{"id":2282,"date":"2011-11-15T22:45:00","date_gmt":"2011-11-16T03:45:00","guid":{"rendered":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/niral\/download\/download-software\/"},"modified":"2018-09-24T14:59:01","modified_gmt":"2018-09-24T18:59:01","slug":"download-software","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/download\/download-software\/","title":{"rendered":"Download Software"},"content":{"rendered":"
\n

Currently supported Software:<\/b><\/h2>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\"FiberViewerLight
\n<\/b><\/td>\n		Go to the FiberViewerLight webpage<\/a><\/span><\/td>\nFiber ViewerLight is an open-source C++ application to analyze fiber bundles. It provides:<\/span>
\n\"arrow.gif\"<\/span> Several methods for clustering<\/span>
\n\"arrow.gif\"<\/span> 3D fibers visualization<\/span>
\n\"arrow.gif\"<\/span> 3D plane selection<\/span><\/td>\n<\/tr>\n
\"dtiatlasfiberanalyzer-logo-v2\"<\/td>\nGo to the DTIAtlasFiberAnalyzer (DTI Fiber Tract Statistics) webpage<\/span><\/a><\/td>\nDTIAtlasFiberAnalyzer is an open-source C++ application that applies an atlas fiber to all individual subjects from a dataset, extracts fiber profiles, gathers and plots related information (FA map…)<\/span><\/p>\n

\u00a0<\/span><\/td>\n<\/tr>\n

DTI-Reg<\/b><\/span><\/td>\nGo to the DTI-Reg webpage<\/a><\/span><\/td>\nDTI-Reg is an open-source C++ application that performs pair-wise DTI registration, using scalar FA map to drive the registration.<\/span><\/p>\n

\u00a0<\/span><\/td>\n<\/tr>\n

Tractograpy with unscented Kalman Filter<\/b><\/span><\/td>\nGo to the UKF webpage<\/a><\/span><\/td>\nWe present a framework which uses an unscented Kalman filter to perform tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods.<\/span><\/td>\n<\/tr>\n
\"DTIAtlasBuilderIcon\"<\/span><\/td>\nGo to the DTIAtlasBuilder webpage<\/a><\/span><\/span><\/span><\/td>\nThis tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps :
\n\"arrow.gif\" Affine Registration with BRAINSFit
\n\"arrow.gif\" Non Linear Registration with GreedyAtlas
\nA final step will apply the transformations to the original DTI images so that the final average can be computed.<\/span><\/td>\n<\/tr>\n
DTI Process Toolkit<\/b><\/span><\/td>\nGo to the DTI Process webpage<\/a><\/span><\/td>\nDTIProcess is a DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess…<\/span><\/p>\n

\u00a0<\/span><\/td>\n<\/tr>\n

\n

\"CCSeg<\/p>\n<\/td>\n

Go to the CCSeg webpage<\/a><\/span><\/td>\nCCSeg is an open-source C++-based application that allows automatic as well as user-interactive segmentation of the Corpus Callosum. <\/span><\/p>\n

Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation.<\/span><\/td>\n<\/tr>\n

\n

\"NIRAL<\/p>\n<\/td>\n

Go to the NIRAL Utilities webpage<\/a><\/span><\/td>\nNIRAL Utilities are open-source C++ based command line applications that allow image analysis and processing using ITK or VTK libraries<\/span><\/td>\n<\/tr>\n
\"ShapeWorks
\n<\/b><\/td>\n		Go to the ShapeWorks webpage<\/span><\/a><\/span><\/td>\nShapeWorks software is an open-source distribution (initially developped by the SCI Institute) of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization:
\n\"arrow.gif\"<\/span> Data preprocessing
\n\"arrow.gif\"<\/span> Group-wise particle-based shape correspondence
\n\"arrow.gif\"<\/span> Data visualization<\/span><\/td>\n<\/tr>\n
\n

\"DTIPrep<\/p>\n<\/td>\n

Go to the DTIPrep webpage<\/a><\/span><\/td>\nDTIPrep performs a “Study-specific Protocol” based automatic pipeline for DWI\/DTI quality control and preparation:
\n\"arrow.gif\"<\/span> Image\/diffusion information check
\n\"arrow.gif\"<\/span> Interlace-wise and gradient-wise intensity and motion check
\n\"arrow.gif\"<\/span> Head motion and Eddy current artifact correction
\n\"arrow.gif\"<\/span> DTI computation<\/span><\/td>\n<\/tr>\n
\n

\"AutoSeg<\/p>\n<\/td>\n

Go to the AutoSeg webpage<\/a><\/span><\/td>\nAutoSeg is an end-to-end application that performs automatic brain tissue classification and structural segmentation:
\n\"arrow.gif\"<\/span> Atlas-based EM tissue segmentation
\n\"arrow.gif\"<\/span> Atlas-based subcortical structure segmentation and lobar parcellation
\n\"arrow.gif\"<\/span> Regional histogram analysis<\/span><\/td>\n<\/tr>\n
\n

\"GAMBIT<\/p>\n<\/td>\n

Go to the GAMBIT webpage<\/a><\/span><\/td>\nGAMBIT is an end-to-end application allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements:
\n\"arrow.gif\"<\/span> Voxel-based cortical thickness
\n\"arrow.gif\"<\/span> White matter cortical surface creation and inflation
\n\"arrow.gif\"<\/span> Group-wise shape correspondence using ShapeWorks<\/span><\/td>\n<\/tr>\n
\n

\"ARCTIC<\/p>\n<\/td>\n

Go to the ARCTIC webpage<\/a><\/span><\/td>\nARCTIC (Automatic Regional Cortical ThICkness) is a cross-platform end-to-end application allowing individual analysis of cortical thickness. It can be run within Slicer3 as an external module or directly as a command line:
\n\"arrow.gif\"<\/span> Brain tissue segmentation
\n\"arrow.gif\"<\/span> Lobar cortical thickness analysis
\n\"arrow.gif\"<\/span> White and gray matter mesh creation<\/span><\/td>\n<\/tr>\n
\n

\"SPHARM-PDM<\/p>\n<\/td>\n

Go to the NITRC SPHARM-PDM page<\/a><\/span><\/td>\nThe SPHARM shape analysis toolset is used for doing local statistical shape analysis. ITK based.<\/span><\/td>\n<\/tr>\n
\n

\"MriWatcherIcon\"<\/p>\n<\/td>\n

Go to the NITRC MriWatcher page<\/a><\/span><\/td>\nMriWatcher is a vizualisation tool for MRI images (.gipl,.mha,.hdr).
\n<\/span> \"arrow.gif\" Coupled cursors to show the differences between images
\n<\/span> \"arrow.gif\" Load an overlay images
\n<\/span> \"arrow.gif\" Screenshot<\/span><\/td>\n<\/tr>\n
\n

\"HeadCircumferenceIcon\"<\/p>\n<\/td>\n

Go to the HeadCircumference webpage<\/span><\/span><\/a><\/td>\nProgram which compute head circumference based on a 3D image
\n<\/span> \"arrow.gif\" Use Fourier harmonics to parametrize the contour
\n<\/span> \"arrow.gif\" Embedded tutorial
\n<\/span> \"arrow.gif\" Store results in an excel spreadsheet automatically<\/span><\/td>\n<\/tr>\n
\n

\"MakeAtlasScriptsLogoSmall2\"<\/p>\n<\/td>\n

Go to the MakeAtlasScripts – Rodent webpage<\/span><\/span><\/a><\/td>\nSets of BatchMake scripts to process rodent images<\/span><\/p>\n

\"arrow.gif\" Perform alignment, skullstripping, average computation, parcellation, region based statistics <\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Non-supported Software:<\/b><\/span> <\/b> <\/b><\/h2>\n

NeuroLib download page<\/b><\/p>\n

Other deprecated software<\/span> <\/b><\/a><\/p>\n

CCSeg is an open-source C++-based application developed at UNC-Chapel Hill that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation<\/span><\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

Currently supported Software: Go to the FiberViewerLight webpage Fiber ViewerLight is an open-source C++ application to analyze fiber bundles. It provides: Several methods for clustering 3D fibers visualization 3D plane selection Go to the DTIAtlasFiberAnalyzer (DTI Fiber Tract Statistics) webpage DTIAtlasFiberAnalyzer is an open-source C++ application that applies an atlas fiber to all individual subjects … Read more<\/a><\/p>\n","protected":false},"author":45190,"featured_media":0,"parent":2231,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2282","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/pages\/2282","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/users\/45190"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/comments?post=2282"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/pages\/2282\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/pages\/2231"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/wp-json\/wp\/v2\/media?parent=2282"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}