages.
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There are many excellent DTI tools including ::[[http://afni.nimh.nih.gov/afni | AFNI]]:, ::[[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide | CAMINO]]:, ::[[https://www.mristudio.org/ | DTI Studio]]:, ::[[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html | FSL]]: to name a few, that provide important functions in most users' existing DTI analysis pipeline, such as tensor reconstruction. However, none of these programs currently output their DTI volumes in a common data format. An important contribution of DTI-TK is in providing necessary tools for users to
to:
There are many excellent DTI tools including [[http://afni.nimh.nih.gov/afni | AFNI]], [[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide | CAMINO]], [[https://www.mristudio.org/ | DTI Studio]], [[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html | FSL]] to name a few, that provide important functions in most users' existing DTI analysis pipeline, such as tensor reconstruction. However, none of these programs currently output their DTI volumes in a common data format. An important contribution of DTI-TK is in providing necessary tools for users to
Changed lines 5-11 from:
to:
There are many excellent DTI tools including ::[[http://afni.nimh.nih.gov/afni | AFNI]]:, ::[[http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.Guide | CAMINO]]:, ::[[https://www.mristudio.org/ | DTI Studio]]:, ::[[http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_dtifit.html | FSL]]: to name a few, that provide important functions in most users' existing DTI analysis pipeline, such as tensor reconstruction. However, none of these programs currently output their DTI volumes in a common data format. An important contribution of DTI-TK is in providing necessary tools for users to
# convert the DTI volumes output from these popular packages into an open standard -- the NIfTI tensor format
# convert the NIfTI tensor format back to the DTI volumes in the native formats of these packages.
This makes it possible for users that have existing pipelines using any of these popular packages to take advantage of DTI-TK. Here, we describe the details of the tools that enable DTI-TK to work seamlessly with other DTI packages.
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!!! Interoperability with Major DTI Tools
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:: [[Documentation.SingleTensorFT | SingleTensorFT]]: A tool for many common tensorial volume processing.
:: [[Documentation.TractTool | TractTool]]: A tool for many common tensorial volume processing.
to:
:: [[Documentation.SingleTensorFT | SingleTensorFT]]: A command that generates white matter tractography corresponding to a specific mask defined by the user.
:: [[Documentation.TractTool | TractTool]]: Using TractTool allows you to limit the tractography to tracts of interest defined by ROIs.
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: [[Documentation.SingleTensorFT | SingleTensorFT]]: A tool for many common tensorial volume processing.
: [[Documentation.TractTool | TractTool]]: A tool for many common tensorial volume processing.
to:
:: [[Documentation.SingleTensorFT | SingleTensorFT]]: A tool for many common tensorial volume processing.
:: [[Documentation.TractTool | TractTool]]: A tool for many common tensorial volume processing.
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: [[Documentation.SingleTensorFT | SingleTensorFT]]: A tool for many common tensorial volume processing.
: [[Documentation.TractTool | TractTool]]: A tool for many common tensorial volume processing.
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:: [[Documentation.TVtool | TVtool]]: to:
:: [[Documentation.TVtool | TVtool]]: A tool for many common tensorial volume processing.
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:: [[TVTool.Documentation | TVTool]]: to:
:: [[Documentation.TVtool | TVtool]]:
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: [[TVTool.Documentation | TVTool]]: to:
:: [[TVTool.Documentation | TVTool]]:
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:: [[TVTool.Documentation | TVTool]]:
to:
: [[TVTool.Documentation | TVTool]]:
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(:noleft:) (:notitle:)(:title DTI-TK Documentation:) to:
(:noleft:) (:notitle:)(:title DTI-TK Documentation:)
! DTI-TK Documentation
!!! Documentation for specific tools
:: [[TVTool.Documentation | TVTool]]:
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(:noleft:) (:notitle:)(:title DTI-TK Documentation:)
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