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Type: LONI Pipeline Licence: by-sa

Workflow Direct Hippocampal Mapping (1)

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Overview - Direct Hippo Mapping The workflow takes volumetric masks of hippocampi from two groups, generates surfaces from each mask, and maps these surfaces to a hippocampal atlas. It also computes thickness and displacement feature on the surfaces and evaluates the statistical significance of the differences between the two groups with respect to these measurements.   Problem addressed by this workflow Automatically establishing correspondences between points on hippocampal ...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: User Pipeline

Workflow BrainParser: Automated Volume Calculation ... (1)

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This workflow takes raw un-skull-stripped volumes and generates tables of the volumes for all 56 ROIs currently automatically extracted using LONI BrainParser.   Problem addressed by this workflow Computing and tabulating the Brain Volumes of 56 cortical and sub-cortical ROIs. This workflow also generates DX models of all 56 ROIs which can be viewed as a scene in ShapeViewer.   Detailed Workflow Usage & Specifications Input: Any volumetric file format can be use...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: User Pipeline

Workflow Automated Brain Tissue Extraction and Volu... (1)

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This workflow takes raw un-skull-stripped volumes and generates tables of the volumes for all 56 ROIs currently automatically extracted using LONI BrainParser.   Problem addressed by this workflow Computing and tabulating the Brain Volumes of 56 cortical and sub-cortical ROIs. This workflow also generates DX models of all 56 ROIs which can be viewed as a scene in ShapeViewer.   Detailed Workflow Usage & Specifications Input: Any volumetric file format can be use...

Created: 2011-04-06 | Last updated: 2011-07-14

Credits: User Pipeline

Workflow Minimum Deformation Template (MDT) Atlasin... (1)

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This pipeline present the redesigned automated workflow for constructing the Minimum Distance Template (MDT) atlas for a given population, based on one specific image modality (e.g., sMRI). There will be two specific validation examples based on 100+ ICBM subjects: Quantitative: The ICBM data will be registered to the MDT, NRU and ICBM 462 atlases and mean displacement stats across all subjects will be reported for each voxel. The distributions of these mean displacement magnitud...

Created: 2011-04-06 | Last updated: 2011-07-14

Credits: User Pipeline

Workflow Automated Cortical Surface Extraction Work... (1)

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This workflow takes raw un-skull-stripped volumes and generates a cortical surface model using FreeSurfer? and CCB tools. Problem addressed by this workflow There are many ways to generate cortical surface models based on MRI data. Here is one of them. Eventually, there will be a new Learning-based Cortical Surface Modeling Pipeline, as well.   Input is Raw MRI T1-weighted volume CCB/FreeSurfer Cortical Surface extractor that the SIG-Shape team developed and we validated ...

Created: 2011-04-06 | Last updated: 2011-07-14

Credits: User Pipeline

Workflow Local Shape Analysis (LSA) Workflow (1)

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This workflow takes raw un-skull-stripped volumes in 2 groups/populations and an ROI index to generate a color-coded shape object using the per-vertex local p-values of some local shape-measure (e.g., displacement, atrophy, Jacobian, curvature, etc). It also outputs the p-values color-map superimposed on the mean shape. Problem addressed by this workflow   Identifying local group differences between 2 populations in one specific ROI. This workflow also generates mean-shape DX mo...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: User Pipeline

Workflow Automated Image Registration (1)

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This is a simple registration workflow. The structural MRI images are aligned to a standard brain image by using AIR registration tools. To build this workflow follow the steps mentioned on the following pages. URL: http://www.loni.ucla.edu/Software/AIR Try this Pipeline Workflow Now!

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: User Pipeline

Workflow Sub-Volume Probabilistic Atlas Segmentaito... (1)

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This workflow takes a raw unskull-stripped volume and a brain mask of the volume to create a tissue segmented image.This workflow is based on a novel genetic algorithm based finite mixture model and a local 3D Markov random field segmentation algorithm based on iterative conditional modes algorithm. Problem addressed by this workflow   This workflow performs tissue segmentation on the brain volumes using genetic algorithm based finite mixture model (GAMIXTURE), local 3D Markov ...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: User Pipeline

Workflow Global Shape Analysis Workflow (1)

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This workflow takes raw un-skull-stripped volumes in multiple groups/populations, or a Study-Design, and generates a scene file containing the models of the ROIs where the groups are different. It also reports the global 56 regional p-values. Problem addressed by this workflow   Identifying the group differences between 2 populations in the global shapes of 56 cortical and sub-cortical ROIs. This workflow also generates DX models of all 56 ROIs which can be viewed as a scene in Sh...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: User Pipeline

Workflow Microsatellite-based Ancestry and Parentag... (1)

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GENEPOP is genetics software package that does the following types of analyses: Hardy Weinberg Exact Tests Linkage Disequilibrium Population Differentiation Nm estimates Basic Information, Fis and gene diversities Fst & other correlations File Conversion Additional Miscellaneous Utilities     Problems addressed by this GENEPOP workflow This specific GENEPOP workflow computes the following: Testing : Hardy-W...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: User Pipeline

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