Pipeline's Workflows

BayesAss+ estiamtion of populations migrat... (1)

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BayesAss+ is a program that estimates recent migration rates between populations using MCMC. It also estimates each individual’s immigrant ancestry, the generation in which immigration occurred (i.e. the individual can be assigned as an immigrant from a specific population, a non-immigrant, or the offspring of an immigrant and a non-immigrant), the population (as opposed to the sample) allele frequencies, inbreeding (F) values within each population, and genotypes at any locus wit...

Created: 2012-03-08

Credits: Pipeline

Fdist2 Simulation Pipeline Workflow (1)

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Fdist2 is a simulation program to detect loci that might be under selection in samples from structured populations.   Workflow Usage & Specifications The workflow reads an input file "fdist_params2.dat", which consists of 6 lines. This file must only contain numbers in the format described: Total number of demes (100 max). No of populations sampled (must be less than or equal to total number of demes). Expected Fst for infinite allele, infinite island model. Sample si...

Created: 2012-03-08 | Last updated: 2012-03-08

Credits: Pipeline

Migrate Pipeline Workflow (1)

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Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.     Workflow Usage & Specifications Migrate can use the following data types: •Sequence data using Felsenstein's 84 model with or without site rate variation, •Single nucleotide poly...

Created: 2012-03-08

Credits: Pipeline

Mouse Brain Image Analysis: General Linear... (1)

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Overview - General Linear Model The workflow runs voxelwise statistics on two populations of mice. Each of the populations has been scanned prior to injection of a label and at four subsequent timepoints.   Problem addressed by this workflow The workflow addresses several problems. First of all, it performs co-registration between the subjects from the two populations and at different timepoints. It then scales all images. Finally, it runs a multiple linear regression module t...

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

Credits: Pipeline

Automated BrainSuite Cortical Surface Extr... (1)

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Overview - BrainSuite Cortical Surface Extraction The workflow takes a skull stripped volume as input and runs a multi-stage process, extracting the cortical surface and splitting it into hemispheres.   Problem addressed by this workflow Generating a shape model of the cortical surface from a 3D volume.   Detailed Workflow Usage & Specifications Tissue Classification The next step in the Brainsuite09 cortical surface identification sequence is tissue classificatio...

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

Credits: Pipeline

First Level within subject fMRI processing (1)

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Overview - fMRI-FEAT workflow This is a simple with-in subject fMRI analysis workflow. It takes 3D fMRI images and structural images of a subject and performs FSLmerge, BET (if the data is not already skull stripped) and first level FEAT processing.   Problem addressed by this workflow FSLMerge, BET and FEAT first level analysis can be performed using this workflow on one or more subjects that require the same processing. The design FSF file is generate using the FSL FEAT inte...

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

Credits: Pipeline

Image Registration Meta Algorithm (IRMA) (1)

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Overview - Workflow-Title In this workflow different registration algorithms are applied to the same image and the image that is best registered to the template is chosen as the output top candidate.   Problem addressed by this workflow In this workflow various registration algorithm is performed on the same subject. The algorithm that gives the best result is chosen. This might be different for different input images. This workflow is robust and picks the best-registered imag...

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

Credits: Pipeline

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: Pipeline

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: Pipeline

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: Pipeline