Workflows

Create Linear Combinations (1)

• Download

This process creates new attributes based on all combinations of coefficients for two attributes, i.e. it produces all linear combinations c1 * att1 + c2 * att2 by looping through a set of possible values for c1 and c2 and all their different combinations.

Created: 2011-04-08

Blast Report from ID (1)

• Download

This workflow retrieves a fasta sequence or blast report from an id. Firstly, given some inputs (e.g. ids:EDL10223.1, format:fasta, style:default and db:emblcds), it returns the sequence in fasta format associated to those inputs using the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). Next, we obtain a Blast report from this fasta sequence and some others parameters. The final result in that case corresponds with the same fasta sequence introduced...

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

Credits: Hectorj2f

Quality control processing of GEO datasets (2)

The workflow performs a quality control process on gene expression data sets stored in the Gene Expression Omnibus database. The QC process is performed using Bioconductor R packages. A variety of statistics are produced by the workflow including a diagnostic plot from snm normalisation and nucleotide composition bias.

Created: 2011-04-06 | Last updated: 2011-04-11

Credits: Peter Li Bhmecham

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

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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