CCB Pipeline Workflows - Documentation and Usage

Overview

This page contains all newly added complete Pipeline Neuroimaging Solutions (data, modules and workflows) that are developed, included and documented as part of the latest LONI Pipeline environment release.

• Classification of Computational Challenges and Currently available LONI end-to-end Solutions
• Interactive View of the the LONI Research and Resource Developments -- data object types, data manipulation protocols and resource challenges via a graphical interface.

MDT Atlasing Workflow

Minimum Distance Template (MDT) Atlasing Workflow and tensor-based morphometry (TBM)

Automated Tissue Volume Extraction Workflow

This workflow takes raw un-skull-stripped volumes and generates tables of the total, GM, WM and CSF volumes.

Automated 56-ROI Brain Volume Extraction Workflow

This workflow takes raw un-skull-stripped volumes and generates tables of the volumes for all 56 ROIs currently automatically extracted using LONI BrainParser.

Global Shape Analysis (GSA) Workflow

This workflow takes raw un-skull-stripped volumes in 2 groups/populations, or a Study-Design, and generates a scene file containing the models of the ROIs where the 2 groups are different. It also reports the global 56 regional p-values.

Local Shape Analysis (LSA) Workflow

This workflow takes raw un-skull-stripped volumes in 2 groups/populations, or a Study-Design, and an ROI index, to generate a locally color-coded Map of the group differences superimposed on the mean shape for the chosen ROI.

Graphical-Model-based Multivariate Analysis (GAMMA) Workflow

This Graphical-Model-based Multivariate Analysis (GAMMA) workflow provides a mechanism for Bayesian data-mining and analysis of high-dimensional data (e.g., neuroimaging data analysis, primarily lesion-based studies, functional MR-based studies, and morphometric studies).

Cortical Surface Extraction Workflow

This workflow takes raw un-skull-stripped volumes and generates a model of the cortical surface.

Automated Complete Cortical Thickness Workflow

This workflow takes raw un-skull-stripped volumes and generates the Left and Right cortical surfaces. It also estimates the cortical thickness at each vertex on the cortical surfaces and maps these GM-thickness values on each vertex. The results may be viewed using ShapeViewer.

Elastic Surface Warping

Elastic Surface Warping Protocol includes a collection of surfaces and anatomical contours on those surfaces, this process will warp the surfaces to an atlas. The atlas may be provided by the user or created from the average of the provided contours. The resulting warped surfaces will have anatomically homologous vertices, which allow the user to perform statistics on anatomically homologous regions on the surfaces across the subjects.

SVPASEG Workflow

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.

ROBEX: Robust Brain Extraction

ROBEX is a parameter-less skull-stripping algorithm that removes non-bran tissue from the MRI using a shape model+free deformation as generative model and a random forest as discriminative model. ROBEX requires the brain to be oriented in the "standard" way.

DTI/DSI Workflow

This workflow takes diffusion images (dicom/Nifti) and performs DTI/DSI reconstruction and fiber tracking.

First Level with-in subject fMRI processing 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.

Higher Level 2 group comparison fMRI processing Workflow

This is a simple 2-sample higher-level fMRI analysis workflow. It takes first level feat directories and performs 2-group higher level FEAT analysis (2 groups and 2EVs in the example workflow) and outputs 2 comparisons, Grp 1 > Grp2 and Grp2 > Grp1.

BrainSuite Cortical Surface Extraction

Cortical surface extraction using BrainSuite09 tools

Cortical Surface Labeling

Use BrainParser to auto-segment the brain, BrainSuite09 and FreeSurfer to extract the cortical surface, and ShapeTools library to project the labels onto the resulting shapes

Direct Hippocampal Mapping

Based on intrinsic shape context, an algorithm automatically detects landmark curves and generates a mapping between source and target hippocampal surfaces

DICOM Anonymizer

Change the fields in DICOM header

DICOM Summarize

Extract specified fields in DICOM header

IRMA Workflow

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.

SSMA Workflow

In this workflow different brain skull-stripping algorithms are applied to the same image and a consensus mapping is used to generate a new meta-skull-stripped volume.

Automatic Registration Toolbox

Nonlinear registration of two volumes

PCA Registration

Automatic Segmentation training/testing

Deformable Organisms Skullstripping

Deformable Organisms Skullstripping

Rat Brain Functional Analysis

Statistical comparison of functional data from two groups of rats

Mouse Workflows

General Linear Model
Tensor Based Morphometry

Pluto Workflows

Pluto fMRI/Diffusion connectomics workflows

Bioinformatics Workflows

This list represents the currently available informatics and genomics Pipeline modules are workflows (November 2010). This PDF Document also includes a guide to the use of these informatics protocols. See this 50-minute video stream demonstrating the Pipeline's functionality for managing bioinformatics and genomics analyses protocols.

Bioinformatics BLAST Workflow EMBOSS Bioinformatics Workflows mrFAST Bioinformatics Workflows GWASS Genomics Workflows PLINK GWAS Workflows Step I Processing: Mapping and Assembly with Qualities (MAQ), SAMtools, Bowtie, CNVer Workflows Step II Processing: Data Quality Control (QC) and Cleaning using Genome Analysis Toolkit (GATK) and SAMtools Workflows

Additional features, extensions and recommendations for improvement of the Genomics and Informatics capabilities of the Pipeline are available here.

The Genomics and Informatics Project code pages

• GoogleCode Informatics Project Page
• SourceForge Informatics Project Page

2011 Pipeline Genomics and Informatics Efforts

Pipeline invocation of R-scripts

The Pipeline environment enables the integration of statistical computing R-language scripts with other computational tools within the Pipeline environment.

Pipeline invocation of Matlab-scripts

The Pipeline environment enables the integration of Matlab scripts with other computational tools within the Pipeline environment.

Basic fMRI Preprocessing

This is a basic fMRI data preprocessing workflow. The output of this workflow can be entered into one's statistical engine of choice.

Arterial Spin Labeling (ASL) Workflow

Arterial Spin Labeling (ASL) Pipeline workflow takes as input Baseline CBF maps, Alpha_Measurement, the T1Estimate Directory that contains all the T1Estimate files, and T1W_3D, and generates baseline CBF NIFTI volume.

Image Converters

A list of tools used to convert images between the various standard file formats

Advanced Normalization Tools (ANTs)

The purpose of this workflow is to take a label volume for an atlas (in this case the JHU 'Eve' atlas), and nonlinearly register it to two subjects using ANTs (Advanced Normalization Tools).

Template Workflow Usage/Docs page

Template Workflow Usage/Docs page

Committing Pipeline Workflows to core Pipeline server library

• IVO DINOV: Confirm that source code is in LONI SVN repo and validate application build.
• ALEN/SHRUTHI: Test the stand-alone application on known good datasets. Validate results.
• SYS ADMINS: Install application in /usr/local of cerebro-rcc and Cranium cluster.
• ALEN/SHRUTHI: Integrate the application into a Pipeline workflow. Test on development cluster and validate results.
• ALEN/SHRUTHI: Test on production cluster and validate results.
• ALEN/SHRUTHI:Deploy workflow on * Development (Server:Cranium-Dev) * Production(Server:Cranium-Prod) * Try-Me (contact Amanda) * Training (Server:Cranium-edu)
• Module/Workflow Wiki page (docs and usage).
• PIPELINE Group: Add workflow to Pipeline distribution.