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DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://picsl.upenn.edu/ | PICSL]]), University of Pennsylvania, under the supervision of Prof. James C Gee.
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ | Prof. Paul Yushkevich at PICSL]] now help maintain and develop DTI-TK.
to:
DTI-TK has been developed as part of Dr Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://picsl.upenn.edu/ | PICSL]]), University of Pennsylvania, under the supervision of Dr James C Gee.
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ | Dr Paul Yushkevich at PICSL]] now help maintain and develop DTI-TK.
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Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ | Prof. Paul Yushkevich at PICSL] now help maintain and develop DTI-TK.
to:
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ | Prof. Paul Yushkevich at PICSL]] now help maintain and develop DTI-TK.
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Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ I Prof. Paul Yushkevich at PICSL] now help maintain and develop DTI-TK.
to:
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ | Prof. Paul Yushkevich at PICSL] now help maintain and develop DTI-TK.
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DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://www.picsl.upenn.edu/|PICSL]]), University of Pennsylvania, under the supervision of Dr. James C Gee.
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ I Paul Yushkevich at PICSL] now help maintain and develop DTI-TK.
to:
DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://picsl.upenn.edu/ | PICSL]]), University of Pennsylvania, under the supervision of Prof. James C Gee.
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ I Prof. Paul Yushkevich at PICSL] now help maintain and develop DTI-TK.
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Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and several members of PICSL now help maintain and develop DTI-TK.
to:
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and [[http://picsl.upenn.edu/people/faculty-staff/paul-yushkevich/ I Paul Yushkevich at PICSL] now help maintain and develop DTI-TK.
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(:comment !!What is DTI-TK? :)
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!! How Much Does it Cost?
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!!! How Much Does it Cost?
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!! What Can DTI-TK do for Me? to:
!!! What Can DTI-TK do for Me? Changed line 36 from:
!! What can't DTI-TK do for Me? to:
!!! What can't DTI-TK do for Me? Changed line 43 from:
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!!! How Can I Contribute?
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(:comment !!What is DTI-TK? :)
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* Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio to:
* Interoperability with other popular DTI tools: AFNI, [[http://cmic.cs.ucl.ac.uk/camino | Camino]], FSL & DTIStudio
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DTI-TK does not replicate the core functionalities of many existing popular DTI packages, such as CAMINO or DTIStudio but is designed to allow users of these existing tools to leverage DTI-TK in a pain-free way. The Interoperability page gives detailed descriptions of how DTI-TK enables the seamless integration of DTI-TK with your favorite DTI tool.
to:
DTI-TK does not replicate the core functionalities of many existing popular DTI packages, such as CAMINO or DTIStudio but is designed to allow users of these existing tools to leverage DTI-TK in a pain-free way. The [[Documentation.Interoperability | Interoperability]] page gives detailed descriptions of how DTI-TK enables the seamless integration of DTI-TK with your favorite DTI tool.
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Gary, now at [[http://cmic.cs.ucl.ac.uk/Centre for Medical Image Computing (CMIC)]], University College London, and several members of PICSL now help maintain and develop DTI-TK.
to:
Gary, now at [[http://cmic.cs.ucl.ac.uk/mig//index.php?n=People.GHZhang | Microstructure Imaging Group]] of [[http://cmic.cs.ucl.ac.uk | Centre for Medical Image Computing (CMIC) ]] and [[http://www.cs.ucl.ac.uk | Department of Computer Science]], [[http://www.ucl.ac.uk | University College London]], and several members of PICSL now help maintain and develop DTI-TK.
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* If you are a software developer, you can contribute to DTI-TK as it is an open source application. To become a developer, join us on [[http://sourceforge.net/projects/dti-tk/| SourceForge]]. to:
* If you are a software developer, you can contribute to DTI-TK as it is an open source application. To become a developer, join us on [[http://sourceforge.net/projects/dti-tk/| SourceForge]].
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DTI-TK is free software, provided under ------ the %newwin% [[http://www.gnu.org/licenses/gpl-3.0.txt|General Public License]]. DTI-TK binaries are provided free of charge for academic or commercial use. Development and continued maintenance of DTI-TK have been made possible by grants from the U.S. National Institutes of Health and by the generous time investments from members of the DTI-TK developer community.
to:
DTI-TK is free software, provided under the %newwin% [[http://www.gnu.org/licenses/gpl-3.0.txt|General Public License]]. DTI-TK binaries are provided free of charge for academic or non-commercial use. Development and continued maintenance of DTI-TK have been made possible by grants from the U.S. National Institutes of Health and by the generous time investments from members of the DTI-TK developer community.
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There are a growing number of researcher groups that have adopted DTI-TK, including several top research groups in diffusion imaging, such as Dr Carlo Pierpaoli's group at NIH and Dr Andrew Alexander's group at University of Wisconsin at Madison. To find out who is publishing with DTI-TK, check out the [[Publications.users|list of publications]] used DTI-TK, which we update regularly.
to:
There are a growing number of researcher groups that have adopted DTI-TK, including several top research groups in diffusion imaging, such as Dr Carlo Pierpaoli's group at NIH and Dr Andrew Alexander's group at University of Wisconsin at Madison. To find out who is publishing with DTI-TK, check out the [[Publications.users|list of publications used DTI-TK]], which we update regularly.
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There is a growing number of researcher now using DTI-TK, including several top research groups, such as Dr Carlo Pierpaoli's group at NIH and Dr Andrew Alexander's group at University of Wisconsin at Madison. Here is a full [[Publications.users|list of publications]] used DTI-TK, which we update regularly.
to:
There are a growing number of researcher groups that have adopted DTI-TK, including several top research groups in diffusion imaging, such as Dr Carlo Pierpaoli's group at NIH and Dr Andrew Alexander's group at University of Wisconsin at Madison. To find out who is publishing with DTI-TK, check out the [[Publications.users|list of publications]] used DTI-TK, which we update regularly.
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DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://www.picsl.upenn.edu/|PICSL]]), University of Pennsylvania, under the supervision of Dr. James C Gee. Several members of PICSL now help maintain and develop DTI-TK.
to:
DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://www.picsl.upenn.edu/|PICSL]]), University of Pennsylvania, under the supervision of Dr. James C Gee.
Gary, now at [[http://cmic.cs.ucl.ac.uk/|Centre for Medical Image Computing (CMIC)]], University College London, and several members of PICSL now help maintain and develop DTI-TK.
!! Who uses DTI-TK?
There is a growing number of researcher now using DTI-TK, including several top research groups, such as Dr Carlo Pierpaoli's group at NIH and Dr Andrew Alexander's group at University of Wisconsin at Madison. Here is a full [[Publications.users|list of publications]] used DTI-TK, which we update regularly.
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DTI-TK is a spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data.
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DTI-TK is a spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data. '''A [[http://dx.doi.org/10.1016/j.neuroimage.2011.01.038 | 2011 study published in NeuroImage]] ranks DTI-TK the top-performing tool in its class.'''
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!!! What Can DTI-TK do for Me?
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!! What Can DTI-TK do for Me? Changed line 33 from:
!!! What can't DTI-TK do for Me?
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!! What can't DTI-TK do for Me? Changed line 41 from:
!!! How Can I Contribute?
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!!! How Much Does it Cost?
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!! How Much Does it Cost?
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%rframe% Attach:WM_morphometry_with_DTITK.png
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DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://www.picsl.upenn.edu/|PICSL]]), University of Pennsylvania, under the supervision of Dr. James C Gee.
to:
DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://www.picsl.upenn.edu/|PICSL]]), University of Pennsylvania, under the supervision of Dr. James C Gee. Several members of PICSL now help maintain and develop DTI-TK.
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DTI-TK is a very convenient tool that allows you to register, analyze and visualize DTI images very easily. If you know how to use very simple unix command lines, then using DTI-TK is very easy!
!!! What can't DTI-TK do for Me?
DTI-TK does not replicate the core functionalities of many existing popular DTI packages, such as CAMINO or DTIStudio but is designed to allow users of these existing tools to leverage DTI-TK in a pain-free way. The Interoperability page gives detailed descriptions of how DTI-TK enables the seamless integration of DTI-TK with your favorite DTI tool.
What is not supported by DTI-TK?
* tensor reconstruction -constructing diffusion tensor images from raw diffusion-weighted images and related preprocessing support
* Probabilistic fiber tractography
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You can help make DTI-TK better in two ways:
* If you use DTI-TK and report its successes and failures, you will help identify bugs and missing features. Use the 'Bugs' link at the top of this page to report bugs.
* If you are a software developer, you can contribute to DTI-TK as it is an open source application. To become a developer, join us on [[http://sourceforge.net/projects/dti-tk/| SourceForge]].
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DTI-TK has been developed as part of Gary Zhang's [[http://www.nitrc.org/frs/download.php/996/phdthesis.pdf|Ph.D. thesis]] at Penn Image Computing and Science Laboratory ([[http://www.picsl.upenn.edu/|PICSL]]), University of Pennsylvania, under the supervision of Dr. James C Gee.
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DTI-TK is free software, provided under ------ the %newwin% [[http://www.gnu.org/licenses/gpl-3.0.txt|General Public License]]. ITK-SNAP binaries are provided free of charge for academic or commercial use. Development and continued maintenance of ITK-SNAP have been made possible by grants and contracts from the U.S. National Institutes of Health (NIBIB, NLM) and by the generous time investments from members of the ITK-SNAP developer community.
Since ITK-SNAP is free, there's no technical support number to call. We do our best to answer questions on the [[mailing lists]] in a timely manner, but we count on other users to offer answers as well. Often, ITK-SNAP development is done on a volunteer basis. Please keep that in mind when you use ITK-SNAP.
to:
DTI-TK is free software, provided under ------ the %newwin% [[http://www.gnu.org/licenses/gpl-3.0.txt|General Public License]]. DTI-TK binaries are provided free of charge for academic or commercial use. Development and continued maintenance of DTI-TK have been made possible by grants from the U.S. National Institutes of Health and by the generous time investments from members of the DTI-TK developer community.
Since DTI-TK is free, there's no technical support number to call. We do our best to answer questions on the [[mailing lists]] in a timely manner, but we count on other users to offer answers as well. Often, DTI-TK development is done on a volunteer basis. Please keep that in mind when you use DTI-TK.
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!!! Who Develops ITK-SNAP?
to:
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%rframe% Attach:sshot01.png
SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, SNAP provides a number of supporting utilities. Some of the core advantages of SNAP include
* Linked cursor for seamless 3D navigation
* Manual segmentation in three orthogonal planes at once
* Friendly UI for selecting active contour segmentation parameters
* Support for many different 3D image formats, including NIfTI
* Support for concurrent, linked viewing and segmentation of multiple images
* Limited support for color images (e.g., diffusion tensor maps)
* 3D cut-plane tool for fast post-processing of segmentation results
* Extensive tutorial
to:
%rframe% Attach:ellipsoid_axial.png
DTI-TK is a spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data.
* open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes
* tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization
* pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies
* built-in cluster-computing support: support for open source Sun Grid Engine (SGE)
* Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio
* Interoperability with ITK-SNAP: support multi-modal visualization and segmentation
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ITK-SNAP is free software, provided under the %newwin% [[http://www.gnu.org/licenses/gpl-3.0.txt|General Public License]]. ITK-SNAP binaries are provided free of charge for academic or commercial use. Development and continued maintenance of ITK-SNAP have been made possible by grants and contracts from the U.S. National Institutes of Health (NIBIB, NLM) and by the generous time investments from members of the ITK-SNAP developer community.
to:
DTI-TK is free software, provided under ------ the %newwin% [[http://www.gnu.org/licenses/gpl-3.0.txt|General Public License]]. ITK-SNAP binaries are provided free of charge for academic or commercial use. Development and continued maintenance of ITK-SNAP have been made possible by grants and contracts from the U.S. National Institutes of Health (NIBIB, NLM) and by the generous time investments from members of the ITK-SNAP developer community.
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Current ITK-SNAP development efforts are led by Paul Yushkevich, Ph.D., of the %newwin% [[http://picsl.upenn.edu | Penn Image Computing and Science Laboratory (PICSL)]] at the Department of Radiology at the University of Pennsylvania. Several members of the lab, and Hui (Gary) Zhang in particular, have contributed to ITK-SNAP development. Previous versions of SNAP were developed under the guidance of Guido Gerig, Ph.D., at the University of North Carolina at Chapel Hill and ETH Zurich. A number of scientists at other academic centers have contributed code and ideas to ITK-SNAP. See the [[Credits]] for complete information.
!!! What Can SNAP do for Me?
If you are a clinical researcher in neurology, radiology, psychiatry, surgery, or any other field that uses medical images, you may be able to use ITK-SNAP to enhance your productivity. Unlike many current image processing tools, ITK-SNAP was designed to be easy to learn and use for people without a computer science or engineering background.
If you are in the business of developing software applications that work with medical images, you may be able to incorporate parts of SNAP into your software. You can also use SNAP as a model of a user friendly application developed on top of ITK.
to:
!!! What Can DTI-TK do for Me?
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You can help make SNAP better in two ways. First, if you use SNAP and report its successes and failures, you will help identify bugs and missing features. Use the 'Bugs' link at the top of this page to report bugs. Second, if you are a software developer, you can contribute to SNAP by writing code. SNAP is an open source application, built on top of the %newwin%[[http://www.itk.org | Insight Toolkit (ITK)]]. To become a developer, join us on %newwin%[[http://sourceforge.net/projects/itk-snap | SourceForge]].
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(:title ITK-SNAP Home Page:)
!ITK-SNAP Home Page
!!! What is ITK-SNAP?
to:
(:title DTI-TK Home Page:)
!IDTI-TK Home Page
!!! What is DTI-TK?
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Welcome to PmWiki!
A local copy of PmWiki's
documentation has been installed along with the software,
and is available via the [[PmWiki/documentation index]].
To continue setting up PmWiki, see [[PmWiki/initial setup tasks]].
The [[PmWiki/basic editing]] page describes how to create pages
in PmWiki. You can practice editing in the [[wiki sandbox]].
More information about PmWiki is available from http://www.pmwiki.org .
to:
(:noleft:) (:notitle:)
(:title ITK-SNAP Home Page:)
!ITK-SNAP Home Page
!!! What is ITK-SNAP?
%rframe% Attach:sshot01.png
SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, SNAP provides a number of supporting utilities. Some of the core advantages of SNAP include
* Linked cursor for seamless 3D navigation
* Manual segmentation in three orthogonal planes at once
* Friendly UI for selecting active contour segmentation parameters
* Support for many different 3D image formats, including NIfTI
* Support for concurrent, linked viewing and segmentation of multiple images
* Limited support for color images (e.g., diffusion tensor maps)
* 3D cut-plane tool for fast post-processing of segmentation results
* Extensive tutorial
!!! How Much Does it Cost?
ITK-SNAP is free software, provided under the %newwin% [[http://www.gnu.org/licenses/gpl-3.0.txt|General Public License]]. ITK-SNAP binaries are provided free of charge for academic or commercial use. Development and continued maintenance of ITK-SNAP have been made possible by grants and contracts from the U.S. National Institutes of Health (NIBIB, NLM) and by the generous time investments from members of the ITK-SNAP developer community.
Since ITK-SNAP is free, there's no technical support number to call. We do our best to answer questions on the [[mailing lists]] in a timely manner, but we count on other users to offer answers as well. Often, ITK-SNAP development is done on a volunteer basis. Please keep that in mind when you use ITK-SNAP.
!!! Who Develops ITK-SNAP?
Current ITK-SNAP development efforts are led by Paul Yushkevich, Ph.D., of the %newwin% [[http://picsl.upenn.edu | Penn Image Computing and Science Laboratory (PICSL)]] at the Department of Radiology at the University of Pennsylvania. Several members of the lab, and Hui (Gary) Zhang in particular, have contributed to ITK-SNAP development. Previous versions of SNAP were developed under the guidance of Guido Gerig, Ph.D., at the University of North Carolina at Chapel Hill and ETH Zurich. A number of scientists at other academic centers have contributed code and ideas to ITK-SNAP. See the [[Credits]] for complete information.
!!! What Can SNAP do for Me?
If you are a clinical researcher in neurology, radiology, psychiatry, surgery, or any other field that uses medical images, you may be able to use ITK-SNAP to enhance your productivity. Unlike many current image processing tools, ITK-SNAP was designed to be easy to learn and use for people without a computer science or engineering background.
If you are in the business of developing software applications that work with medical images, you may be able to incorporate parts of SNAP into your software. You can also use SNAP as a model of a user friendly application developed on top of ITK.
!!! How Can I Contribute?
You can help make SNAP better in two ways. First, if you use SNAP and report its successes and failures, you will help identify bugs and missing features. Use the 'Bugs' link at the top of this page to report bugs. Second, if you are a software developer, you can contribute to SNAP by writing code. SNAP is an open source application, built on top of the %newwin%[[http://www.itk.org | Insight Toolkit (ITK)]]. To become a developer, join us on %newwin%[[http://sourceforge.net/projects/itk-snap | SourceForge]].
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