Workflows

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: Pipeline

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: Pipeline

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: Pipeline

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: Pipeline

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: Pipeline

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: Pipeline

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: Pipeline

Integrated Mapping and Assembly with Quali... (1)

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This workflow contains the first step of a genomics data analysis protocol designed and implemented by Federica Torri, Fabio Macciardi and Ivo Dinov to process large number of sequence data outputted by the Illumina sequencing pipeline. See Step II analysis (GATK/QC/Cleaning) here. This protocol is implemented using the LONI Pipeline environment and includes the following types of computational resources: Mapping and Assembly with Qualities (MAQ) Sequence Alignment and Mapping t...

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

Credits: Pipeline

PLINK Association workflow (1)

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PLINK is an open-source genome association analysis (GWAS) suite of tools providing a range of basic, large-scale computationally-efficient analyses. PLINK may be used for analysis of genotype/phenotype data, but requires some outside data-preprocessing (e.g., study design and planning, generating genotype or CNV calls from raw data). Support for visualization, annotation and storage of results is provided via gPLINK and Haploview.   The PLINK Association workflow provides testi...

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

Credits: Pipeline

GWASS Impute (1)

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Genome-wide Association Study Software (GWASS) package provides genomics tools facilitating the analysis of genome-wide association studies. These tools were used in the design and analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC)   IMPUTE2 is a GWASS program for phasing observed genotypes and imputing missing genotypes. It includes basic and advanced functions. URL: http://www.loni.ucla.edu/twiki/bin/view/CCB/Pipe...

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

Credits: Pipeline