feat FSL group analysis

Created: 2009-01-28 17:25:34      Last updated: 2009-01-28 17:36:07

This workflow is to be run on results obtained from this one (couldn't manage to find a clean solution for merging those two in Scufl).

Processor "feat_group":

1. builds the experiment intput (design) file from template and input parameters

2. calls feat FSL

Processor "roi" reads activation maps produced by feat_group, extract a region of interest and compute the mean, stdev, max and min activation within it.

Here is a sample input in VBrowser's XML dialect.

Below is detailed the meaning of input parameters.

 

<h1>Files to be swept on (thus iterated with a cross pdct)</h1>

* designFile_template: template for input design file.

* region_of_interest: binary mask of the ROI in .nii.gz format

<h1>Analysis-related files (to be combined with a dot)</h1>

* feat_files{1-11}: output of feat individual analysis for patient 1 to 11. Archive in tgz format.

 

 

 

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
https://www.myexperiment.org/workflows/640/download?version=1
[ More InfoExpand ]


Information Workflow Components

Inputs (13)
Processors (6)
Beanshells (1)
Outputs (4)
Links (31)
Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (0)

None

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (8)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.


Uploader

Workflow feat (3)

Thumb
This is an attempt to implement the feat application from the fsl fMRI package www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html into a Scufl workflow. Details are still being polished but the general structure is here. The main problem that we have with such workflows concerns data provenance. Each of the services is typically iterated on hundreds of data sets and keeping track of the produced files is a pain.

Created: 2008-03-18 | Last updated: 2008-05-19

Credits: User Glatard

Workflow Sff2Fasta_Blast_ParseBlast (1)

Thumb
Blast Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/      

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: User Barbera van Schaik User Antoine van Kampen User Angela Luijf User Silvia Olabarriaga